* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
-import java.util.*;\r
+\r
import java.awt.*;\r
\r
-public class Atom {\r
- double x;\r
- double y;\r
- double z;\r
- int number;\r
- String name;\r
- String resName;\r
- int resNumber;\r
- int type;\r
- Color color;\r
- String chain;\r
+import java.util.*;\r
\r
- public Atom(StringTokenizer str) {\r
- this.number = (new Integer(str.nextToken())).intValue();\r
- this.name = str.nextToken();\r
- this.resName = str.nextToken();\r
\r
- String tmpstr = new String();\r
+public class Atom {\r
+ double x;\r
+ double y;\r
+ double z;\r
+ int number;\r
+ String name;\r
+ String resName;\r
+ int resNumber;\r
+ int type;\r
+ Color color;\r
+ String chain;\r
\r
- try {\r
- tmpstr = str.nextToken();\r
+ public Atom(StringTokenizer str) {\r
+ this.number = (new Integer(str.nextToken())).intValue();\r
+ this.name = str.nextToken();\r
+ this.resName = str.nextToken();\r
\r
- this.resNumber = (new Integer(tmpstr).intValue());\r
- this.chain = "A";\r
- this.color = Color.green;\r
+ String tmpstr = new String();\r
\r
- } catch(NumberFormatException e) {\r
- this.chain = tmpstr;\r
+ try {\r
+ tmpstr = str.nextToken();\r
\r
- if (tmpstr.equals("A")) {\r
- this.color = new Color((float)Math.random(),(float)Math.random(),(float)Math.random());\r
- } else {\r
- this.color = Color.red;\r
- }\r
- this.resNumber = (new Integer(str.nextToken()).intValue());\r
- }\r
+ this.resNumber = (new Integer(tmpstr).intValue());\r
+ this.chain = "A";\r
+ this.color = Color.green;\r
+ } catch (NumberFormatException e) {\r
+ this.chain = tmpstr;\r
\r
- this.x = (double)(new Double(str.nextToken()).floatValue());\r
- this.y = (double)(new Double(str.nextToken()).floatValue());\r
- this.z = (double)(new Double(str.nextToken()).floatValue());\r
+ if (tmpstr.equals("A")) {\r
+ this.color = new Color((float) Math.random(),\r
+ (float) Math.random(), (float) Math.random());\r
+ } else {\r
+ this.color = Color.red;\r
+ }\r
\r
- }\r
+ this.resNumber = (new Integer(str.nextToken()).intValue());\r
+ }\r
\r
- public void setColor(Color col) {\r
- this.color = col;\r
- }\r
+ this.x = (double) (new Double(str.nextToken()).floatValue());\r
+ this.y = (double) (new Double(str.nextToken()).floatValue());\r
+ this.z = (double) (new Double(str.nextToken()).floatValue());\r
+ }\r
\r
+ public void setColor(Color col) {\r
+ this.color = col;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
\r
import java.awt.*;\r
\r
-public class Bond {\r
-\r
- float start[];\r
- float end[];\r
-\r
- Color startCol;\r
- Color endCol;\r
-\r
- public myAtom at1;\r
- public myAtom at2;\r
-\r
- public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {\r
- this.start = start;\r
- this.end = end;\r
- this.startCol = at1.color;\r
- this.endCol = at2.color;\r
- this.at1 = at1;\r
- this.at2 = at2;\r
- }\r
- public Bond(Bond bond) {\r
- this.start = new float[3];\r
-\r
- this.start[0] = bond.start[0];\r
- this.start[1] = bond.start[1];\r
- this.start[2] = bond.start[2];\r
-\r
- this.end = new float[3];\r
\r
- this.end[0] = bond.end[0];\r
- this.end[1] = bond.end[1];\r
- this.end[2] = bond.end[2];\r
-\r
- this.startCol = bond.startCol;\r
- this.endCol = bond.endCol;\r
- }\r
-\r
- public void print() {\r
- System.out.println("Start " + start[0] + " "+ start[1] + " " + start[2]);\r
- System.out.println("End " + end[0] + " "+ end[1] + " " + end[2]);\r
- }\r
-\r
- public float length() {\r
- float len = (end[0] - start[0])*(end[0] - start[0]) +\r
- (end[1] - start[1])*(end[1] - start[1]) +\r
- (end[2] - start[2])*(end[2] - start[2]);\r
-\r
- len = (float)(Math.sqrt(len));\r
-\r
- return len;\r
- }\r
- public void translate(float x, float y, float z) {\r
- start[0] = (start[0] + x);\r
- end[0] = (end[0] + x);\r
-\r
- start[1] = (start[1] + y);\r
- end[1] = (end[1] + y);\r
-\r
- start[2] = (start[2] + z);\r
- end[2] = (end[2] + z);\r
- }\r
+public class Bond {\r
+ float[] start;\r
+ float[] end;\r
+ Color startCol;\r
+ Color endCol;\r
+ public myAtom at1;\r
+ public myAtom at2;\r
+\r
+ public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {\r
+ this.start = start;\r
+ this.end = end;\r
+ this.startCol = at1.color;\r
+ this.endCol = at2.color;\r
+ this.at1 = at1;\r
+ this.at2 = at2;\r
+ }\r
+\r
+ public Bond(Bond bond) {\r
+ this.start = new float[3];\r
+\r
+ this.start[0] = bond.start[0];\r
+ this.start[1] = bond.start[1];\r
+ this.start[2] = bond.start[2];\r
+\r
+ this.end = new float[3];\r
+\r
+ this.end[0] = bond.end[0];\r
+ this.end[1] = bond.end[1];\r
+ this.end[2] = bond.end[2];\r
+\r
+ this.startCol = bond.startCol;\r
+ this.endCol = bond.endCol;\r
+ }\r
+\r
+ public void print() {\r
+ System.out.println("Start " + start[0] + " " + start[1] + " " +\r
+ start[2]);\r
+ System.out.println("End " + end[0] + " " + end[1] + " " + end[2]);\r
+ }\r
+\r
+ public float length() {\r
+ float len = ((end[0] - start[0]) * (end[0] - start[0])) +\r
+ ((end[1] - start[1]) * (end[1] - start[1])) +\r
+ ((end[2] - start[2]) * (end[2] - start[2]));\r
+\r
+ len = (float) (Math.sqrt(len));\r
+\r
+ return len;\r
+ }\r
+\r
+ public void translate(float x, float y, float z) {\r
+ start[0] = (start[0] + x);\r
+ end[0] = (end[0] + x);\r
+\r
+ start[1] = (start[1] + y);\r
+ end[1] = (end[1] + y);\r
+\r
+ start[2] = (start[2] + z);\r
+ end[2] = (end[2] + z);\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
\r
public class MCMatrix {\r
- float matrix[][];\r
- float tmp[][];\r
-\r
- float mycos;\r
- float mysin;\r
- float myconst = (float)(Math.PI/180);\r
-\r
- public MCMatrix(int rows, int cols) {\r
- matrix = new float[rows][cols];\r
- tmp = new float[rows][cols];\r
- }\r
-\r
- public void addElement(int i, int j, float value) {\r
- matrix[i][j] = value;\r
- }\r
-\r
- public void print() {\r
- System.out.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);\r
- System.out.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);\r
- System.out.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);\r
- }\r
-\r
- public void rotatex(float degrees) {\r
- mycos = (float)(Math.cos(degrees*myconst));\r
- mysin = (float)(Math.sin(degrees*myconst));\r
-\r
- tmp[0][0] = 1;\r
- tmp[0][1] = 0;\r
- tmp[0][2] = 0;\r
- tmp[1][0] = 0;\r
- tmp[1][1] = mycos;\r
- tmp[1][2] = mysin;\r
- tmp[2][0] = 0;\r
- tmp[2][1] = -mysin;\r
- tmp[2][2] = mycos;\r
- preMultiply(tmp);\r
- }\r
-\r
- public void rotatez(float degrees) {\r
- mycos = (float)(Math.cos(degrees*myconst));\r
- mysin = (float)(Math.sin(degrees*myconst));\r
-\r
- tmp[0][0] = mycos;\r
- tmp[0][1] = -mysin;\r
- tmp[0][2] = 0;\r
- tmp[1][0] = mysin;\r
- tmp[1][1] = mycos;\r
- tmp[1][2] = 0;\r
- tmp[2][0] = 0;\r
- tmp[2][1] = 0;\r
- tmp[2][2] = 1;\r
-\r
- preMultiply(tmp);\r
- }\r
-\r
- public void rotatey(float degrees) {\r
- mycos = (float)(Math.cos(degrees*myconst));\r
- mysin = (float)(Math.sin(degrees*myconst));\r
-\r
- tmp[0][0] = mycos;\r
- tmp[0][1] = 0;\r
- tmp[0][2] = -mysin;\r
- tmp[1][0] = 0;\r
- tmp[1][1] = 1;\r
- tmp[1][2] = 0;\r
- tmp[2][0] = mysin;\r
- tmp[2][1] = 0;\r
- tmp[2][2] = mycos;\r
-\r
- preMultiply(tmp);\r
- }\r
-\r
- public float[] vectorMultiply(float[] vect) {\r
- float temp[] = new float[3];\r
-\r
- temp[0] = vect[0];\r
- temp[1] = vect[1];\r
- temp[2] = vect[2];\r
-\r
- for (int i = 0; i < 3; i++) {\r
- temp[i] = (float)matrix[i][0]*vect[0] + (float)matrix[i][1]*vect[1] +(float)matrix[i][2]*vect[2];\r
+ float[][] matrix;\r
+ float[][] tmp;\r
+ float mycos;\r
+ float mysin;\r
+ float myconst = (float) (Math.PI / 180);\r
+\r
+ public MCMatrix(int rows, int cols) {\r
+ matrix = new float[rows][cols];\r
+ tmp = new float[rows][cols];\r
}\r
\r
- vect[0] = temp[0];\r
- vect[1] = temp[1];\r
- vect[2] = temp[2];\r
+ public void addElement(int i, int j, float value) {\r
+ matrix[i][j] = value;\r
+ }\r
\r
- return vect;\r
- }\r
+ public void print() {\r
+ System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +\r
+ matrix[0][2]);\r
+ System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +\r
+ matrix[1][2]);\r
+ System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +\r
+ matrix[2][2]);\r
+ }\r
\r
- public void preMultiply(float mat[][]) {\r
- float tmp[][] = new float[3][3];\r
+ public void rotatex(float degrees) {\r
+ mycos = (float) (Math.cos(degrees * myconst));\r
+ mysin = (float) (Math.sin(degrees * myconst));\r
+\r
+ tmp[0][0] = 1;\r
+ tmp[0][1] = 0;\r
+ tmp[0][2] = 0;\r
+ tmp[1][0] = 0;\r
+ tmp[1][1] = mycos;\r
+ tmp[1][2] = mysin;\r
+ tmp[2][0] = 0;\r
+ tmp[2][1] = -mysin;\r
+ tmp[2][2] = mycos;\r
+ preMultiply(tmp);\r
+ }\r
\r
- for (int i = 0; i < 3 ; i++) {\r
- for (int j = 0; j < 3; j++ ) {\r
- tmp[i][j] = mat[i][0]*matrix[0][j] +\r
- mat[i][1]*matrix[1][j] +\r
- mat[i][2]*matrix[2][j];\r
- }\r
+ public void rotatez(float degrees) {\r
+ mycos = (float) (Math.cos(degrees * myconst));\r
+ mysin = (float) (Math.sin(degrees * myconst));\r
+\r
+ tmp[0][0] = mycos;\r
+ tmp[0][1] = -mysin;\r
+ tmp[0][2] = 0;\r
+ tmp[1][0] = mysin;\r
+ tmp[1][1] = mycos;\r
+ tmp[1][2] = 0;\r
+ tmp[2][0] = 0;\r
+ tmp[2][1] = 0;\r
+ tmp[2][2] = 1;\r
+\r
+ preMultiply(tmp);\r
}\r
\r
- for (int i = 0; i < 3 ; i++) {\r
- for (int j = 0; j < 3; j++ ) {\r
- matrix[i][j] = tmp[i][j];\r
- }\r
+ public void rotatey(float degrees) {\r
+ mycos = (float) (Math.cos(degrees * myconst));\r
+ mysin = (float) (Math.sin(degrees * myconst));\r
+\r
+ tmp[0][0] = mycos;\r
+ tmp[0][1] = 0;\r
+ tmp[0][2] = -mysin;\r
+ tmp[1][0] = 0;\r
+ tmp[1][1] = 1;\r
+ tmp[1][2] = 0;\r
+ tmp[2][0] = mysin;\r
+ tmp[2][1] = 0;\r
+ tmp[2][2] = mycos;\r
+\r
+ preMultiply(tmp);\r
}\r
- }\r
\r
- public void postMultiply(float mat[][]) {\r
- float tmp[][] = new float[3][3];\r
+ public float[] vectorMultiply(float[] vect) {\r
+ float[] temp = new float[3];\r
+\r
+ temp[0] = vect[0];\r
+ temp[1] = vect[1];\r
+ temp[2] = vect[2];\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ temp[i] = ((float) matrix[i][0] * vect[0]) +\r
+ ((float) matrix[i][1] * vect[1]) +\r
+ ((float) matrix[i][2] * vect[2]);\r
+ }\r
\r
- for (int i = 0; i < 3 ; i++) {\r
- for (int j = 0; j < 3; j++ ) {\r
- tmp[i][j] = matrix[i][0]*mat[0][j] +\r
- matrix[i][1]*mat[1][j] +\r
- matrix[i][2]*mat[2][j];\r
- }\r
+ vect[0] = temp[0];\r
+ vect[1] = temp[1];\r
+ vect[2] = temp[2];\r
+\r
+ return vect;\r
}\r
\r
- for (int i = 0; i < 3 ; i++) {\r
- for (int j = 0; j < 3; j++ ) {\r
- matrix[i][j] = tmp[i][j];\r
- }\r
+ public void preMultiply(float[][] mat) {\r
+ float[][] tmp = new float[3][3];\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ tmp[i][j] = (mat[i][0] * matrix[0][j]) +\r
+ (mat[i][1] * matrix[1][j]) + (mat[i][2] * matrix[2][j]);\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ matrix[i][j] = tmp[i][j];\r
+ }\r
+ }\r
}\r
- }\r
-\r
- public void setIdentity() {\r
- matrix[0][0] = 1;\r
- matrix[1][1] = 1;\r
- matrix[2][2] = 1;\r
- matrix[0][1] = 0;\r
- matrix[0][2] = 0;\r
- matrix[1][0] = 0;\r
- matrix[1][2] = 0;\r
- matrix[2][0] = 0;\r
- matrix[2][1] = 0;\r
- }\r
-}\r
\r
+ public void postMultiply(float[][] mat) {\r
+ float[][] tmp = new float[3][3];\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ tmp[i][j] = (matrix[i][0] * mat[0][j]) +\r
+ (matrix[i][1] * mat[1][j]) + (matrix[i][2] * mat[2][j]);\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ matrix[i][j] = tmp[i][j];\r
+ }\r
+ }\r
+ }\r
\r
+ public void setIdentity() {\r
+ matrix[0][0] = 1;\r
+ matrix[1][1] = 1;\r
+ matrix[2][2] = 1;\r
+ matrix[0][1] = 0;\r
+ matrix[0][2] = 0;\r
+ matrix[1][0] = 0;\r
+ matrix[1][2] = 0;\r
+ matrix[2][0] = 0;\r
+ matrix[2][1] = 0;\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
\r
import jalview.datamodel.*;\r
+\r
import jalview.schemes.ResidueProperties;\r
\r
import java.awt.*;\r
+\r
import java.util.*;\r
\r
\r
public class PDBChain {\r
+ public String id;\r
+ public Vector bonds = new Vector();\r
+ public Vector atoms = new Vector();\r
+ public Vector residues = new Vector();\r
+ public int offset;\r
+ public Sequence sequence;\r
+ public boolean isVisible = false;\r
+ public int pdbstart = 0;\r
+ public int pdbend = 0;\r
+ public int seqstart = 0;\r
+ public int seqend = 0;\r
+\r
+ //public DrawableSequence ds;\r
+ public PDBChain(String id) {\r
+ this.id = id;\r
+ }\r
\r
- public String id;\r
- public Vector bonds = new Vector();\r
- public Vector atoms = new Vector();\r
- public Vector residues = new Vector();\r
- public int offset;\r
-\r
- public Sequence sequence;\r
- public boolean isVisible = false;\r
-\r
- public int pdbstart=0, pdbend=0, seqstart=0, seqend=0;\r
-\r
- //public DrawableSequence ds;\r
-\r
- public PDBChain(String id) {\r
- this.id = id;\r
- }\r
-\r
+ public String print() {\r
+ String tmp = "";\r
\r
- public String print() {\r
- String tmp = "";\r
- for (int i=0; i < bonds.size() ;i++) {\r
- tmp = tmp + ((Bond)bonds.elementAt(i)).at1.resName + " " + ((Bond)bonds.elementAt(i)).at1.resNumber +" " + offset+ "\n";\r
- }\r
- return tmp;\r
- }\r
- public void makeCaBondList() {\r
- for (int i = 0; i < (residues.size() - 1) ; i++) {\r
- Residue tmpres = (Residue)residues.elementAt(i);\r
- Residue tmpres2 = (Residue)residues.elementAt(i+1);\r
- myAtom at1 = tmpres.findAtom("CA");\r
- myAtom at2 = tmpres2.findAtom("CA");\r
- if ((at1 != null) && (at2 != null)) {\r
- if (at1.chain.equals(at2.chain)) {\r
- makeBond(at1,at2);\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void makeBond(myAtom at1, myAtom at2) {\r
- float[] start = new float[3];\r
- float[] end = new float[3];\r
-\r
- start[0] = at1.x;\r
- start[1] = at1.y;\r
- start[2] = at1.z;\r
-\r
- end[0] = at2.x;\r
- end[1] = at2.y;\r
- end[2] = at2.z;\r
-\r
- bonds.addElement(new Bond(start, end, at1,at2));\r
- }\r
-\r
- public void makeResidueList() {\r
- int count = 0;\r
- String seq = "";\r
- for (int i = 0; i < atoms.size(); i++) {\r
-\r
- myAtom tmp = (myAtom)atoms.elementAt(i);\r
- String resName = tmp.resName;\r
- int resNumber = tmp.resNumber;\r
- int res = resNumber;\r
-\r
- if (i ==0) {\r
- offset = resNumber;\r
- }\r
- Vector resAtoms = new Vector();\r
-\r
- resAtoms.addElement((myAtom)atoms.elementAt(i));\r
- i++;\r
- resNumber = ((myAtom)atoms.elementAt(i)).resNumber;\r
-\r
- //Add atoms to a vector while the residue number\r
- //remains the same\r
- while ((resNumber == res) && (i < atoms.size())) {\r
-\r
- resAtoms.addElement((myAtom)atoms.elementAt(i));\r
- i++;\r
- if (i < atoms.size()) {\r
- resNumber = ((myAtom)atoms.elementAt(i)).resNumber;\r
- } else {\r
- resNumber++;\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " +\r
+ ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +\r
+ "\n";\r
}\r
- }\r
-\r
- //We need this to keep in step with the outer for i = loop\r
- i--;\r
-\r
- //Make a new Residue object with the new atoms vector\r
- residues.addElement(new Residue(resAtoms, resNumber - 1,count));\r
- count++;\r
- Residue tmpres = (Residue)residues.lastElement();\r
- myAtom tmpat = (myAtom)tmpres.atoms.elementAt(0);\r
-\r
- // Keep totting up the sequence\r
- if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {\r
- System.err.println("PDBReader:Null aa3Hash for " + tmpat.resName);\r
- } else {\r
- String tmpres2 =\r
- ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];\r
- seq = seq + tmpres2;\r
- }\r
- // System.out.println(tmpat.resName + " " + tmpres2);\r
+\r
+ return tmp;\r
}\r
- sequence = new Sequence("PDB_seq",seq,1,seq.length());\r
- System.out.println("PDB Sequence is :\nSequence = " + seq);\r
- System.out.println("No of residues = " +residues.size());\r
- }\r
-\r
- public void setChargeColours() {\r
- for (int i = 0; i < bonds.size(); i++) {\r
- try {\r
- Bond b = (Bond)bonds.elementAt(i);\r
-\r
- if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {\r
- b.startCol = Color.red;\r
- } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {\r
- b.startCol = Color.blue;\r
- } else if (b.at1.resName.toUpperCase().equals("CYS")) {\r
- b.startCol = Color.yellow;\r
- } else {\r
- int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();\r
- b.startCol = Color.lightGray;\r
- }\r
- if (b.at2.resName.toUpperCase().equals("ASP") || b.at2.resName.toUpperCase().equals("GLU")) {\r
- b.endCol = Color.red;\r
- } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {\r
- b.endCol = Color.blue;\r
- } else if (b.at2.resName.toUpperCase().equals("CYS")) {\r
- b.endCol = Color.yellow;\r
- } else {\r
- int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();\r
- b.endCol = Color.lightGray;\r
+\r
+ public void makeCaBondList() {\r
+ for (int i = 0; i < (residues.size() - 1); i++) {\r
+ Residue tmpres = (Residue) residues.elementAt(i);\r
+ Residue tmpres2 = (Residue) residues.elementAt(i + 1);\r
+ myAtom at1 = tmpres.findAtom("CA");\r
+ myAtom at2 = tmpres2.findAtom("CA");\r
+\r
+ if ((at1 != null) && (at2 != null)) {\r
+ if (at1.chain.equals(at2.chain)) {\r
+ makeBond(at1, at2);\r
+ }\r
+ }\r
}\r
- } catch (Exception e) {\r
- Bond b = (Bond)bonds.elementAt(i);\r
- b.startCol = Color.gray;\r
- b.endCol = Color.gray;\r
- }\r
}\r
- }\r
\r
- public void setHydrophobicityColours() {\r
- float hydmin = (float)ResidueProperties.getHydmin();\r
- float hydmax = (float)ResidueProperties.getHydmax();\r
- double[] hyd = ResidueProperties.getHyd();\r
+ public void makeBond(myAtom at1, myAtom at2) {\r
+ float[] start = new float[3];\r
+ float[] end = new float[3];\r
\r
- Hashtable AA3Hash = ResidueProperties.getAA3Hash();\r
+ start[0] = at1.x;\r
+ start[1] = at1.y;\r
+ start[2] = at1.z;\r
\r
- for (int i = 0; i < bonds.size(); i++) {\r
- try {\r
- Bond b = (Bond)bonds.elementAt(i);\r
+ end[0] = at2.x;\r
+ end[1] = at2.y;\r
+ end[2] = at2.z;\r
\r
- int atno = ((Integer)AA3Hash.get(b.at1.resName.toUpperCase())).intValue();\r
- float red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);\r
+ bonds.addElement(new Bond(start, end, at1, at2));\r
+ }\r
\r
- if (red > (float)1.0) {\r
- red = (float)1.0;\r
- }\r
- if (red < (float)0.0) {\r
- red = (float)0.0;\r
+ public void makeResidueList() {\r
+ int count = 0;\r
+ String seq = "";\r
+\r
+ for (int i = 0; i < atoms.size(); i++) {\r
+ myAtom tmp = (myAtom) atoms.elementAt(i);\r
+ String resName = tmp.resName;\r
+ int resNumber = tmp.resNumber;\r
+ int res = resNumber;\r
+\r
+ if (i == 0) {\r
+ offset = resNumber;\r
+ }\r
+\r
+ Vector resAtoms = new Vector();\r
+\r
+ resAtoms.addElement((myAtom) atoms.elementAt(i));\r
+ i++;\r
+ resNumber = ((myAtom) atoms.elementAt(i)).resNumber;\r
+\r
+ //Add atoms to a vector while the residue number\r
+ //remains the same\r
+ while ((resNumber == res) && (i < atoms.size())) {\r
+ resAtoms.addElement((myAtom) atoms.elementAt(i));\r
+ i++;\r
+\r
+ if (i < atoms.size()) {\r
+ resNumber = ((myAtom) atoms.elementAt(i)).resNumber;\r
+ } else {\r
+ resNumber++;\r
+ }\r
+ }\r
+\r
+ //We need this to keep in step with the outer for i = loop\r
+ i--;\r
+\r
+ //Make a new Residue object with the new atoms vector\r
+ residues.addElement(new Residue(resAtoms, resNumber - 1, count));\r
+ count++;\r
+\r
+ Residue tmpres = (Residue) residues.lastElement();\r
+ myAtom tmpat = (myAtom) tmpres.atoms.elementAt(0);\r
+\r
+ // Keep totting up the sequence\r
+ if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {\r
+ System.err.println("PDBReader:Null aa3Hash for " +\r
+ tmpat.resName);\r
+ } else {\r
+ String tmpres2 = ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()\r
+ .get(tmpat.resName)).intValue()];\r
+ seq = seq + tmpres2;\r
+ }\r
+\r
+ // System.out.println(tmpat.resName + " " + tmpres2);\r
}\r
\r
- b.startCol = new Color(red,(float)0.0,(float)1.0-red);\r
- atno = ((Integer)AA3Hash.get(b.at2.resName.toUpperCase())).intValue();\r
-\r
- red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);\r
+ sequence = new Sequence("PDB_seq", seq, 1, seq.length());\r
+ System.out.println("PDB Sequence is :\nSequence = " + seq);\r
+ System.out.println("No of residues = " + residues.size());\r
+ }\r
\r
- if (red > (float)1.0) {\r
- red = (float)1.0;\r
+ public void setChargeColours() {\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ try {\r
+ Bond b = (Bond) bonds.elementAt(i);\r
+\r
+ if (b.at1.resName.toUpperCase().equals("ASP") ||\r
+ b.at1.resName.toUpperCase().equals("GLU")) {\r
+ b.startCol = Color.red;\r
+ } else if (b.at1.resName.toUpperCase().equals("LYS") ||\r
+ b.at1.resName.toUpperCase().equals("ARG")) {\r
+ b.startCol = Color.blue;\r
+ } else if (b.at1.resName.toUpperCase().equals("CYS")) {\r
+ b.startCol = Color.yellow;\r
+ } else {\r
+ int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();\r
+ b.startCol = Color.lightGray;\r
+ }\r
+\r
+ if (b.at2.resName.toUpperCase().equals("ASP") ||\r
+ b.at2.resName.toUpperCase().equals("GLU")) {\r
+ b.endCol = Color.red;\r
+ } else if (b.at2.resName.toUpperCase().equals("LYS") ||\r
+ b.at2.resName.toUpperCase().equals("ARG")) {\r
+ b.endCol = Color.blue;\r
+ } else if (b.at2.resName.toUpperCase().equals("CYS")) {\r
+ b.endCol = Color.yellow;\r
+ } else {\r
+ int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();\r
+ b.endCol = Color.lightGray;\r
+ }\r
+ } catch (Exception e) {\r
+ Bond b = (Bond) bonds.elementAt(i);\r
+ b.startCol = Color.gray;\r
+ b.endCol = Color.gray;\r
+ }\r
}\r
- if (red < (float)0.0) {\r
- red = (float)0.0;\r
- }\r
-\r
- b.endCol = new Color(red,(float)0.2,(float)1.0-red);\r
- } catch (Exception e) {\r
- Bond b = (Bond)bonds.elementAt(i);\r
- b.startCol = Color.gray;\r
- b.endCol = Color.gray;\r
- }\r
}\r
- }\r
-\r
\r
- public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {\r
-jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);\r
+ public void setHydrophobicityColours() {\r
+ float hydmin = (float) ResidueProperties.getHydmin();\r
+ float hydmax = (float) ResidueProperties.getHydmax();\r
+ double[] hyd = ResidueProperties.getHyd();\r
\r
+ Hashtable AA3Hash = ResidueProperties.getAA3Hash();\r
\r
- for (int i = 0; i < bonds.size(); i++) {\r
- Bond tmp = (Bond)bonds.elementAt(i);\r
- try {\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ try {\r
+ Bond b = (Bond) bonds.elementAt(i);\r
\r
- if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {\r
+ int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();\r
+ float red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);\r
\r
- int pos = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;\r
- int index = seq.findIndex(pos);\r
+ if (red > (float) 1.0) {\r
+ red = (float) 1.0;\r
+ }\r
\r
+ if (red < (float) 0.0) {\r
+ red = (float) 0.0;\r
+ }\r
\r
- tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);\r
+ b.startCol = new Color(red, (float) 0.0, (float) 1.0 - red);\r
+ atno = ((Integer) AA3Hash.get(b.at2.resName.toUpperCase())).intValue();\r
\r
- } else {\r
- tmp.startCol = Color.gray;\r
- }\r
+ red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);\r
\r
- if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {\r
+ if (red > (float) 1.0) {\r
+ red = (float) 1.0;\r
+ }\r
\r
- int pos = seqstart + (tmp.at2.resNumber - pdbstart-offset);\r
- int index = seq.findIndex(pos);\r
+ if (red < (float) 0.0) {\r
+ red = (float) 0.0;\r
+ }\r
\r
- tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);\r
+ b.endCol = new Color(red, (float) 0.2, (float) 1.0 - red);\r
+ } catch (Exception e) {\r
+ Bond b = (Bond) bonds.elementAt(i);\r
+ b.startCol = Color.gray;\r
+ b.endCol = Color.gray;\r
+ }\r
+ }\r
+ }\r
\r
- } else {\r
- tmp.endCol = Color.gray;\r
+ public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {\r
+ jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmp = (Bond) bonds.elementAt(i);\r
+\r
+ try {\r
+ if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&\r
+ (tmp.at1.resNumber <= ((offset + pdbend) - 1))) {\r
+ int pos = seqstart +\r
+ (tmp.at1.resNumber - pdbstart - offset);\r
+ int index = seq.findIndex(pos);\r
+\r
+ tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),\r
+ seq, index);\r
+ } else {\r
+ tmp.startCol = Color.gray;\r
+ }\r
+\r
+ if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&\r
+ (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {\r
+ int pos = seqstart +\r
+ (tmp.at2.resNumber - pdbstart - offset);\r
+ int index = seq.findIndex(pos);\r
+\r
+ tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),\r
+ seq, index);\r
+ } else {\r
+ tmp.endCol = Color.gray;\r
+ }\r
+ } catch (Exception e) {\r
+ tmp.startCol = Color.lightGray;\r
+ tmp.endCol = Color.lightGray;\r
+ }\r
}\r
- } catch (Exception e) {\r
- tmp.startCol = Color.lightGray;\r
- tmp.endCol = Color.lightGray;\r
- }\r
}\r
- }\r
-\r
- public void setChainColours() {\r
- for (int i = 0; i < bonds.size(); i++) {\r
- Bond tmp = (Bond)bonds.elementAt(i);\r
- try {\r
- tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);\r
- tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);\r
- } catch (Exception e) {\r
- tmp.startCol = Color.lightGray;\r
- tmp.endCol = Color.lightGray;\r
- }\r
+\r
+ public void setChainColours() {\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmp = (Bond) bonds.elementAt(i);\r
+\r
+ try {\r
+ tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);\r
+ tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);\r
+ } catch (Exception e) {\r
+ tmp.startCol = Color.lightGray;\r
+ tmp.endCol = Color.lightGray;\r
+ }\r
+ }\r
}\r
- }\r
}\r
-\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
\r
import jalview.datamodel.*;\r
+\r
import java.io.*;\r
+\r
import java.net.*;\r
+\r
import java.util.*;\r
\r
\r
public class PDBfile extends jalview.io.FileParse {\r
+ public Vector chains = new Vector();\r
+ Vector lineArray = new Vector();\r
\r
- public Vector chains = new Vector();\r
+ public PDBfile(String[] lines) {\r
+ for (int i = 0; i < lines.length; i++)\r
+ lineArray.addElement(lines[i]);\r
\r
- Vector lineArray = new Vector();\r
-\r
- public PDBfile(String [] lines)\r
- {\r
- for(int i=0; i<lines.length; i++)\r
- lineArray.addElement(lines[i]);\r
+ noLines = lineArray.size();\r
+ parse();\r
+ }\r
\r
- noLines = lineArray.size();\r
- parse();\r
- }\r
+ public PDBfile(String inFile, String inType) throws IOException {\r
+ super(inFile, inType);\r
\r
- public PDBfile(String inFile, String inType) throws IOException {\r
+ String line;\r
+ this.lineArray = new Vector();\r
\r
- super(inFile,inType);\r
+ BufferedReader dataIn;\r
\r
- String line;\r
- this.lineArray = new Vector();\r
- BufferedReader dataIn;\r
+ if (inType.equals("File")) {\r
+ dataIn = new BufferedReader(new FileReader(inFile));\r
+ }\r
+ else {\r
+ URL url = new URL(inFile);\r
+ this.fileSize = 0;\r
+ dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ }\r
\r
- if (inType.equals("File"))\r
- dataIn = new BufferedReader(new FileReader( inFile ));\r
+ while ((line = dataIn.readLine()) != null) {\r
+ lineArray.addElement(line);\r
+ }\r
\r
- else\r
- {\r
- URL url = new URL(inFile);\r
- this.fileSize = 0;\r
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
- }\r
+ noLines = lineArray.size();\r
\r
- while ((line = dataIn.readLine()) != null) {\r
- lineArray.addElement(line);\r
+ parse();\r
}\r
- noLines = lineArray.size();\r
\r
- parse();\r
+ public void parse() {\r
+ for (int i = 0; i < lineArray.size(); i++) {\r
+ StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)\r
+ .toString());\r
+\r
+ if (str.hasMoreTokens()) {\r
+ String inStr = str.nextToken();\r
+\r
+ if (inStr.indexOf("ATOM") != -1) {\r
+ try {\r
+ myAtom tmpatom = new myAtom(str);\r
+\r
+ if (findChain(tmpatom.chain) != null) {\r
+ // System.out.println("Adding to chain " + tmpatom.chain);\r
+ findChain(tmpatom.chain).atoms.addElement(tmpatom);\r
+ } else {\r
+ // System.out.println("Making chain " + tmpatom.chain);\r
+ PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
+ chains.addElement(tmpchain);\r
+ tmpchain.atoms.addElement(tmpatom);\r
+ }\r
+ } catch (NumberFormatException e) {\r
+ System.err.println("Caught" + e);\r
+ System.err.println("Record not added to PDB model:" +\r
+ lineArray.elementAt(i).toString());\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
-}\r
+ makeResidueList();\r
+ makeCaBondList();\r
\r
+ // for (int i=0; i < chains.size() ; i++) {\r
+ // String pog = ((PDBChain)chains.elementAt(i)).print();\r
+ // System.out.println(pog);\r
+ // }\r
+ }\r
\r
- public void parse() {\r
-\r
- for (int i = 0; i < lineArray.size(); i++) {\r
- StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());\r
- if (str.hasMoreTokens()) {\r
- String inStr = str.nextToken();\r
-\r
- if (inStr.indexOf("ATOM") != -1) {\r
- try {\r
- myAtom tmpatom = new myAtom(str);\r
- if (findChain(tmpatom.chain) != null) {\r
- // System.out.println("Adding to chain " + tmpatom.chain);\r
- findChain(tmpatom.chain).atoms.addElement(tmpatom);\r
- } else {\r
- // System.out.println("Making chain " + tmpatom.chain);\r
- PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
- chains.addElement(tmpchain);\r
- tmpchain.atoms.addElement(tmpatom);\r
- }\r
- } catch(NumberFormatException e) {\r
- System.err.println("Caught" + e);\r
- System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString());\r
- }\r
+ public void makeResidueList() {\r
+ for (int i = 0; i < chains.size(); i++) {\r
+ ((PDBChain) chains.elementAt(i)).makeResidueList();\r
}\r
- }\r
- }\r
- makeResidueList();\r
- makeCaBondList();\r
- // for (int i=0; i < chains.size() ; i++) {\r
- // String pog = ((PDBChain)chains.elementAt(i)).print();\r
- // System.out.println(pog);\r
- // }\r
- }\r
-\r
- public void makeResidueList() {\r
- for (int i=0; i < chains.size() ; i++) {\r
- ((PDBChain)chains.elementAt(i)).makeResidueList();\r
}\r
- }\r
- public void makeCaBondList() {\r
- for (int i=0; i < chains.size() ; i++) {\r
- ((PDBChain)chains.elementAt(i)).makeCaBondList();\r
- }\r
- }\r
-\r
- public PDBChain findChain(String id) {\r
- for (int i=0; i < chains.size(); i++) {\r
- // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);\r
- if (((PDBChain)chains.elementAt(i)).id.equals(id)) {\r
- return (PDBChain)chains.elementAt(i);\r
- }\r
+\r
+ public void makeCaBondList() {\r
+ for (int i = 0; i < chains.size(); i++) {\r
+ ((PDBChain) chains.elementAt(i)).makeCaBondList();\r
+ }\r
}\r
- return null;\r
- }\r
\r
+ public PDBChain findChain(String id) {\r
+ for (int i = 0; i < chains.size(); i++) {\r
+ // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);\r
+ if (((PDBChain) chains.elementAt(i)).id.equals(id)) {\r
+ return (PDBChain) chains.elementAt(i);\r
+ }\r
+ }\r
\r
- public void setChargeColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setChargeColours();\r
+ return null;\r
}\r
- }\r
\r
- public void setHydrophobicityColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();\r
- }\r
- }\r
-\r
- public void colourBySequence(Sequence seq) {\r
-//SMJS TODO\r
-// int max = seq.maxchain;\r
-// if (seq.maxchain != -1) {\r
-// ((PDBChain)chains.elementAt(max)).colourBySequence(seq);\r
-// }\r
- }\r
-\r
- public void setChainColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setChainColours();\r
+ public void setChargeColours() {\r
+ for (int i = 0; i < chains.size(); i++) {\r
+ ((PDBChain) chains.elementAt(i)).setChargeColours();\r
+ }\r
}\r
- }\r
- public static void main(String[] args) {\r
- try {\r
- PDBfile pdb = new PDBfile("enkp1.pdb","File");\r
- } catch(IOException e) {\r
- System.out.println(e);\r
- e.printStackTrace();\r
- System.exit(0);\r
+\r
+ public void setHydrophobicityColours() {\r
+ for (int i = 0; i < chains.size(); i++) {\r
+ ((PDBChain) chains.elementAt(i)).setHydrophobicityColours();\r
+ }\r
}\r
- }\r
-}\r
\r
+ public void colourBySequence(Sequence seq) {\r
+ //SMJS TODO\r
+ // int max = seq.maxchain;\r
+ // if (seq.maxchain != -1) {\r
+ // ((PDBChain)chains.elementAt(max)).colourBySequence(seq);\r
+ // }\r
+ }\r
\r
+ public void setChainColours() {\r
+ for (int i = 0; i < chains.size(); i++) {\r
+ ((PDBChain) chains.elementAt(i)).setChainColours();\r
+ }\r
+ }\r
\r
+ public static void main(String[] args) {\r
+ try {\r
+ PDBfile pdb = new PDBfile("enkp1.pdb", "File");\r
+ } catch (IOException e) {\r
+ System.out.println(e);\r
+ e.printStackTrace();\r
+ System.exit(0);\r
+ }\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
\r
import java.util.*;\r
\r
\r
public class Residue {\r
- Vector atoms = new Vector();\r
-\r
- int number;\r
- int count;\r
- int seqnumber;\r
-\r
- public Residue(Vector atoms, int number, int count) {\r
- this.atoms = atoms;\r
- this.number = number;\r
- this.count = count;\r
- }\r
+ Vector atoms = new Vector();\r
+ int number;\r
+ int count;\r
+ int seqnumber;\r
+\r
+ public Residue(Vector atoms, int number, int count) {\r
+ this.atoms = atoms;\r
+ this.number = number;\r
+ this.count = count;\r
+ }\r
\r
- public myAtom findAtom(String name) {\r
+ public myAtom findAtom(String name) {\r
+ for (int i = 0; i < atoms.size(); i++) {\r
+ if (((myAtom) atoms.elementAt(i)).name.equals(name)) {\r
+ return (myAtom) atoms.elementAt(i);\r
+ }\r
+ }\r
\r
- for (int i = 0; i < atoms.size(); i++) {\r
- if (((myAtom)atoms.elementAt(i)).name.equals(name)) {\r
- return (myAtom)atoms.elementAt(i);\r
- }\r
+ return null;\r
}\r
- return null;\r
- }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
\r
import java.util.*;\r
\r
-public class Zsort {\r
-\r
- public static void Zsort(Vector bonds) {\r
-\r
- sort(bonds,0,bonds.size()-1);\r
- }\r
-\r
-\r
-\r
- public static void sort(Vector bonds,int p, int r) {\r
- int q;\r
\r
- if (p < r) {\r
- q = partition(bonds,p,r);\r
- sort(bonds,p,q);\r
- sort(bonds,q+1,r);\r
+public class Zsort {\r
+ public static void Zsort(Vector bonds) {\r
+ sort(bonds, 0, bonds.size() - 1);\r
}\r
- }\r
-\r
- private static int partition(Vector bonds, int p, int r) {\r
- float x = ((Bond)bonds.elementAt(p)).start[2];\r
- int i = p-1;\r
- int j = r+1;\r
\r
- while(true) {\r
- do {\r
- j = j-1;\r
- } while (j >= 0 && ((Bond)bonds.elementAt(j)).start[2] > x);\r
+ public static void sort(Vector bonds, int p, int r) {\r
+ int q;\r
\r
- do {\r
- i = i+1;\r
- } while (i < bonds.size() && ((Bond)bonds.elementAt(i)).start[2] < x);\r
+ if (p < r) {\r
+ q = partition(bonds, p, r);\r
+ sort(bonds, p, q);\r
+ sort(bonds, q + 1, r);\r
+ }\r
+ }\r
\r
- if ( i < j) {\r
- Bond tmp = (Bond)bonds.elementAt(i);\r
- bonds.setElementAt(bonds.elementAt(j),i);\r
- bonds.setElementAt(tmp,j);\r
- } else {\r
- return j;\r
- }\r
+ private static int partition(Vector bonds, int p, int r) {\r
+ float x = ((Bond) bonds.elementAt(p)).start[2];\r
+ int i = p - 1;\r
+ int j = r + 1;\r
+\r
+ while (true) {\r
+ do {\r
+ j = j - 1;\r
+ } while ((j >= 0) && (((Bond) bonds.elementAt(j)).start[2] > x));\r
+\r
+ do {\r
+ i = i + 1;\r
+ } while ((i < bonds.size()) &&\r
+ (((Bond) bonds.elementAt(i)).start[2] < x));\r
+\r
+ if (i < j) {\r
+ Bond tmp = (Bond) bonds.elementAt(i);\r
+ bonds.setElementAt(bonds.elementAt(j), i);\r
+ bonds.setElementAt(tmp, j);\r
+ } else {\r
+ return j;\r
+ }\r
+ }\r
}\r
- }\r
}\r
-\r
-\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
\r
-import java.util.*;\r
import java.awt.*;\r
\r
-public class myAtom {\r
- float x;\r
- float y;\r
- float z;\r
-\r
- public int number;\r
- public String name;\r
- public String resName;\r
- public int resNumber;\r
- public int type;\r
- public Color color;\r
- public String chain;\r
- public boolean isSelected = false;\r
+import java.util.*;\r
\r
- public myAtom(StringTokenizer str) {\r
\r
- this.number = (new Integer(str.nextToken())).intValue();\r
- this.name = str.nextToken();\r
- this.resName = str.nextToken();\r
+public class myAtom {\r
+ float x;\r
+ float y;\r
+ float z;\r
+ public int number;\r
+ public String name;\r
+ public String resName;\r
+ public int resNumber;\r
+ public int type;\r
+ public Color color;\r
+ public String chain;\r
+ public boolean isSelected = false;\r
\r
- String tmpstr = new String();\r
+ public myAtom(StringTokenizer str) {\r
+ this.number = (new Integer(str.nextToken())).intValue();\r
+ this.name = str.nextToken();\r
+ this.resName = str.nextToken();\r
\r
- try {\r
- tmpstr = str.nextToken();\r
- this.resNumber = (new Integer(tmpstr).intValue());\r
- this.chain = "A";\r
- this.color = Color.lightGray;\r
+ String tmpstr = new String();\r
\r
- } catch(NumberFormatException e) {\r
- this.chain = tmpstr;\r
+ try {\r
+ tmpstr = str.nextToken();\r
+ this.resNumber = (new Integer(tmpstr).intValue());\r
+ this.chain = "A";\r
+ this.color = Color.lightGray;\r
+ } catch (NumberFormatException e) {\r
+ this.chain = tmpstr;\r
\r
- if (tmpstr.equals("A")) {\r
- this.color = Color.lightGray;\r
+ if (tmpstr.equals("A")) {\r
+ this.color = Color.lightGray;\r
+ } else {\r
+ this.color = Color.red;\r
+ }\r
\r
- } else {\r
- this.color = Color.red;\r
- }\r
+ this.resNumber = (new Integer(str.nextToken()).intValue());\r
+ }\r
\r
- this.resNumber = (new Integer(str.nextToken()).intValue());\r
+ this.x = (float) (new Float(str.nextToken()).floatValue());\r
+ this.y = (float) (new Float(str.nextToken()).floatValue());\r
+ this.z = (float) (new Float(str.nextToken()).floatValue());\r
}\r
\r
- this.x = (float)(new Float(str.nextToken()).floatValue());\r
- this.y = (float)(new Float(str.nextToken()).floatValue());\r
- this.z = (float)(new Float(str.nextToken()).floatValue());\r
- }\r
-\r
- public void setColor(Color col) {\r
- this.color = col;\r
- }\r
+ public void setColor(Color col) {\r
+ this.color = col;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package MCview;\r
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.util.*;\r
-import java.io.*;\r
-import javax.swing.*;\r
-import jalview.analysis.AlignSeq;\r
-import jalview.datamodel.*;\r
-\r
-public class rotCanvas extends JPanel implements KeyListener,\r
- MouseListener,\r
- MouseMotionListener {\r
- MCMatrix idmat = new MCMatrix(3,3);\r
- MCMatrix objmat = new MCMatrix(3,3);\r
-\r
- boolean redrawneeded =true;\r
-\r
- int omx = 0;\r
- int mx = 0;\r
- int omy = 0;\r
- int my = 0;\r
-\r
- public PDBfile pdb;\r
-\r
- int bsize;\r
-\r
- Image img;\r
- Graphics ig;\r
\r
- Dimension prefsize;\r
-\r
- float centre[] = new float[3];\r
- float width[] = new float[3];\r
+import jalview.analysis.AlignSeq;\r
\r
- float maxwidth;\r
- float scale;\r
+import jalview.datamodel.*;\r
\r
- String inStr;\r
- String inType;\r
+// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug\r
+import java.awt.*;\r
+import java.awt.event.*;\r
\r
- boolean depthcue = true;\r
- boolean wire = false;\r
- boolean bymolecule = false;\r
- boolean zbuffer = true;\r
+import java.io.*;\r
\r
- boolean dragging;\r
+import java.util.*;\r
\r
- int xstart;\r
- int xend;\r
- int ystart;\r
- int yend;\r
- int xmid;\r
- int ymid;\r
+import javax.swing.*;\r
\r
- Font font = new Font("Helvetica",Font.PLAIN,10);\r
\r
- public rotCanvas(PDBfile pdb, Sequence sequence, jalview.gui.AlignViewport av) throws IOException {\r
+public class rotCanvas extends JPanel implements KeyListener, MouseListener,\r
+ MouseMotionListener {\r
+ MCMatrix idmat = new MCMatrix(3, 3);\r
+ MCMatrix objmat = new MCMatrix(3, 3);\r
+ boolean redrawneeded = true;\r
+ int omx = 0;\r
+ int mx = 0;\r
+ int omy = 0;\r
+ int my = 0;\r
+ public PDBfile pdb;\r
+ int bsize;\r
+ Image img;\r
+ Graphics ig;\r
+ Dimension prefsize;\r
+ float[] centre = new float[3];\r
+ float[] width = new float[3];\r
+ float maxwidth;\r
+ float scale;\r
+ String inStr;\r
+ String inType;\r
+ boolean depthcue = true;\r
+ boolean wire = false;\r
+ boolean bymolecule = false;\r
+ boolean zbuffer = true;\r
+ boolean dragging;\r
+ int xstart;\r
+ int xend;\r
+ int ystart;\r
+ int yend;\r
+ int xmid;\r
+ int ymid;\r
+ Font font = new Font("Helvetica", Font.PLAIN, 10);\r
+\r
+ public rotCanvas(PDBfile pdb, Sequence sequence,\r
+ jalview.gui.AlignViewport av) throws IOException {\r
+ int max = -10;\r
+ int maxchain = -1;\r
+ int pdbstart = 0;\r
+ int pdbend = 0;\r
+ int seqstart = 0;\r
+ int seqend = 0;\r
+\r
+ for (int i = 0; i < pdb.chains.size(); i++) {\r
+ // Now lets compare the sequences to get\r
+ // the start and end points.\r
+ java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(),\r
+ ".");\r
+ String newString = "";\r
+\r
+ while (str.hasMoreTokens()) {\r
+ newString += str.nextToken();\r
+ }\r
\r
- int max = -10;\r
- int maxchain = -1;\r
- int pdbstart=0, pdbend=0, seqstart =0, seqend=0;\r
+ // Align the sequence to the pdb\r
+ AlignSeq as = new AlignSeq(sequence,\r
+ ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");\r
+ as.calcScoreMatrix();\r
+ as.traceAlignment();\r
+ as.printAlignment();\r
+\r
+ if (as.maxscore > max) {\r
+ max = as.maxscore;\r
+ maxchain = i;\r
+\r
+ pdbstart = as.seq2start;\r
+ pdbend = as.seq2end;\r
+ seqstart = as.seq1start - 1;\r
+ seqend = as.seq1end - 1;\r
+ }\r
\r
+ System.out.println("PDB start/end " + pdbstart + " " + pdbend);\r
+ System.out.println("SEQ start/end " + seqstart + " " + seqend);\r
+ }\r
\r
- for (int i=0; i < pdb.chains.size(); i++) {\r
- // Now lets compare the sequences to get\r
- // the start and end points.\r
+ ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;\r
+ ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend;\r
+ ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart;\r
+ ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend;\r
+ ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;\r
+ ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;\r
+ ((PDBChain) pdb.chains.elementAt(maxchain)).colourBySequence(av,\r
+ sequence);\r
+\r
+ this.pdb = pdb;\r
+ this.prefsize = new Dimension(getWidth(), getHeight());\r
+\r
+ //Initialize the matrices to identity\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ if (i != j) {\r
+ idmat.addElement(i, j, 0);\r
+ objmat.addElement(i, j, 0);\r
+ } else {\r
+ idmat.addElement(i, j, 1);\r
+ objmat.addElement(i, j, 1);\r
+ }\r
+ }\r
+ }\r
\r
- java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(), ".");\r
- String newString = "";\r
+ addMouseMotionListener(this);\r
+ addMouseListener(this);\r
+ addKeyListener(this);\r
\r
- while (str.hasMoreTokens()) {\r
- newString += str.nextToken();\r
- }\r
- // Align the sequence to the pdb\r
- AlignSeq as = new AlignSeq(sequence,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
-\r
- if (as.maxscore > max) {\r
- max = as.maxscore;\r
- maxchain = i;\r
-\r
- pdbstart = as.seq2start;\r
- pdbend = as.seq2end;\r
- seqstart = as.seq1start - 1 ;\r
- seqend = as.seq1end -1;\r
- }\r
-\r
- System.out.println("PDB start/end " + pdbstart + " " + pdbend);\r
- System.out.println("SEQ start/end " + seqstart + " " + seqend);\r
+ addPDBfile();\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
}\r
\r
+ public void addPDBfile() {\r
+ findCentre();\r
+ findWidth();\r
\r
- ( (PDBChain)pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;\r
- ( (PDBChain)pdb.chains.elementAt(maxchain)).pdbend = pdbend;\r
- ( (PDBChain)pdb.chains.elementAt(maxchain)).seqstart = seqstart;\r
- ( (PDBChain)pdb.chains.elementAt(maxchain)).seqend = seqend;\r
- ( (PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;\r
- ( (PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;\r
- ( (PDBChain)pdb.chains.elementAt(maxchain)).colourBySequence(av, sequence);\r
+ scale = findScale();\r
\r
+ System.out.println("Scale factor = " + scale);\r
+ }\r
\r
+ public void deleteBonds() {\r
+ scale = 0;\r
+ maxwidth = 0;\r
\r
- this.pdb = pdb;\r
- this.prefsize = new Dimension( getWidth(), getHeight());\r
+ width[0] = 0;\r
+ width[1] = 0;\r
+ width[2] = 0;\r
\r
- //Initialize the matrices to identity\r
+ centre[0] = 0;\r
+ centre[1] = 0;\r
+ centre[2] = 0;\r
\r
- for (int i = 0; i < 3; i++) {\r
- for (int j = 0; j < 3 ; j++) {\r
- if (i != j) {\r
- idmat.addElement(i,j,0);\r
- objmat.addElement(i,j,0);\r
- } else {\r
- idmat.addElement(i,j,1);\r
- objmat.addElement(i,j,1);\r
+ for (int i = 0; i < pdb.chains.size(); i++) {\r
+ ((PDBChain) pdb.chains.elementAt(i)).bonds = null;\r
}\r
- }\r
}\r
\r
- addMouseMotionListener(this);\r
- addMouseListener(this);\r
- addKeyListener(this);\r
-\r
- addPDBfile();\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
-\r
- }\r
+ public void findWidth() {\r
+ float[] max = new float[3];\r
+ float[] min = new float[3];\r
\r
- public void addPDBfile() {\r
- findCentre();\r
- findWidth();\r
+ max[0] = (float) -1e30;\r
+ max[1] = (float) -1e30;\r
+ max[2] = (float) -1e30;\r
\r
- scale = findScale();\r
+ min[0] = (float) 1e30;\r
+ min[1] = (float) 1e30;\r
+ min[2] = (float) 1e30;\r
\r
- System.out.println("Scale factor = " + scale);\r
- }\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++) {\r
+ if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {\r
+ Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
\r
- public void deleteBonds() {\r
- scale = 0;\r
- maxwidth = 0;\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmp = (Bond) bonds.elementAt(i);\r
\r
- width[0] = 0;\r
- width[1] = 0;\r
- width[2] = 0;\r
+ if (tmp.start[0] >= max[0]) {\r
+ max[0] = tmp.start[0];\r
+ }\r
\r
- centre[0] = 0;\r
- centre[1] = 0;\r
- centre[2] = 0;\r
+ if (tmp.start[1] >= max[1]) {\r
+ max[1] = tmp.start[1];\r
+ }\r
\r
- for (int i=0; i < pdb.chains.size(); i++) {\r
- ((PDBChain)pdb.chains.elementAt(i)).bonds = null;\r
- }\r
- }\r
+ if (tmp.start[2] >= max[2]) {\r
+ max[2] = tmp.start[2];\r
+ }\r
\r
- public void findWidth() {\r
- float max[] = new float[3];\r
- float min[] = new float[3];\r
+ if (tmp.start[0] <= min[0]) {\r
+ min[0] = tmp.start[0];\r
+ }\r
\r
- max[0] = (float)-1e30;\r
- max[1] = (float)-1e30;\r
- max[2] = (float)-1e30;\r
+ if (tmp.start[1] <= min[1]) {\r
+ min[1] = tmp.start[1];\r
+ }\r
\r
- min[0] = (float)1e30;\r
- min[1] = (float)1e30;\r
- min[2] = (float)1e30;\r
+ if (tmp.start[2] <= min[2]) {\r
+ min[2] = tmp.start[2];\r
+ }\r
\r
- for (int ii=0; ii < pdb.chains.size(); ii++) {\r
- if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {\r
+ if (tmp.end[0] >= max[0]) {\r
+ max[0] = tmp.end[0];\r
+ }\r
\r
- Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+ if (tmp.end[1] >= max[1]) {\r
+ max[1] = tmp.end[1];\r
+ }\r
\r
- for (int i = 0; i < bonds.size(); i++) {\r
- Bond tmp = (Bond)bonds.elementAt(i);\r
-\r
- if (tmp.start[0] >= max[0])\r
- max[0] = tmp.start[0];\r
- if (tmp.start[1] >= max[1])\r
- max[1] = tmp.start[1];\r
- if (tmp.start[2] >= max[2])\r
- max[2] = tmp.start[2];\r
- if (tmp.start[0] <= min[0])\r
- min[0] = tmp.start[0];\r
- if (tmp.start[1] <= min[1])\r
- min[1] = tmp.start[1];\r
- if (tmp.start[2] <= min[2])\r
- min[2] = tmp.start[2];\r
-\r
- if (tmp.end[0] >= max[0])\r
- max[0] = tmp.end[0];\r
- if (tmp.end[1] >= max[1])\r
- max[1] = tmp.end[1];\r
- if (tmp.end[2] >= max[2])\r
- max[2] = tmp.end[2];\r
- if (tmp.end[0] <= min[0])\r
- min[0] = tmp.end[0];\r
- if (tmp.end[1] <= min[1])\r
- min[1] = tmp.end[1];\r
- if (tmp.end[2] <= min[2])\r
- min[2] = tmp.end[2];\r
- }\r
- }\r
- }\r
+ if (tmp.end[2] >= max[2]) {\r
+ max[2] = tmp.end[2];\r
+ }\r
\r
- System.out.println("xmax " + max[0] + " min " + min[0]);\r
- System.out.println("ymax " + max[1] + " min " + min[1]);\r
- System.out.println("zmax " + max[2] + " min " + min[2]);\r
+ if (tmp.end[0] <= min[0]) {\r
+ min[0] = tmp.end[0];\r
+ }\r
\r
- width[0] = (float)Math.abs(max[0] - min[0]);\r
- width[1] = (float)Math.abs(max[1] - min[1]);\r
- width[2] = (float)Math.abs(max[2] - min[2]);\r
+ if (tmp.end[1] <= min[1]) {\r
+ min[1] = tmp.end[1];\r
+ }\r
\r
- maxwidth = width[0];\r
+ if (tmp.end[2] <= min[2]) {\r
+ min[2] = tmp.end[2];\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- if (width[1] > width[0])\r
- maxwidth = width[1];\r
- if (width[2] > width[1])\r
- maxwidth = width[2];\r
+ System.out.println("xmax " + max[0] + " min " + min[0]);\r
+ System.out.println("ymax " + max[1] + " min " + min[1]);\r
+ System.out.println("zmax " + max[2] + " min " + min[2]);\r
\r
- System.out.println("Maxwidth = " + maxwidth);\r
- }\r
+ width[0] = (float) Math.abs(max[0] - min[0]);\r
+ width[1] = (float) Math.abs(max[1] - min[1]);\r
+ width[2] = (float) Math.abs(max[2] - min[2]);\r
\r
- public float findScale() {\r
- int dim, width, height;\r
+ maxwidth = width[0];\r
\r
- if ( getWidth() != 0) {\r
- width = getWidth();\r
- height = getHeight();\r
+ if (width[1] > width[0]) {\r
+ maxwidth = width[1];\r
+ }\r
\r
- } else {\r
- width = prefsize.width;\r
- height = prefsize.height;\r
- }\r
+ if (width[2] > width[1]) {\r
+ maxwidth = width[2];\r
+ }\r
\r
- if (width < height) {\r
- dim = width;\r
- } else {\r
- dim = height;\r
+ System.out.println("Maxwidth = " + maxwidth);\r
}\r
\r
- return (float)(dim/(1.5d*maxwidth));\r
- }\r
-\r
+ public float findScale() {\r
+ int dim;\r
+ int width;\r
+ int height;\r
\r
+ if (getWidth() != 0) {\r
+ width = getWidth();\r
+ height = getHeight();\r
+ } else {\r
+ width = prefsize.width;\r
+ height = prefsize.height;\r
+ }\r
\r
- public void findCentre() {\r
- float xtot = 0;\r
- float ytot = 0;\r
- float ztot = 0;\r
+ if (width < height) {\r
+ dim = width;\r
+ } else {\r
+ dim = height;\r
+ }\r
\r
- int bsize = 0;\r
- //Find centre coordinate\r
+ return (float) (dim / (1.5d * maxwidth));\r
+ }\r
\r
- for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
- if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {\r
+ public void findCentre() {\r
+ float xtot = 0;\r
+ float ytot = 0;\r
+ float ztot = 0;\r
\r
- Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+ int bsize = 0;\r
\r
- bsize += bonds.size();\r
+ //Find centre coordinate\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++) {\r
+ if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {\r
+ Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
\r
- for (int i = 0; i < bonds.size(); i++) {\r
+ bsize += bonds.size();\r
\r
- xtot = xtot + ((Bond)bonds.elementAt(i)).start[0] +\r
- ((Bond)bonds.elementAt(i)).end[0];\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +\r
+ ((Bond) bonds.elementAt(i)).end[0];\r
\r
- ytot = ytot + ((Bond)bonds.elementAt(i)).start[1] +\r
- ((Bond)bonds.elementAt(i)).end[1];\r
+ ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +\r
+ ((Bond) bonds.elementAt(i)).end[1];\r
\r
- ztot = ztot + ((Bond)bonds.elementAt(i)).start[2] +\r
- ((Bond)bonds.elementAt(i)).end[2];\r
+ ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +\r
+ ((Bond) bonds.elementAt(i)).end[2];\r
+ }\r
+ }\r
}\r
- }\r
+\r
+ centre[0] = xtot / (2 * (float) bsize);\r
+ centre[1] = ytot / (2 * (float) bsize);\r
+ centre[2] = ztot / (2 * (float) bsize);\r
}\r
\r
- centre[0] = xtot / (2 * (float)bsize);\r
- centre[1] = ytot / (2 * (float)bsize);\r
- centre[2] = ztot / (2 * (float)bsize);\r
- }\r
+ public void paint(Graphics g) {\r
+ //Only create the image at the beginning -\r
+ //this saves much memory usage\r
+ if ((img == null) || (prefsize.width != getWidth()) ||\r
+ (prefsize.height != getHeight())) {\r
+ prefsize.width = getWidth();\r
+ prefsize.height = getHeight();\r
\r
- public void paint(Graphics g) {\r
- //Only create the image at the beginning -\r
- //this saves much memory usage\r
- if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {\r
- prefsize.width = getWidth();\r
- prefsize.height = getHeight();\r
+ scale = findScale();\r
+ img = createImage(prefsize.width, prefsize.height);\r
+ ig = img.getGraphics();\r
\r
- scale = findScale();\r
- img = createImage(prefsize.width,prefsize.height);\r
- ig = img.getGraphics();\r
+ redrawneeded = true;\r
+ }\r
\r
- redrawneeded = true;\r
- }\r
+ if (redrawneeded == true) {\r
+ drawBackground(ig, Color.black);\r
+ drawScene(ig);\r
+ redrawneeded = false;\r
+ } else {\r
+ ig = img.getGraphics();\r
+ }\r
\r
- if (redrawneeded == true) {\r
- drawBackground(ig,Color.black);\r
- drawScene(ig);\r
- redrawneeded = false;\r
- } else {\r
- ig = img.getGraphics();\r
+ g.drawImage(img, 0, 0, this);\r
}\r
\r
- g.drawImage(img,0,0,this);\r
- }\r
+ public void drawBackground(Graphics g, Color col) {\r
+ g.setColor(col);\r
+ g.fillRect(0, 0, prefsize.width, prefsize.height);\r
+ }\r
\r
- public void drawBackground(Graphics g, Color col) {\r
- g.setColor(col);\r
- g.fillRect(0,0,prefsize.width,prefsize.height);\r
- }\r
+ public void drawScene(Graphics g) {\r
+ // Sort the bonds by z coord\r
+ Vector bonds = new Vector();\r
\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++) {\r
+ if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {\r
+ Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
\r
- public void drawScene(Graphics g) {\r
- // Sort the bonds by z coord\r
+ for (int i = 0; i < tmp.size(); i++) {\r
+ bonds.addElement(tmp.elementAt(i));\r
+ }\r
+ }\r
+ }\r
\r
- Vector bonds = new Vector();\r
+ if (zbuffer) {\r
+ Zsort.Zsort(bonds);\r
+ }\r
\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmpBond = (Bond) bonds.elementAt(i);\r
+\r
+ xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +\r
+ (getWidth() / 2));\r
+ ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +\r
+ (getHeight() / 2));\r
+\r
+ xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +\r
+ (getWidth() / 2));\r
+ yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +\r
+ (getHeight() / 2));\r
+\r
+ xmid = (xend + xstart) / 2;\r
+ ymid = (yend + ystart) / 2;\r
+\r
+ if (depthcue && !bymolecule) {\r
+ if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {\r
+ g.setColor(tmpBond.startCol.darker().darker());\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+\r
+ g.setColor(tmpBond.endCol.darker().darker());\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {\r
+ g.setColor(tmpBond.startCol.darker());\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+\r
+ g.setColor(tmpBond.endCol.darker());\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ } else {\r
+ g.setColor(tmpBond.startCol);\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+\r
+ g.setColor(tmpBond.endCol);\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ }\r
+ } else if (depthcue && bymolecule) {\r
+ if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {\r
+ g.setColor(Color.green.darker().darker());\r
+ drawLine(g, xstart, ystart, xend, yend);\r
+ } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {\r
+ g.setColor(Color.green.darker());\r
+ drawLine(g, xstart, ystart, xend, yend);\r
+ } else {\r
+ g.setColor(Color.green);\r
+ drawLine(g, xstart, ystart, xend, yend);\r
+ }\r
+ } else if (!depthcue && !bymolecule) {\r
+ g.setColor(tmpBond.startCol);\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+ g.setColor(tmpBond.endCol);\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ } else {\r
+ drawLine(g, xstart, ystart, xend, yend);\r
+ }\r
+ }\r
+ }\r
\r
- for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
- if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {\r
+ public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {\r
+ if (!wire) {\r
+ if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {\r
+ g.drawLine(x1, y1, x2, y2);\r
+ g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);\r
+ g.drawLine(x1, y1 - 1, x2, y2 - 1);\r
+ } else {\r
+ g.setColor(g.getColor().brighter());\r
+ g.drawLine(x1, y1, x2, y2);\r
+ g.drawLine(x1 + 1, y1, x2 + 1, y2);\r
+ g.drawLine(x1 - 1, y1, x2 - 1, y2);\r
+ }\r
+ } else {\r
+ g.drawLine(x1, y1, x2, y2);\r
+ }\r
+ }\r
\r
- Vector tmp = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+ public Dimension minimumsize() {\r
+ return prefsize;\r
+ }\r
\r
- for (int i=0; i < tmp.size(); i++) {\r
- bonds.addElement(tmp.elementAt(i));\r
- }\r
- }\r
+ public Dimension preferredsize() {\r
+ return prefsize;\r
}\r
\r
- if (zbuffer) {\r
- Zsort.Zsort(bonds);\r
+ public void keyTyped(KeyEvent evt) {\r
}\r
\r
- for (int i = 0; i < bonds.size(); i++) {\r
- Bond tmpBond = (Bond)bonds.elementAt(i);\r
+ public void keyReleased(KeyEvent evt) {\r
+ }\r
\r
- xstart = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);\r
- ystart = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);\r
+ public void keyPressed(KeyEvent evt) {\r
+ int key = evt.getKeyChar();\r
+\r
+ if (evt.getKeyCode() == KeyEvent.VK_UP) {\r
+ scale = (float) (scale * 1.1);\r
+ redrawneeded = true;\r
+ repaint();\r
+ } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {\r
+ scale = (float) (scale * 0.9);\r
+ redrawneeded = true;\r
+ repaint();\r
+ } else if (key == 'w') {\r
+ wire = !wire;\r
+ System.out.println("wireframe " + wire);\r
+ redrawneeded = true;\r
+ repaint();\r
+ } else if (key == 'd') {\r
+ depthcue = !depthcue;\r
+ System.out.println("Depth cueing is " + depthcue);\r
+ redrawneeded = true;\r
+ repaint();\r
+ } else if (key == 'm') {\r
+ bymolecule = !bymolecule;\r
+ System.out.println("Bymolecule is " + bymolecule);\r
+ redrawneeded = true;\r
+ repaint();\r
+ } else if (key == 'z') {\r
+ zbuffer = !zbuffer;\r
+ System.out.println("Z buffering is " + zbuffer);\r
+ redrawneeded = true;\r
+ repaint();\r
+ } else if (key == 'c') {\r
+ bymolecule = false;\r
+ pdb.setChainColours();\r
+ System.out.println("Colouring by chain");\r
+ redrawneeded = true;\r
+ repaint();\r
+ } else if (key == 'h') {\r
+ bymolecule = false;\r
+ pdb.setHydrophobicityColours();\r
+ System.out.println("Colouring by hydrophobicity");\r
+ redrawneeded = true;\r
+ repaint();\r
+ } else if (key == 'q') {\r
+ bymolecule = false;\r
+ pdb.setChargeColours();\r
+ System.out.println("Colouring charges and cysteines");\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
\r
- xend = (int)((tmpBond.end[0] - centre[0])*scale + getWidth()/2);\r
- yend = (int)((tmpBond.end[1] - centre[1])*scale + getHeight()/2);\r
+ return;\r
+ }\r
\r
- xmid = (xend+xstart)/2;\r
- ymid = (yend+ystart)/2;\r
+ public void mousePressed(MouseEvent e) {\r
+ mx = e.getX();\r
+ my = e.getY();\r
+ omx = mx;\r
+ omy = my;\r
+ dragging = false;\r
+ }\r
\r
+ public void mouseMoved(MouseEvent e) {\r
+ myAtom fatom = null;\r
\r
- if (depthcue && !bymolecule) {\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++) {\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
\r
- if (tmpBond.start[2] < (centre[2] - maxwidth/6)) {\r
- g.setColor(tmpBond.startCol.darker().darker());\r
- drawLine(g,xstart,ystart,xmid,ymid);\r
+ if (chain.isVisible) {\r
+ Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
\r
- g.setColor(tmpBond.endCol.darker().darker());\r
- drawLine(g,xmid,ymid,xend,yend);\r
- } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {\r
- g.setColor(tmpBond.startCol.darker());\r
- drawLine(g,xstart,ystart,xmid,ymid);\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmpBond = (Bond) bonds.elementAt(i);\r
+ int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +\r
+ (getWidth() / 2));\r
\r
- g.setColor(tmpBond.endCol.darker());\r
- drawLine(g,xmid,ymid,xend,yend);\r
- } else {\r
- g.setColor(tmpBond.startCol);\r
- drawLine(g,xstart,ystart,xmid,ymid);\r
+ if (Math.abs(truex - e.getX()) <= 2) {\r
+ int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +\r
+ (getHeight() / 2));\r
\r
- g.setColor(tmpBond.endCol);\r
- drawLine(g,xmid,ymid,xend,yend);\r
+ if (Math.abs(truey - e.getY()) <= 2) {\r
+ fatom = tmpBond.at1;\r
+ }\r
+ }\r
+ }\r
+ }\r
}\r
- } else if (depthcue && bymolecule) {\r
- if (tmpBond.start[2] < (centre[2] - maxwidth/6)) {\r
- g.setColor(Color.green.darker().darker());\r
- drawLine(g,xstart,ystart,xend,yend);\r
-\r
- } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {\r
- g.setColor(Color.green.darker());\r
- drawLine(g,xstart,ystart,xend,yend);\r
\r
+ if (fatom != null) {\r
+ this.setToolTipText(fatom.resName);\r
} else {\r
- g.setColor(Color.green);\r
- drawLine(g,xstart,ystart,xend,yend);\r
-\r
+ this.setToolTipText(null);\r
}\r
- } else if (!depthcue && !bymolecule) {\r
- g.setColor(tmpBond.startCol);\r
- drawLine(g,xstart,ystart,xmid,ymid);\r
- g.setColor(tmpBond.endCol);\r
- drawLine(g,xmid,ymid,xend,yend);\r
-\r
- } else {\r
- drawLine(g,xstart,ystart,xend,yend);\r
- }\r
}\r
- }\r
\r
- public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {\r
- if (!wire) {\r
-\r
- if (((float)Math.abs(y2-y1)/(float)Math.abs(x2-x1)) < 0.5) {\r
-\r
- g.drawLine(x1,y1,x2,y2);\r
- g.drawLine(x1+1,y1+1,x2+1,y2+1);\r
- g.drawLine(x1,y1-1,x2,y2-1);\r
- } else {\r
- g.setColor(g.getColor().brighter());\r
- g.drawLine(x1,y1,x2,y2);\r
- g.drawLine(x1+1,y1,x2+1,y2);\r
- g.drawLine(x1-1,y1,x2-1,y2);\r
+ public void mouseClicked(MouseEvent e) {\r
+ }\r
\r
- }\r
- } else {\r
- g.drawLine(x1,y1,x2,y2);\r
+ public void mouseEntered(MouseEvent e) {\r
}\r
- }\r
-\r
- public Dimension minimumsize() {\r
- return prefsize;\r
- }\r
- public Dimension preferredsize() {\r
- return prefsize;\r
- }\r
-\r
- public void keyTyped(KeyEvent evt) { }\r
- public void keyReleased(KeyEvent evt) { }\r
- public void keyPressed(KeyEvent evt) {\r
- int key = evt.getKeyChar();\r
-\r
- if (evt.getKeyCode() == KeyEvent.VK_UP) {\r
- scale = (float)(scale * 1.1);\r
- redrawneeded = true;\r
- repaint();\r
-\r
- } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {\r
- scale = (float)(scale * 0.9);\r
- redrawneeded = true;\r
- repaint();\r
-\r
- } else if (key == 'w') {\r
-\r
- wire = !wire;\r
- System.out.println("wireframe " + wire);\r
- redrawneeded = true;\r
- repaint();\r
-\r
- } else if (key == 'd') {\r
- depthcue = !depthcue;\r
- System.out.println("Depth cueing is " + depthcue);\r
- redrawneeded = true;\r
- repaint();\r
-\r
- } else if (key == 'm') {\r
- bymolecule = !bymolecule;\r
- System.out.println("Bymolecule is " + bymolecule);\r
- redrawneeded = true;\r
- repaint();\r
-\r
- } else if (key == 'z') {\r
- zbuffer = !zbuffer;\r
- System.out.println("Z buffering is " + zbuffer);\r
- redrawneeded = true;\r
- repaint();\r
-\r
- } else if (key == 'c') {\r
- bymolecule = false;\r
- pdb.setChainColours();\r
- System.out.println("Colouring by chain");\r
- redrawneeded = true;\r
- repaint();\r
-\r
- } else if (key == 'h') {\r
- bymolecule = false;\r
- pdb.setHydrophobicityColours();\r
- System.out.println("Colouring by hydrophobicity");\r
- redrawneeded = true;\r
- repaint();\r
-\r
- } else if (key == 'q') {\r
- bymolecule = false;\r
- pdb.setChargeColours();\r
- System.out.println("Colouring charges and cysteines");\r
- redrawneeded = true;\r
- repaint();\r
\r
+ public void mouseExited(MouseEvent e) {\r
}\r
- return;\r
- }\r
\r
- public void mousePressed(MouseEvent e)\r
- {\r
+ public void mouseDragged(MouseEvent evt) {\r
+ int x = evt.getX();\r
+ int y = evt.getY();\r
+ mx = x;\r
+ my = y;\r
\r
- mx = e.getX();\r
- my = e.getY();\r
- omx = mx;\r
- omy = my;\r
- dragging = false;\r
-}\r
+ MCMatrix objmat = new MCMatrix(3, 3);\r
+ objmat.setIdentity();\r
\r
- public void mouseMoved(MouseEvent e)\r
- {\r
- myAtom fatom = null;\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
-\r
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
- if (chain.isVisible)\r
- {\r
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
- for (int i = 0; i < bonds.size(); i++)\r
- {\r
- Bond tmpBond = (Bond) bonds.elementAt(i);\r
- int truex = (int) ( (tmpBond.start[0] - centre[0]) * scale +\r
- getWidth() / 2);\r
- if (Math.abs(truex - e.getX()) <= 2)\r
- {\r
- int truey = (int) ( (tmpBond.start[1] - centre[1]) * scale +\r
- getHeight() / 2);\r
- if (Math.abs(truey - e.getY()) <= 2)\r
- fatom = tmpBond.at1;\r
- }\r
+ if ((evt.getModifiers() & Event.META_MASK) != 0) {\r
+ objmat.rotatez((float) ((mx - omx)));\r
+ } else {\r
+ objmat.rotatex((float) ((my - omy)));\r
+ objmat.rotatey((float) ((omx - mx)));\r
}\r
- }\r
- }\r
- if(fatom!=null)\r
- {\r
- this.setToolTipText(fatom.resName);\r
- }\r
- else\r
- this.setToolTipText(null);\r
- }\r
-\r
- public void mouseClicked(MouseEvent e) { }\r
- public void mouseEntered(MouseEvent e) { }\r
- public void mouseExited(MouseEvent e) { }\r
-\r
- public void mouseDragged(MouseEvent evt) {\r
- int x = evt.getX();\r
- int y = evt.getY();\r
- mx = x;\r
- my = y;\r
-\r
- MCMatrix objmat = new MCMatrix(3,3);\r
- objmat.setIdentity();\r
-\r
- if ((evt.getModifiers() & Event.META_MASK) != 0) {\r
- objmat.rotatez((float)((mx-omx)));\r
- } else {\r
- objmat.rotatex((float)((my-omy)));\r
- objmat.rotatey((float)((omx-mx)));\r
- }\r
\r
- //Alter the bonds\r
- for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
- Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+ //Alter the bonds\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++) {\r
+ Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
\r
- for (int i = 0; i < bonds.size(); i++) {\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmpBond = (Bond) bonds.elementAt(i);\r
\r
- Bond tmpBond = (Bond)bonds.elementAt(i);\r
+ //Translate the bond so the centre is 0,0,0\r
+ tmpBond.translate(-centre[0], -centre[1], -centre[2]);\r
\r
- //Translate the bond so the centre is 0,0,0\r
- tmpBond.translate(-centre[0],-centre[1],-centre[2]);\r
-\r
- //Now apply the rotation matrix\r
- tmpBond.start = objmat.vectorMultiply(tmpBond.start);\r
- tmpBond.end = objmat.vectorMultiply(tmpBond.end);\r
-\r
- //Now translate back again\r
- tmpBond.translate(centre[0],centre[1],centre[2]);\r
- }\r
- }\r
+ //Now apply the rotation matrix\r
+ tmpBond.start = objmat.vectorMultiply(tmpBond.start);\r
+ tmpBond.end = objmat.vectorMultiply(tmpBond.end);\r
\r
- objmat = null;\r
+ //Now translate back again\r
+ tmpBond.translate(centre[0], centre[1], centre[2]);\r
+ }\r
+ }\r
\r
- omx = mx;\r
- omy = my;\r
+ objmat = null;\r
\r
- redrawneeded = true;\r
+ omx = mx;\r
+ omy = my;\r
\r
- paint(this.getGraphics());\r
+ redrawneeded = true;\r
\r
- dragging = true;\r
- return;\r
- }\r
+ paint(this.getGraphics());\r
\r
- public void mouseReleased(MouseEvent evt) {\r
- int x = evt.getX();\r
- int y = evt.getY();\r
+ dragging = true;\r
\r
- if (!dragging) {\r
- myAtom tmp = findAtom(x,y);\r
+ return;\r
}\r
- drawLabels();\r
- return;\r
- }\r
-\r
- public void drawLabels() {\r
- redrawneeded = true;\r
- paint(this.getGraphics());\r
-\r
- for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
\r
- PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);\r
-\r
- if (chain.isVisible) {\r
-\r
- Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
-\r
- for (int i = 0; i < bonds.size(); i++) {\r
- Bond tmpBond = (Bond)bonds.elementAt(i);\r
-\r
- if (tmpBond.at1.isSelected) {\r
- labelAtom(img.getGraphics(),tmpBond,1);\r
- }\r
-\r
- if (tmpBond.at2.isSelected) {\r
- labelAtom(img.getGraphics(),tmpBond,2);\r
- }\r
+ public void mouseReleased(MouseEvent evt) {\r
+ int x = evt.getX();\r
+ int y = evt.getY();\r
\r
+ if (!dragging) {\r
+ myAtom tmp = findAtom(x, y);\r
}\r
- }\r
- }\r
-\r
- this.getGraphics().drawImage(img,0,0,this);\r
-\r
- dragging = false;\r
-\r
- }\r
-\r
- public void labelAtom(Graphics g,Bond b, int n) {\r
\r
- g.setFont(font);\r
+ drawLabels();\r
\r
- if (n ==1) {\r
-\r
- int xstart = (int)((b.start[0] - centre[0])*scale + getWidth()/2);\r
- int ystart = (int)((b.start[1] - centre[1])*scale + getHeight()/2);\r
-\r
- g.setColor(Color.red);\r
- g.drawString(b.at1.resName + "-" + b.at1.resNumber,xstart,ystart);\r
+ return;\r
}\r
\r
- if (n ==2) {\r
+ public void drawLabels() {\r
+ redrawneeded = true;\r
+ paint(this.getGraphics());\r
\r
- int xstart = (int)((b.end[0] - centre[0])*scale + getWidth()/2);\r
- int ystart = (int)((b.end[1] - centre[1])*scale + getHeight()/2);\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++) {\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
\r
- g.setColor(Color.red);\r
- g.drawString(b.at2.resName + "-" + b.at2.resNumber,xstart,ystart);\r
- }\r
- }\r
+ if (chain.isVisible) {\r
+ Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmpBond = (Bond) bonds.elementAt(i);\r
\r
- public myAtom findAtom(int x, int y) {\r
- myAtom fatom = null;\r
+ if (tmpBond.at1.isSelected) {\r
+ labelAtom(img.getGraphics(), tmpBond, 1);\r
+ }\r
\r
- int foundchain = -1;\r
+ if (tmpBond.at2.isSelected) {\r
+ labelAtom(img.getGraphics(), tmpBond, 2);\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
+ this.getGraphics().drawImage(img, 0, 0, this);\r
\r
- PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);\r
+ dragging = false;\r
+ }\r
\r
- if (chain.isVisible) {\r
+ public void labelAtom(Graphics g, Bond b, int n) {\r
+ g.setFont(font);\r
\r
- Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+ if (n == 1) {\r
+ int xstart = (int) (((b.start[0] - centre[0]) * scale) +\r
+ (getWidth() / 2));\r
+ int ystart = (int) (((b.start[1] - centre[1]) * scale) +\r
+ (getHeight() / 2));\r
\r
- for (int i = 0; i < bonds.size(); i++) {\r
- Bond tmpBond = (Bond)bonds.elementAt(i);\r
+ g.setColor(Color.red);\r
+ g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);\r
+ }\r
\r
- int truex = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);\r
+ if (n == 2) {\r
+ int xstart = (int) (((b.end[0] - centre[0]) * scale) +\r
+ (getWidth() / 2));\r
+ int ystart = (int) (((b.end[1] - centre[1]) * scale) +\r
+ (getHeight() / 2));\r
\r
- if (Math.abs(truex - x) <= 2) {\r
+ g.setColor(Color.red);\r
+ g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);\r
+ }\r
+ }\r
\r
- int truey = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);\r
+ public myAtom findAtom(int x, int y) {\r
+ myAtom fatom = null;\r
+\r
+ int foundchain = -1;\r
+\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++) {\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
+\r
+ if (chain.isVisible) {\r
+ Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmpBond = (Bond) bonds.elementAt(i);\r
+\r
+ int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +\r
+ (getWidth() / 2));\r
+\r
+ if (Math.abs(truex - x) <= 2) {\r
+ int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +\r
+ (getHeight() / 2));\r
+\r
+ if (Math.abs(truey - y) <= 2) {\r
+ System.out.println("Found match");\r
+ System.out.println(x + " " + y);\r
+ System.out.println(truex + " " + truey);\r
+ System.out.println(tmpBond.start[0] + " " +\r
+ tmpBond.start[1]);\r
+ System.out.println("Atom 1 = " +\r
+ tmpBond.at1.resName + " " +\r
+ tmpBond.at1.resNumber + " " +\r
+ tmpBond.at1.chain);\r
+ fatom = tmpBond.at1;\r
+ fatom.isSelected = !fatom.isSelected;\r
+ foundchain = ii;\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- if (Math.abs(truey - y) <= 2) {\r
+ if (fatom != null) //)&& chain.ds != null)\r
+ {\r
+ chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
\r
- System.out.println("Found match");\r
- System.out.println(x + " " + y);\r
- System.out.println(truex + " " + truey);\r
- System.out.println(tmpBond.start[0] + " " + tmpBond.start[1]);\r
- System.out.println("Atom 1 = " + tmpBond.at1.resName + " " +\r
- tmpBond.at1.resNumber + " " + tmpBond.at1.chain);\r
- fatom = tmpBond.at1;\r
- fatom.isSelected = !fatom.isSelected;\r
- foundchain = ii;\r
+ // SMJS TODO\r
+ // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;\r
+ // int pos = chain.ds.findIndex(tmp);\r
+ // System.out.println("Found seq " + chain.ds.name + " " + tmp + " " + pos);\r
}\r
- }\r
}\r
- }\r
-\r
- if (fatom != null) //)&& chain.ds != null)\r
- {\r
- chain = (PDBChain)pdb.chains.elementAt(foundchain);\r
- // SMJS TODO\r
- // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;\r
- // int pos = chain.ds.findIndex(tmp);\r
- // System.out.println("Found seq " + chain.ds.name + " " + tmp + " " + pos);\r
- }\r
\r
+ return fatom;\r
}\r
- return fatom;\r
- }\r
-\r
- public void update(Graphics g) {\r
- paint(g);\r
- }\r
\r
+ public void update(Graphics g) {\r
+ paint(g);\r
+ }\r
}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public interface JPredWS extends java.rmi.Remote {
- public java.lang.String predict(ext.vamsas.Sequence in0) throws java.rmi.RemoteException;
- public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0) throws java.rmi.RemoteException;
- public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException;
- public ext.vamsas.JpredResult getresult(java.lang.String in0) throws java.rmi.RemoteException;
-}
+*/\r
+package ext.vamsas;\r
+\r
+public interface JPredWS extends java.rmi.Remote {\r
+ public java.lang.String predict(ext.vamsas.Sequence in0)\r
+ throws java.rmi.RemoteException;\r
+\r
+ public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0)\r
+ throws java.rmi.RemoteException;\r
+\r
+ public ext.vamsas.Secstructpred getpredict(java.lang.String in0)\r
+ throws java.rmi.RemoteException;\r
+\r
+ public ext.vamsas.JpredResult getresult(java.lang.String in0)\r
+ throws java.rmi.RemoteException;\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public interface JPredWSService extends javax.xml.rpc.Service {
- public java.lang.String getjpredAddress();
-
- public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException;
-
- public ext.vamsas.JPredWS getjpred(java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
-}
+*/\r
+package ext.vamsas;\r
+\r
+public interface JPredWSService extends javax.xml.rpc.Service {\r
+ public java.lang.String getjpredAddress();\r
+\r
+ public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException;\r
+\r
+ public ext.vamsas.JPredWS getjpred(java.net.URL portAddress)\r
+ throws javax.xml.rpc.ServiceException;\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class JPredWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JPredWSService {
-
- public JPredWSServiceLocator() {
- }
-
-
- public JPredWSServiceLocator(org.apache.axis.EngineConfiguration config) {
- super(config);
- }
-
- // Use to get a proxy class for jpred
- private java.lang.String jpred_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred";
-
- public java.lang.String getjpredAddress() {
- return jpred_address;
- }
-
- // The WSDD service name defaults to the port name.
- private java.lang.String jpredWSDDServiceName = "jpred";
-
- public java.lang.String getjpredWSDDServiceName() {
- return jpredWSDDServiceName;
- }
-
- public void setjpredWSDDServiceName(java.lang.String name) {
- jpredWSDDServiceName = name;
- }
-
- public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException {
- java.net.URL endpoint;
- try {
- endpoint = new java.net.URL(jpred_address);
- }
- catch (java.net.MalformedURLException e) {
- throw new javax.xml.rpc.ServiceException(e);
- }
- return getjpred(endpoint);
- }
-
- public ext.vamsas.JPredWS getjpred(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
- try {
- ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(portAddress, this);
- _stub.setPortName(getjpredWSDDServiceName());
- return _stub;
- }
- catch (org.apache.axis.AxisFault e) {
- return null;
- }
- }
-
- public void setjpredEndpointAddress(java.lang.String address) {
- jpred_address = address;
- }
-
+*/\r
+package ext.vamsas;\r
+\r
+public class JPredWSServiceLocator extends org.apache.axis.client.Service\r
+ implements ext.vamsas.JPredWSService {\r
+ // Use to get a proxy class for jpred\r
+ private java.lang.String jpred_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred";\r
+\r
+ // The WSDD service name defaults to the port name.\r
+ private java.lang.String jpredWSDDServiceName = "jpred";\r
+ private java.util.HashSet ports = null;\r
+\r
+ public JPredWSServiceLocator() {\r
+ }\r
+\r
+ public JPredWSServiceLocator(org.apache.axis.EngineConfiguration config) {\r
+ super(config);\r
+ }\r
+\r
+ public java.lang.String getjpredAddress() {\r
+ return jpred_address;\r
+ }\r
+\r
+ public java.lang.String getjpredWSDDServiceName() {\r
+ return jpredWSDDServiceName;\r
+ }\r
+\r
+ public void setjpredWSDDServiceName(java.lang.String name) {\r
+ jpredWSDDServiceName = name;\r
+ }\r
+\r
+ public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException {\r
+ java.net.URL endpoint;\r
+\r
+ try {\r
+ endpoint = new java.net.URL(jpred_address);\r
+ } catch (java.net.MalformedURLException e) {\r
+ throw new javax.xml.rpc.ServiceException(e);\r
+ }\r
+\r
+ return getjpred(endpoint);\r
+ }\r
+\r
+ public ext.vamsas.JPredWS getjpred(java.net.URL portAddress)\r
+ throws javax.xml.rpc.ServiceException {\r
+ try {\r
+ ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(portAddress,\r
+ this);\r
+ _stub.setPortName(getjpredWSDDServiceName());\r
+\r
+ return _stub;\r
+ } catch (org.apache.axis.AxisFault e) {\r
+ return null;\r
+ }\r
+ }\r
+\r
+ public void setjpredEndpointAddress(java.lang.String address) {\r
+ jpred_address = address;\r
+ }\r
+\r
/**
- * For the given interface, get the stub implementation.
- * If this service has no port for the given interface,
- * then ServiceException is thrown.
- */
- public java.rmi.Remote getPort(Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
- try {
- if (ext.vamsas.JPredWS.class.isAssignableFrom(serviceEndpointInterface)) {
- ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(new java.net.URL(jpred_address), this);
- _stub.setPortName(getjpredWSDDServiceName());
- return _stub;
- }
- }
- catch (java.lang.Throwable t) {
- throw new javax.xml.rpc.ServiceException(t);
- }
- throw new javax.xml.rpc.ServiceException("There is no stub implementation for the interface: " + (serviceEndpointInterface == null ? "null" : serviceEndpointInterface.getName()));
- }
-
+ * For the given interface, get the stub implementation.
+ * If this service has no port for the given interface,
+ * then ServiceException is thrown.
+ */\r
+ public java.rmi.Remote getPort(Class serviceEndpointInterface)\r
+ throws javax.xml.rpc.ServiceException {\r
+ try {\r
+ if (ext.vamsas.JPredWS.class.isAssignableFrom(\r
+ serviceEndpointInterface)) {\r
+ ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(new java.net.URL(\r
+ jpred_address), this);\r
+ _stub.setPortName(getjpredWSDDServiceName());\r
+\r
+ return _stub;\r
+ }\r
+ } catch (java.lang.Throwable t) {\r
+ throw new javax.xml.rpc.ServiceException(t);\r
+ }\r
+\r
+ throw new javax.xml.rpc.ServiceException(\r
+ "There is no stub implementation for the interface: " +\r
+ ((serviceEndpointInterface == null) ? "null"\r
+ : serviceEndpointInterface.getName()));\r
+ }\r
+\r
/**
- * For the given interface, get the stub implementation.
- * If this service has no port for the given interface,
- * then ServiceException is thrown.
- */
- public java.rmi.Remote getPort(javax.xml.namespace.QName portName, Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
- if (portName == null) {
- return getPort(serviceEndpointInterface);
- }
- java.lang.String inputPortName = portName.getLocalPart();
- if ("jpred".equals(inputPortName)) {
- return getjpred();
- }
- else {
- java.rmi.Remote _stub = getPort(serviceEndpointInterface);
- ((org.apache.axis.client.Stub) _stub).setPortName(portName);
- return _stub;
- }
- }
-
- public javax.xml.namespace.QName getServiceName() {
- return new javax.xml.namespace.QName("vamsas", "JPredWSService");
- }
-
- private java.util.HashSet ports = null;
-
- public java.util.Iterator getPorts() {
- if (ports == null) {
- ports = new java.util.HashSet();
- ports.add(new javax.xml.namespace.QName("vamsas", "jpred"));
- }
- return ports.iterator();
- }
-
+ * For the given interface, get the stub implementation.
+ * If this service has no port for the given interface,
+ * then ServiceException is thrown.
+ */\r
+ public java.rmi.Remote getPort(javax.xml.namespace.QName portName,\r
+ Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {\r
+ if (portName == null) {\r
+ return getPort(serviceEndpointInterface);\r
+ }\r
+\r
+ java.lang.String inputPortName = portName.getLocalPart();\r
+\r
+ if ("jpred".equals(inputPortName)) {\r
+ return getjpred();\r
+ } else {\r
+ java.rmi.Remote _stub = getPort(serviceEndpointInterface);\r
+ ((org.apache.axis.client.Stub) _stub).setPortName(portName);\r
+\r
+ return _stub;\r
+ }\r
+ }\r
+\r
+ public javax.xml.namespace.QName getServiceName() {\r
+ return new javax.xml.namespace.QName("vamsas", "JPredWSService");\r
+ }\r
+\r
+ public java.util.Iterator getPorts() {\r
+ if (ports == null) {\r
+ ports = new java.util.HashSet();\r
+ ports.add(new javax.xml.namespace.QName("vamsas", "jpred"));\r
+ }\r
+\r
+ return ports.iterator();\r
+ }\r
+\r
/**
- * Set the endpoint address for the specified port name.
- */
- public void setEndpointAddress(java.lang.String portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
- if ("jpred".equals(portName)) {
- setjpredEndpointAddress(address);
- }
- else { // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
- }
- }
-
+* Set the endpoint address for the specified port name.
+*/\r
+ public void setEndpointAddress(java.lang.String portName,\r
+ java.lang.String address) throws javax.xml.rpc.ServiceException {\r
+ if ("jpred".equals(portName)) {\r
+ setjpredEndpointAddress(address);\r
+ } else { // Unknown Port Name\r
+ throw new javax.xml.rpc.ServiceException(\r
+ " Cannot set Endpoint Address for Unknown Port" + portName);\r
+ }\r
+ }\r
+\r
/**
- * Set the endpoint address for the specified port name.
- */
- public void setEndpointAddress(javax.xml.namespace.QName portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
- setEndpointAddress(portName.getLocalPart(), address);
- }
-
-}
+* Set the endpoint address for the specified port name.
+*/\r
+ public void setEndpointAddress(javax.xml.namespace.QName portName,\r
+ java.lang.String address) throws javax.xml.rpc.ServiceException {\r
+ setEndpointAddress(portName.getLocalPart(), address);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class JpredResult extends ext.vamsas.Result implements java.io.Serializable {
- private java.lang.String aligfile;
- private java.lang.String predfile;
-
- public JpredResult() {
- }
-
- public JpredResult(
- java.lang.String aligfile,
- java.lang.String predfile) {
- this.aligfile = aligfile;
- this.predfile = predfile;
- }
-
-
+*/\r
+package ext.vamsas;\r
+\r
+public class JpredResult extends ext.vamsas.Result\r
+ implements java.io.Serializable {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(JpredResult.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "JpredResult"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("aligfile");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "aligfile"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("predfile");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "predfile"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
+ private java.lang.String aligfile;\r
+ private java.lang.String predfile;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public JpredResult() {\r
+ }\r
+\r
+ public JpredResult(java.lang.String aligfile, java.lang.String predfile) {\r
+ this.aligfile = aligfile;\r
+ this.predfile = predfile;\r
+ }\r
+\r
/**
- * Gets the aligfile value for this JpredResult.
- *
- * @return aligfile
- */
- public java.lang.String getAligfile() {
- return aligfile;
- }
-
-
+ * Gets the aligfile value for this JpredResult.
+ *
+ * @return aligfile
+ */\r
+ public java.lang.String getAligfile() {\r
+ return aligfile;\r
+ }\r
+\r
/**
- * Sets the aligfile value for this JpredResult.
- *
- * @param aligfile
- */
- public void setAligfile(java.lang.String aligfile) {
- this.aligfile = aligfile;
- }
-
-
+ * Sets the aligfile value for this JpredResult.
+ *
+ * @param aligfile
+ */\r
+ public void setAligfile(java.lang.String aligfile) {\r
+ this.aligfile = aligfile;\r
+ }\r
+\r
/**
- * Gets the predfile value for this JpredResult.
- *
- * @return predfile
- */
- public java.lang.String getPredfile() {
- return predfile;
- }
-
-
+ * Gets the predfile value for this JpredResult.
+ *
+ * @return predfile
+ */\r
+ public java.lang.String getPredfile() {\r
+ return predfile;\r
+ }\r
+\r
/**
- * Sets the predfile value for this JpredResult.
- *
- * @param predfile
- */
- public void setPredfile(java.lang.String predfile) {
- this.predfile = predfile;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof JpredResult)) return false;
- JpredResult other = (JpredResult) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = super.equals(obj) &&
- ((this.aligfile==null && other.getAligfile()==null) ||
- (this.aligfile!=null &&
- this.aligfile.equals(other.getAligfile()))) &&
- ((this.predfile==null && other.getPredfile()==null) ||
- (this.predfile!=null &&
- this.predfile.equals(other.getPredfile())));
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = super.hashCode();
- if (getAligfile() != null) {
- _hashCode += getAligfile().hashCode();
- }
- if (getPredfile() != null) {
- _hashCode += getPredfile().hashCode();
- }
- __hashCodeCalc = false;
- return _hashCode;
- }
-
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(JpredResult.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("aligfile");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "aligfile"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("predfile");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "predfile"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- typeDesc.addFieldDesc(elemField);
- }
-
+ * Sets the predfile value for this JpredResult.
+ *
+ * @param predfile
+ */\r
+ public void setPredfile(java.lang.String predfile) {\r
+ this.predfile = predfile;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof JpredResult)) {\r
+ return false;\r
+ }\r
+\r
+ JpredResult other = (JpredResult) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = super.equals(obj) &&\r
+ (((this.aligfile == null) && (other.getAligfile() == null)) ||\r
+ ((this.aligfile != null) &&\r
+ this.aligfile.equals(other.getAligfile()))) &&\r
+ (((this.predfile == null) && (other.getPredfile() == null)) ||\r
+ ((this.predfile != null) &&\r
+ this.predfile.equals(other.getPredfile())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = super.hashCode();\r
+\r
+ if (getAligfile() != null) {\r
+ _hashCode += getAligfile().hashCode();\r
+ }\r
+\r
+ if (getPredfile() != null) {\r
+ _hashCode += getPredfile().hashCode();\r
+ }\r
+\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.JPredWS {
- private java.util.Vector cachedSerClasses = new java.util.Vector();
- private java.util.Vector cachedSerQNames = new java.util.Vector();
- private java.util.Vector cachedSerFactories = new java.util.Vector();
- private java.util.Vector cachedDeserFactories = new java.util.Vector();
-
- static org.apache.axis.description.OperationDesc [] _operations;
-
- static {
- _operations = new org.apache.axis.description.OperationDesc[4];
- _initOperationDesc1();
- }
-
- private static void _initOperationDesc1(){
- org.apache.axis.description.OperationDesc oper;
- oper = new org.apache.axis.description.OperationDesc();
- oper.setName("predict");
- oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence"), ext.vamsas.Sequence.class, org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- oper.setReturnClass(java.lang.String.class);
- oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "predictReturn"));
- oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
- oper.setUse(org.apache.axis.constants.Use.LITERAL);
- _operations[0] = oper;
-
- oper = new org.apache.axis.description.OperationDesc();
- oper.setName("predictOnMsa");
- oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment"), ext.vamsas.Msfalignment.class, org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- oper.setReturnClass(java.lang.String.class);
- oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "predictOnMsaReturn"));
- oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
- oper.setUse(org.apache.axis.constants.Use.LITERAL);
- _operations[1] = oper;
-
- oper = new org.apache.axis.description.OperationDesc();
- oper.setName("getpredict");
- oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.setReturnType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred"));
- oper.setReturnClass(ext.vamsas.Secstructpred.class);
- oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "getpredictReturn"));
- oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
- oper.setUse(org.apache.axis.constants.Use.LITERAL);
- _operations[2] = oper;
-
- oper = new org.apache.axis.description.OperationDesc();
- oper.setName("getresult");
- oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.setReturnType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult"));
- oper.setReturnClass(ext.vamsas.JpredResult.class);
- oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "getresultReturn"));
- oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
- oper.setUse(org.apache.axis.constants.Use.LITERAL);
- _operations[3] = oper;
-
- }
-
- public JpredSoapBindingStub() throws org.apache.axis.AxisFault {
- this(null);
- }
-
- public JpredSoapBindingStub(java.net.URL endpointURL, javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
- this(service);
- super.cachedEndpoint = endpointURL;
- }
-
- public JpredSoapBindingStub(javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
- if (service == null) {
- super.service = new org.apache.axis.client.Service();
- } else {
- super.service = service;
- }
- java.lang.Class cls;
- javax.xml.namespace.QName qName;
- java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
- java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
- java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
- java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
- java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
- java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
- java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
- java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
- java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
- java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
- qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence");
- cachedSerQNames.add(qName);
- cls = ext.vamsas.Sequence.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred");
- cachedSerQNames.add(qName);
- cls = ext.vamsas.Secstructpred.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment");
- cachedSerQNames.add(qName);
- cls = ext.vamsas.Msfalignment.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult");
- cachedSerQNames.add(qName);
- cls = ext.vamsas.JpredResult.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Result");
- cachedSerQNames.add(qName);
- cls = ext.vamsas.Result.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- }
-
- protected org.apache.axis.client.Call createCall() throws java.rmi.RemoteException {
- try {
- org.apache.axis.client.Call _call =
- (org.apache.axis.client.Call) super.service.createCall();
- if (super.maintainSessionSet) {
- _call.setMaintainSession(super.maintainSession);
- }
- if (super.cachedUsername != null) {
- _call.setUsername(super.cachedUsername);
- }
- if (super.cachedPassword != null) {
- _call.setPassword(super.cachedPassword);
- }
- if (super.cachedEndpoint != null) {
- _call.setTargetEndpointAddress(super.cachedEndpoint);
- }
- if (super.cachedTimeout != null) {
- _call.setTimeout(super.cachedTimeout);
- }
- if (super.cachedPortName != null) {
- _call.setPortName(super.cachedPortName);
- }
- java.util.Enumeration keys = super.cachedProperties.keys();
- while (keys.hasMoreElements()) {
- java.lang.String key = (java.lang.String) keys.nextElement();
- _call.setProperty(key, super.cachedProperties.get(key));
- }
- // All the type mapping information is registered
- // when the first call is made.
- // The type mapping information is actually registered in
- // the TypeMappingRegistry of the service, which
- // is the reason why registration is only needed for the first call.
- synchronized (this) {
- if (firstCall()) {
- // must set encoding style before registering serializers
- _call.setEncodingStyle(null);
- for (int i = 0; i < cachedSerFactories.size(); ++i) {
- java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
- javax.xml.namespace.QName qName =
- (javax.xml.namespace.QName) cachedSerQNames.get(i);
- java.lang.Class sf = (java.lang.Class)
- cachedSerFactories.get(i);
- java.lang.Class df = (java.lang.Class)
- cachedDeserFactories.get(i);
- _call.registerTypeMapping(cls, qName, sf, df, false);
- }
- }
- }
- return _call;
- }
- catch (java.lang.Throwable _t) {
- throw new org.apache.axis.AxisFault("Failure trying to get the Call object", _t);
- }
- }
-
- public java.lang.String predict(ext.vamsas.Sequence in0) throws java.rmi.RemoteException {
- if (super.cachedEndpoint == null) {
- throw new org.apache.axis.NoEndPointException();
- }
- org.apache.axis.client.Call _call = createCall();
- _call.setOperation(_operations[0]);
- _call.setUseSOAPAction(true);
- _call.setSOAPActionURI("");
- _call.setEncodingStyle(null);
- _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
- _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "predict"));
-
- setRequestHeaders(_call);
- setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
-
- if (_resp instanceof java.rmi.RemoteException) {
- throw (java.rmi.RemoteException)_resp;
- }
- else {
- extractAttachments(_call);
- try {
- return (java.lang.String) _resp;
- } catch (java.lang.Exception _exception) {
- return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String.class);
- }
- }
- }
-
- public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0) throws java.rmi.RemoteException {
- if (super.cachedEndpoint == null) {
- throw new org.apache.axis.NoEndPointException();
- }
- org.apache.axis.client.Call _call = createCall();
- _call.setOperation(_operations[1]);
- _call.setUseSOAPAction(true);
- _call.setSOAPActionURI("");
- _call.setEncodingStyle(null);
- _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
- _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "predictOnMsa"));
-
- setRequestHeaders(_call);
- setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
-
- if (_resp instanceof java.rmi.RemoteException) {
- throw (java.rmi.RemoteException)_resp;
- }
- else {
- extractAttachments(_call);
- try {
- return (java.lang.String) _resp;
- } catch (java.lang.Exception _exception) {
- return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String.class);
- }
- }
- }
-
- public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException {
- if (super.cachedEndpoint == null) {
- throw new org.apache.axis.NoEndPointException();
- }
- org.apache.axis.client.Call _call = createCall();
- _call.setOperation(_operations[2]);
- _call.setUseSOAPAction(true);
- _call.setSOAPActionURI("");
- _call.setEncodingStyle(null);
- _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
- _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getpredict"));
-
- setRequestHeaders(_call);
- setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
-
- if (_resp instanceof java.rmi.RemoteException) {
- throw (java.rmi.RemoteException)_resp;
- }
- else {
- extractAttachments(_call);
- try {
- return (ext.vamsas.Secstructpred) _resp;
- } catch (java.lang.Exception _exception) {
- return (ext.vamsas.Secstructpred) org.apache.axis.utils.JavaUtils.convert(_resp, ext.vamsas.Secstructpred.class);
- }
- }
- }
-
- public ext.vamsas.JpredResult getresult(java.lang.String in0) throws java.rmi.RemoteException {
- if (super.cachedEndpoint == null) {
- throw new org.apache.axis.NoEndPointException();
- }
- org.apache.axis.client.Call _call = createCall();
- _call.setOperation(_operations[3]);
- _call.setUseSOAPAction(true);
- _call.setSOAPActionURI("");
- _call.setEncodingStyle(null);
- _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
- _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getresult"));
-
- setRequestHeaders(_call);
- setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
-
- if (_resp instanceof java.rmi.RemoteException) {
- throw (java.rmi.RemoteException)_resp;
- }
- else {
- extractAttachments(_call);
- try {
- return (ext.vamsas.JpredResult) _resp;
- } catch (java.lang.Exception _exception) {
- return (ext.vamsas.JpredResult) org.apache.axis.utils.JavaUtils.convert(_resp, ext.vamsas.JpredResult.class);
- }
- }
- }
-
-}
+*/\r
+package ext.vamsas;\r
+\r
+public class JpredSoapBindingStub extends org.apache.axis.client.Stub\r
+ implements ext.vamsas.JPredWS {\r
+ static org.apache.axis.description.OperationDesc[] _operations;\r
+\r
+ static {\r
+ _operations = new org.apache.axis.description.OperationDesc[4];\r
+ _initOperationDesc1();\r
+ }\r
+\r
+ private java.util.Vector cachedSerClasses = new java.util.Vector();\r
+ private java.util.Vector cachedSerQNames = new java.util.Vector();\r
+ private java.util.Vector cachedSerFactories = new java.util.Vector();\r
+ private java.util.Vector cachedDeserFactories = new java.util.Vector();\r
+\r
+ public JpredSoapBindingStub() throws org.apache.axis.AxisFault {\r
+ this(null);\r
+ }\r
+\r
+ public JpredSoapBindingStub(java.net.URL endpointURL,\r
+ javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {\r
+ this(service);\r
+ super.cachedEndpoint = endpointURL;\r
+ }\r
+\r
+ public JpredSoapBindingStub(javax.xml.rpc.Service service)\r
+ throws org.apache.axis.AxisFault {\r
+ if (service == null) {\r
+ super.service = new org.apache.axis.client.Service();\r
+ } else {\r
+ super.service = service;\r
+ }\r
+\r
+ java.lang.Class cls;\r
+ javax.xml.namespace.QName qName;\r
+ java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;\r
+ java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;\r
+ java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;\r
+ java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;\r
+ java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;\r
+ java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;\r
+ java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;\r
+ java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;\r
+ java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;\r
+ java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;\r
+ qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",\r
+ "Sequence");\r
+ cachedSerQNames.add(qName);\r
+ cls = ext.vamsas.Sequence.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",\r
+ "Secstructpred");\r
+ cachedSerQNames.add(qName);\r
+ cls = ext.vamsas.Secstructpred.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",\r
+ "Msfalignment");\r
+ cachedSerQNames.add(qName);\r
+ cls = ext.vamsas.Msfalignment.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",\r
+ "JpredResult");\r
+ cachedSerQNames.add(qName);\r
+ cls = ext.vamsas.JpredResult.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",\r
+ "Result");\r
+ cachedSerQNames.add(qName);\r
+ cls = ext.vamsas.Result.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+ }\r
+\r
+ private static void _initOperationDesc1() {\r
+ org.apache.axis.description.OperationDesc oper;\r
+ oper = new org.apache.axis.description.OperationDesc();\r
+ oper.setName("predict");\r
+ oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"),\r
+ new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence"),\r
+ ext.vamsas.Sequence.class,\r
+ org.apache.axis.description.ParameterDesc.IN, false, false);\r
+ oper.setReturnType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ oper.setReturnClass(java.lang.String.class);\r
+ oper.setReturnQName(new javax.xml.namespace.QName("vamsas",\r
+ "predictReturn"));\r
+ oper.setStyle(org.apache.axis.constants.Style.WRAPPED);\r
+ oper.setUse(org.apache.axis.constants.Use.LITERAL);\r
+ _operations[0] = oper;\r
+\r
+ oper = new org.apache.axis.description.OperationDesc();\r
+ oper.setName("predictOnMsa");\r
+ oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"),\r
+ new javax.xml.namespace.QName("http://dataTypes.vamsas",\r
+ "Msfalignment"), ext.vamsas.Msfalignment.class,\r
+ org.apache.axis.description.ParameterDesc.IN, false, false);\r
+ oper.setReturnType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ oper.setReturnClass(java.lang.String.class);\r
+ oper.setReturnQName(new javax.xml.namespace.QName("vamsas",\r
+ "predictOnMsaReturn"));\r
+ oper.setStyle(org.apache.axis.constants.Style.WRAPPED);\r
+ oper.setUse(org.apache.axis.constants.Use.LITERAL);\r
+ _operations[1] = oper;\r
+\r
+ oper = new org.apache.axis.description.OperationDesc();\r
+ oper.setName("getpredict");\r
+ oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"),\r
+ new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",\r
+ "string"), java.lang.String.class,\r
+ org.apache.axis.description.ParameterDesc.IN, false, false);\r
+ oper.setReturnType(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "Secstructpred"));\r
+ oper.setReturnClass(ext.vamsas.Secstructpred.class);\r
+ oper.setReturnQName(new javax.xml.namespace.QName("vamsas",\r
+ "getpredictReturn"));\r
+ oper.setStyle(org.apache.axis.constants.Style.WRAPPED);\r
+ oper.setUse(org.apache.axis.constants.Use.LITERAL);\r
+ _operations[2] = oper;\r
+\r
+ oper = new org.apache.axis.description.OperationDesc();\r
+ oper.setName("getresult");\r
+ oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"),\r
+ new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",\r
+ "string"), java.lang.String.class,\r
+ org.apache.axis.description.ParameterDesc.IN, false, false);\r
+ oper.setReturnType(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "JpredResult"));\r
+ oper.setReturnClass(ext.vamsas.JpredResult.class);\r
+ oper.setReturnQName(new javax.xml.namespace.QName("vamsas",\r
+ "getresultReturn"));\r
+ oper.setStyle(org.apache.axis.constants.Style.WRAPPED);\r
+ oper.setUse(org.apache.axis.constants.Use.LITERAL);\r
+ _operations[3] = oper;\r
+ }\r
+\r
+ protected org.apache.axis.client.Call createCall()\r
+ throws java.rmi.RemoteException {\r
+ try {\r
+ org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service.createCall();\r
+\r
+ if (super.maintainSessionSet) {\r
+ _call.setMaintainSession(super.maintainSession);\r
+ }\r
+\r
+ if (super.cachedUsername != null) {\r
+ _call.setUsername(super.cachedUsername);\r
+ }\r
+\r
+ if (super.cachedPassword != null) {\r
+ _call.setPassword(super.cachedPassword);\r
+ }\r
+\r
+ if (super.cachedEndpoint != null) {\r
+ _call.setTargetEndpointAddress(super.cachedEndpoint);\r
+ }\r
+\r
+ if (super.cachedTimeout != null) {\r
+ _call.setTimeout(super.cachedTimeout);\r
+ }\r
+\r
+ if (super.cachedPortName != null) {\r
+ _call.setPortName(super.cachedPortName);\r
+ }\r
+\r
+ java.util.Enumeration keys = super.cachedProperties.keys();\r
+\r
+ while (keys.hasMoreElements()) {\r
+ java.lang.String key = (java.lang.String) keys.nextElement();\r
+ _call.setProperty(key, super.cachedProperties.get(key));\r
+ }\r
+\r
+ // All the type mapping information is registered\r
+ // when the first call is made.\r
+ // The type mapping information is actually registered in\r
+ // the TypeMappingRegistry of the service, which\r
+ // is the reason why registration is only needed for the first call.\r
+ synchronized (this) {\r
+ if (firstCall()) {\r
+ // must set encoding style before registering serializers\r
+ _call.setEncodingStyle(null);\r
+\r
+ for (int i = 0; i < cachedSerFactories.size(); ++i) {\r
+ java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);\r
+ javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames.get(i);\r
+ java.lang.Class sf = (java.lang.Class) cachedSerFactories.get(i);\r
+ java.lang.Class df = (java.lang.Class) cachedDeserFactories.get(i);\r
+ _call.registerTypeMapping(cls, qName, sf, df, false);\r
+ }\r
+ }\r
+ }\r
+\r
+ return _call;\r
+ } catch (java.lang.Throwable _t) {\r
+ throw new org.apache.axis.AxisFault("Failure trying to get the Call object",\r
+ _t);\r
+ }\r
+ }\r
+\r
+ public java.lang.String predict(ext.vamsas.Sequence in0)\r
+ throws java.rmi.RemoteException {\r
+ if (super.cachedEndpoint == null) {\r
+ throw new org.apache.axis.NoEndPointException();\r
+ }\r
+\r
+ org.apache.axis.client.Call _call = createCall();\r
+ _call.setOperation(_operations[0]);\r
+ _call.setUseSOAPAction(true);\r
+ _call.setSOAPActionURI("");\r
+ _call.setEncodingStyle(null);\r
+ _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,\r
+ Boolean.FALSE);\r
+ _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,\r
+ Boolean.FALSE);\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setOperationName(new javax.xml.namespace.QName("vamsas", "predict"));\r
+\r
+ setRequestHeaders(_call);\r
+ setAttachments(_call);\r
+\r
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { in0 });\r
+\r
+ if (_resp instanceof java.rmi.RemoteException) {\r
+ throw (java.rmi.RemoteException) _resp;\r
+ } else {\r
+ extractAttachments(_call);\r
+\r
+ try {\r
+ return (java.lang.String) _resp;\r
+ } catch (java.lang.Exception _exception) {\r
+ return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp,\r
+ java.lang.String.class);\r
+ }\r
+ }\r
+ }\r
+\r
+ public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0)\r
+ throws java.rmi.RemoteException {\r
+ if (super.cachedEndpoint == null) {\r
+ throw new org.apache.axis.NoEndPointException();\r
+ }\r
+\r
+ org.apache.axis.client.Call _call = createCall();\r
+ _call.setOperation(_operations[1]);\r
+ _call.setUseSOAPAction(true);\r
+ _call.setSOAPActionURI("");\r
+ _call.setEncodingStyle(null);\r
+ _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,\r
+ Boolean.FALSE);\r
+ _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,\r
+ Boolean.FALSE);\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setOperationName(new javax.xml.namespace.QName("vamsas",\r
+ "predictOnMsa"));\r
+\r
+ setRequestHeaders(_call);\r
+ setAttachments(_call);\r
+\r
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { in0 });\r
+\r
+ if (_resp instanceof java.rmi.RemoteException) {\r
+ throw (java.rmi.RemoteException) _resp;\r
+ } else {\r
+ extractAttachments(_call);\r
+\r
+ try {\r
+ return (java.lang.String) _resp;\r
+ } catch (java.lang.Exception _exception) {\r
+ return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp,\r
+ java.lang.String.class);\r
+ }\r
+ }\r
+ }\r
+\r
+ public ext.vamsas.Secstructpred getpredict(java.lang.String in0)\r
+ throws java.rmi.RemoteException {\r
+ if (super.cachedEndpoint == null) {\r
+ throw new org.apache.axis.NoEndPointException();\r
+ }\r
+\r
+ org.apache.axis.client.Call _call = createCall();\r
+ _call.setOperation(_operations[2]);\r
+ _call.setUseSOAPAction(true);\r
+ _call.setSOAPActionURI("");\r
+ _call.setEncodingStyle(null);\r
+ _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,\r
+ Boolean.FALSE);\r
+ _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,\r
+ Boolean.FALSE);\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setOperationName(new javax.xml.namespace.QName("vamsas",\r
+ "getpredict"));\r
+\r
+ setRequestHeaders(_call);\r
+ setAttachments(_call);\r
+\r
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { in0 });\r
+\r
+ if (_resp instanceof java.rmi.RemoteException) {\r
+ throw (java.rmi.RemoteException) _resp;\r
+ } else {\r
+ extractAttachments(_call);\r
+\r
+ try {\r
+ return (ext.vamsas.Secstructpred) _resp;\r
+ } catch (java.lang.Exception _exception) {\r
+ return (ext.vamsas.Secstructpred) org.apache.axis.utils.JavaUtils.convert(_resp,\r
+ ext.vamsas.Secstructpred.class);\r
+ }\r
+ }\r
+ }\r
+\r
+ public ext.vamsas.JpredResult getresult(java.lang.String in0)\r
+ throws java.rmi.RemoteException {\r
+ if (super.cachedEndpoint == null) {\r
+ throw new org.apache.axis.NoEndPointException();\r
+ }\r
+\r
+ org.apache.axis.client.Call _call = createCall();\r
+ _call.setOperation(_operations[3]);\r
+ _call.setUseSOAPAction(true);\r
+ _call.setSOAPActionURI("");\r
+ _call.setEncodingStyle(null);\r
+ _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,\r
+ Boolean.FALSE);\r
+ _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,\r
+ Boolean.FALSE);\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setOperationName(new javax.xml.namespace.QName("vamsas",\r
+ "getresult"));\r
+\r
+ setRequestHeaders(_call);\r
+ setAttachments(_call);\r
+\r
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { in0 });\r
+\r
+ if (_resp instanceof java.rmi.RemoteException) {\r
+ throw (java.rmi.RemoteException) _resp;\r
+ } else {\r
+ extractAttachments(_call);\r
+\r
+ try {\r
+ return (ext.vamsas.JpredResult) _resp;\r
+ } catch (java.lang.Exception _exception) {\r
+ return (ext.vamsas.JpredResult) org.apache.axis.utils.JavaUtils.convert(_resp,\r
+ ext.vamsas.JpredResult.class);\r
+ }\r
+ }\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class Msfalignment implements java.io.Serializable {
- private java.lang.String msf;
- private java.lang.String notes;
-
- public Msfalignment() {
- }
-
- public Msfalignment(
- java.lang.String msf,
- java.lang.String notes) {
- this.msf = msf;
- this.notes = notes;
- }
-
-
+*/\r
+package ext.vamsas;\r
+\r
+public class Msfalignment implements java.io.Serializable {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Msfalignment.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "Msfalignment"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("msf");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "msf"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("notes");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "notes"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
+ private java.lang.String msf;\r
+ private java.lang.String notes;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Msfalignment() {\r
+ }\r
+\r
+ public Msfalignment(java.lang.String msf, java.lang.String notes) {\r
+ this.msf = msf;\r
+ this.notes = notes;\r
+ }\r
+\r
/**
- * Gets the msf value for this Msfalignment.
- *
- * @return msf
- */
- public java.lang.String getMsf() {
- return msf;
- }
-
-
+ * Gets the msf value for this Msfalignment.
+ *
+ * @return msf
+ */\r
+ public java.lang.String getMsf() {\r
+ return msf;\r
+ }\r
+\r
/**
- * Sets the msf value for this Msfalignment.
- *
- * @param msf
- */
- public void setMsf(java.lang.String msf) {
- this.msf = msf;
- }
-
-
+ * Sets the msf value for this Msfalignment.
+ *
+ * @param msf
+ */\r
+ public void setMsf(java.lang.String msf) {\r
+ this.msf = msf;\r
+ }\r
+\r
/**
- * Gets the notes value for this Msfalignment.
- *
- * @return notes
- */
- public java.lang.String getNotes() {
- return notes;
- }
-
-
+ * Gets the notes value for this Msfalignment.
+ *
+ * @return notes
+ */\r
+ public java.lang.String getNotes() {\r
+ return notes;\r
+ }\r
+\r
/**
- * Sets the notes value for this Msfalignment.
- *
- * @param notes
- */
- public void setNotes(java.lang.String notes) {
- this.notes = notes;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof Msfalignment)) return false;
- Msfalignment other = (Msfalignment) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true &&
- ((this.msf==null && other.getMsf()==null) ||
- (this.msf!=null &&
- this.msf.equals(other.getMsf()))) &&
- ((this.notes==null && other.getNotes()==null) ||
- (this.notes!=null &&
- this.notes.equals(other.getNotes())));
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- if (getMsf() != null) {
- _hashCode += getMsf().hashCode();
- }
- if (getNotes() != null) {
- _hashCode += getNotes().hashCode();
- }
- __hashCodeCalc = false;
- return _hashCode;
- }
-
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(Msfalignment.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("msf");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "msf"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("notes");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "notes"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- typeDesc.addFieldDesc(elemField);
- }
-
+ * Sets the notes value for this Msfalignment.
+ *
+ * @param notes
+ */\r
+ public void setNotes(java.lang.String notes) {\r
+ this.notes = notes;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof Msfalignment)) {\r
+ return false;\r
+ }\r
+\r
+ Msfalignment other = (Msfalignment) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true &&\r
+ (((this.msf == null) && (other.getMsf() == null)) ||\r
+ ((this.msf != null) && this.msf.equals(other.getMsf()))) &&\r
+ (((this.notes == null) && (other.getNotes() == null)) ||\r
+ ((this.notes != null) && this.notes.equals(other.getNotes())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+\r
+ if (getMsf() != null) {\r
+ _hashCode += getMsf().hashCode();\r
+ }\r
+\r
+ if (getNotes() != null) {\r
+ _hashCode += getNotes().hashCode();\r
+ }\r
+\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public interface MuscleWS extends java.rmi.Remote {
- public vamsas.objects.simple.WsJobId align(vamsas.objects.simple.SequenceSet seqSet) throws java.rmi.RemoteException;
- public vamsas.objects.simple.Alignment getalign(java.lang.String job_id) throws java.rmi.RemoteException;
- public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id) throws java.rmi.RemoteException;
- public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId) throws java.rmi.RemoteException;
-}
+*/\r
+package ext.vamsas;\r
+\r
+public interface MuscleWS extends java.rmi.Remote {\r
+ public vamsas.objects.simple.WsJobId align(\r
+ vamsas.objects.simple.SequenceSet seqSet)\r
+ throws java.rmi.RemoteException;\r
+\r
+ public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)\r
+ throws java.rmi.RemoteException;\r
+\r
+ public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)\r
+ throws java.rmi.RemoteException;\r
+\r
+ public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)\r
+ throws java.rmi.RemoteException;\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public interface MuscleWSService extends javax.xml.rpc.Service {
- public java.lang.String getMuscleWSAddress();
-
- public ext.vamsas.MuscleWS getMuscleWS() throws javax.xml.rpc.ServiceException;
-
- public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
-}
+*/\r
+package ext.vamsas;\r
+\r
+public interface MuscleWSService extends javax.xml.rpc.Service {\r
+ public java.lang.String getMuscleWSAddress();\r
+\r
+ public ext.vamsas.MuscleWS getMuscleWS()\r
+ throws javax.xml.rpc.ServiceException;\r
+\r
+ public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)\r
+ throws javax.xml.rpc.ServiceException;\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class MuscleWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.MuscleWSService {
-
- public MuscleWSServiceLocator() {
- }
-
-
- public MuscleWSServiceLocator(org.apache.axis.EngineConfiguration config) {
- super(config);
- }
-
- // Use to get a proxy class for MuscleWS
- private java.lang.String MuscleWS_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/MuscleWS";
-
- public java.lang.String getMuscleWSAddress() {
- return MuscleWS_address;
- }
-
- // The WSDD service name defaults to the port name.
- private java.lang.String MuscleWSWSDDServiceName = "MuscleWS";
-
- public java.lang.String getMuscleWSWSDDServiceName() {
- return MuscleWSWSDDServiceName;
- }
-
- public void setMuscleWSWSDDServiceName(java.lang.String name) {
- MuscleWSWSDDServiceName = name;
- }
-
- public ext.vamsas.MuscleWS getMuscleWS() throws javax.xml.rpc.ServiceException {
- java.net.URL endpoint;
- try {
- endpoint = new java.net.URL(MuscleWS_address);
- }
- catch (java.net.MalformedURLException e) {
- throw new javax.xml.rpc.ServiceException(e);
- }
- return getMuscleWS(endpoint);
- }
-
- public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
- try {
- ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(portAddress, this);
- _stub.setPortName(getMuscleWSWSDDServiceName());
- return _stub;
- }
- catch (org.apache.axis.AxisFault e) {
- return null;
- }
- }
-
- public void setMuscleWSEndpointAddress(java.lang.String address) {
- MuscleWS_address = address;
- }
-
+*/\r
+package ext.vamsas;\r
+\r
+public class MuscleWSServiceLocator extends org.apache.axis.client.Service\r
+ implements ext.vamsas.MuscleWSService {\r
+ // Use to get a proxy class for MuscleWS\r
+ private java.lang.String MuscleWS_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/MuscleWS";\r
+\r
+ // The WSDD service name defaults to the port name.\r
+ private java.lang.String MuscleWSWSDDServiceName = "MuscleWS";\r
+ private java.util.HashSet ports = null;\r
+\r
+ public MuscleWSServiceLocator() {\r
+ }\r
+\r
+ public MuscleWSServiceLocator(org.apache.axis.EngineConfiguration config) {\r
+ super(config);\r
+ }\r
+\r
+ public java.lang.String getMuscleWSAddress() {\r
+ return MuscleWS_address;\r
+ }\r
+\r
+ public java.lang.String getMuscleWSWSDDServiceName() {\r
+ return MuscleWSWSDDServiceName;\r
+ }\r
+\r
+ public void setMuscleWSWSDDServiceName(java.lang.String name) {\r
+ MuscleWSWSDDServiceName = name;\r
+ }\r
+\r
+ public ext.vamsas.MuscleWS getMuscleWS()\r
+ throws javax.xml.rpc.ServiceException {\r
+ java.net.URL endpoint;\r
+\r
+ try {\r
+ endpoint = new java.net.URL(MuscleWS_address);\r
+ } catch (java.net.MalformedURLException e) {\r
+ throw new javax.xml.rpc.ServiceException(e);\r
+ }\r
+\r
+ return getMuscleWS(endpoint);\r
+ }\r
+\r
+ public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)\r
+ throws javax.xml.rpc.ServiceException {\r
+ try {\r
+ ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(portAddress,\r
+ this);\r
+ _stub.setPortName(getMuscleWSWSDDServiceName());\r
+\r
+ return _stub;\r
+ } catch (org.apache.axis.AxisFault e) {\r
+ return null;\r
+ }\r
+ }\r
+\r
+ public void setMuscleWSEndpointAddress(java.lang.String address) {\r
+ MuscleWS_address = address;\r
+ }\r
+\r
/**
- * For the given interface, get the stub implementation.
- * If this service has no port for the given interface,
- * then ServiceException is thrown.
- */
- public java.rmi.Remote getPort(Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
- try {
- if (ext.vamsas.MuscleWS.class.isAssignableFrom(serviceEndpointInterface)) {
- ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(new java.net.URL(MuscleWS_address), this);
- _stub.setPortName(getMuscleWSWSDDServiceName());
- return _stub;
- }
- }
- catch (java.lang.Throwable t) {
- throw new javax.xml.rpc.ServiceException(t);
- }
- throw new javax.xml.rpc.ServiceException("There is no stub implementation for the interface: " + (serviceEndpointInterface == null ? "null" : serviceEndpointInterface.getName()));
- }
-
+ * For the given interface, get the stub implementation.
+ * If this service has no port for the given interface,
+ * then ServiceException is thrown.
+ */\r
+ public java.rmi.Remote getPort(Class serviceEndpointInterface)\r
+ throws javax.xml.rpc.ServiceException {\r
+ try {\r
+ if (ext.vamsas.MuscleWS.class.isAssignableFrom(\r
+ serviceEndpointInterface)) {\r
+ ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(new java.net.URL(\r
+ MuscleWS_address), this);\r
+ _stub.setPortName(getMuscleWSWSDDServiceName());\r
+\r
+ return _stub;\r
+ }\r
+ } catch (java.lang.Throwable t) {\r
+ throw new javax.xml.rpc.ServiceException(t);\r
+ }\r
+\r
+ throw new javax.xml.rpc.ServiceException(\r
+ "There is no stub implementation for the interface: " +\r
+ ((serviceEndpointInterface == null) ? "null"\r
+ : serviceEndpointInterface.getName()));\r
+ }\r
+\r
/**
- * For the given interface, get the stub implementation.
- * If this service has no port for the given interface,
- * then ServiceException is thrown.
- */
- public java.rmi.Remote getPort(javax.xml.namespace.QName portName, Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
- if (portName == null) {
- return getPort(serviceEndpointInterface);
- }
- java.lang.String inputPortName = portName.getLocalPart();
- if ("MuscleWS".equals(inputPortName)) {
- return getMuscleWS();
- }
- else {
- java.rmi.Remote _stub = getPort(serviceEndpointInterface);
- ((org.apache.axis.client.Stub) _stub).setPortName(portName);
- return _stub;
- }
- }
-
- public javax.xml.namespace.QName getServiceName() {
- return new javax.xml.namespace.QName("vamsas", "MuscleWSService");
- }
-
- private java.util.HashSet ports = null;
-
- public java.util.Iterator getPorts() {
- if (ports == null) {
- ports = new java.util.HashSet();
- ports.add(new javax.xml.namespace.QName("vamsas", "MuscleWS"));
- }
- return ports.iterator();
- }
-
+ * For the given interface, get the stub implementation.
+ * If this service has no port for the given interface,
+ * then ServiceException is thrown.
+ */\r
+ public java.rmi.Remote getPort(javax.xml.namespace.QName portName,\r
+ Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {\r
+ if (portName == null) {\r
+ return getPort(serviceEndpointInterface);\r
+ }\r
+\r
+ java.lang.String inputPortName = portName.getLocalPart();\r
+\r
+ if ("MuscleWS".equals(inputPortName)) {\r
+ return getMuscleWS();\r
+ } else {\r
+ java.rmi.Remote _stub = getPort(serviceEndpointInterface);\r
+ ((org.apache.axis.client.Stub) _stub).setPortName(portName);\r
+\r
+ return _stub;\r
+ }\r
+ }\r
+\r
+ public javax.xml.namespace.QName getServiceName() {\r
+ return new javax.xml.namespace.QName("vamsas", "MuscleWSService");\r
+ }\r
+\r
+ public java.util.Iterator getPorts() {\r
+ if (ports == null) {\r
+ ports = new java.util.HashSet();\r
+ ports.add(new javax.xml.namespace.QName("vamsas", "MuscleWS"));\r
+ }\r
+\r
+ return ports.iterator();\r
+ }\r
+\r
/**
- * Set the endpoint address for the specified port name.
- */
- public void setEndpointAddress(java.lang.String portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
- if ("MuscleWS".equals(portName)) {
- setMuscleWSEndpointAddress(address);
- }
- else { // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
- }
- }
-
+* Set the endpoint address for the specified port name.
+*/\r
+ public void setEndpointAddress(java.lang.String portName,\r
+ java.lang.String address) throws javax.xml.rpc.ServiceException {\r
+ if ("MuscleWS".equals(portName)) {\r
+ setMuscleWSEndpointAddress(address);\r
+ } else { // Unknown Port Name\r
+ throw new javax.xml.rpc.ServiceException(\r
+ " Cannot set Endpoint Address for Unknown Port" + portName);\r
+ }\r
+ }\r
+\r
/**
- * Set the endpoint address for the specified port name.
- */
- public void setEndpointAddress(javax.xml.namespace.QName portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
- setEndpointAddress(portName.getLocalPart(), address);
- }
-
-}
+* Set the endpoint address for the specified port name.
+*/\r
+ public void setEndpointAddress(javax.xml.namespace.QName portName,\r
+ java.lang.String address) throws javax.xml.rpc.ServiceException {\r
+ setEndpointAddress(portName.getLocalPart(), address);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.MuscleWS {
- private java.util.Vector cachedSerClasses = new java.util.Vector();
- private java.util.Vector cachedSerQNames = new java.util.Vector();
- private java.util.Vector cachedSerFactories = new java.util.Vector();
- private java.util.Vector cachedDeserFactories = new java.util.Vector();
-
- static org.apache.axis.description.OperationDesc [] _operations;
-
- static {
- _operations = new org.apache.axis.description.OperationDesc[4];
- _initOperationDesc1();
- }
-
- private static void _initOperationDesc1(){
- org.apache.axis.description.OperationDesc oper;
- oper = new org.apache.axis.description.OperationDesc();
- oper.setName("align");
- oper.addParameter(new javax.xml.namespace.QName("", "seqSet"), new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"), vamsas.objects.simple.SequenceSet.class, org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
- oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
- oper.setReturnQName(new javax.xml.namespace.QName("", "alignReturn"));
- oper.setStyle(org.apache.axis.constants.Style.RPC);
- oper.setUse(org.apache.axis.constants.Use.ENCODED);
- _operations[0] = oper;
-
- oper = new org.apache.axis.description.OperationDesc();
- oper.setName("getalign");
- oper.addParameter(new javax.xml.namespace.QName("", "job_id"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
- oper.setReturnClass(vamsas.objects.simple.Alignment.class);
- oper.setReturnQName(new javax.xml.namespace.QName("", "getalignReturn"));
- oper.setStyle(org.apache.axis.constants.Style.RPC);
- oper.setUse(org.apache.axis.constants.Use.ENCODED);
- _operations[1] = oper;
-
- oper = new org.apache.axis.description.OperationDesc();
- oper.setName("getResult");
- oper.addParameter(new javax.xml.namespace.QName("", "job_id"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "MsaResult"));
- oper.setReturnClass(vamsas.objects.simple.MsaResult.class);
- oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));
- oper.setStyle(org.apache.axis.constants.Style.RPC);
- oper.setUse(org.apache.axis.constants.Use.ENCODED);
- _operations[2] = oper;
-
- oper = new org.apache.axis.description.OperationDesc();
- oper.setName("cancel");
- oper.addParameter(new javax.xml.namespace.QName("", "jobId"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
- oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
- oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));
- oper.setStyle(org.apache.axis.constants.Style.RPC);
- oper.setUse(org.apache.axis.constants.Use.ENCODED);
- _operations[3] = oper;
-
- }
-
- public MuscleWSSoapBindingStub() throws org.apache.axis.AxisFault {
- this(null);
- }
-
- public MuscleWSSoapBindingStub(java.net.URL endpointURL, javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
- this(service);
- super.cachedEndpoint = endpointURL;
- }
-
- public MuscleWSSoapBindingStub(javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
- if (service == null) {
- super.service = new org.apache.axis.client.Service();
- } else {
- super.service = service;
- }
- java.lang.Class cls;
- javax.xml.namespace.QName qName;
- java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
- java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
- java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
- java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
- java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
- java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
- java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
- java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
- java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
- java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence");
- cachedSerQNames.add(qName);
- cls = vamsas.objects.simple.Sequence.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
- cachedSerQNames.add(qName);
- cls = vamsas.objects.simple.Sequence[].class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(arraysf);
- cachedDeserFactories.add(arraydf);
-
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "MsaResult");
- cachedSerQNames.add(qName);
- cls = vamsas.objects.simple.MsaResult.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet");
- cachedSerQNames.add(qName);
- cls = vamsas.objects.simple.SequenceSet.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("http://simple.objects.vamsas", "Object");
- cachedSerQNames.add(qName);
- cls = vamsas.objects.simple.Object.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment");
- cachedSerQNames.add(qName);
- cls = vamsas.objects.simple.Alignment.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId");
- cachedSerQNames.add(qName);
- cls = vamsas.objects.simple.WsJobId.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");
- cachedSerQNames.add(qName);
- cls = java.lang.String[].class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(arraysf);
- cachedDeserFactories.add(arraydf);
-
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
- cachedSerQNames.add(qName);
- cls = vamsas.objects.simple.Result.class;
- cachedSerClasses.add(cls);
- cachedSerFactories.add(beansf);
- cachedDeserFactories.add(beandf);
-
- }
-
- protected org.apache.axis.client.Call createCall() throws java.rmi.RemoteException {
- try {
- org.apache.axis.client.Call _call =
- (org.apache.axis.client.Call) super.service.createCall();
- if (super.maintainSessionSet) {
- _call.setMaintainSession(super.maintainSession);
- }
- if (super.cachedUsername != null) {
- _call.setUsername(super.cachedUsername);
- }
- if (super.cachedPassword != null) {
- _call.setPassword(super.cachedPassword);
- }
- if (super.cachedEndpoint != null) {
- _call.setTargetEndpointAddress(super.cachedEndpoint);
- }
- if (super.cachedTimeout != null) {
- _call.setTimeout(super.cachedTimeout);
- }
- if (super.cachedPortName != null) {
- _call.setPortName(super.cachedPortName);
- }
- java.util.Enumeration keys = super.cachedProperties.keys();
- while (keys.hasMoreElements()) {
- java.lang.String key = (java.lang.String) keys.nextElement();
- _call.setProperty(key, super.cachedProperties.get(key));
- }
- // All the type mapping information is registered
- // when the first call is made.
- // The type mapping information is actually registered in
- // the TypeMappingRegistry of the service, which
- // is the reason why registration is only needed for the first call.
- synchronized (this) {
- if (firstCall()) {
- // must set encoding style before registering serializers
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
- for (int i = 0; i < cachedSerFactories.size(); ++i) {
- java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
- javax.xml.namespace.QName qName =
- (javax.xml.namespace.QName) cachedSerQNames.get(i);
- java.lang.Class sf = (java.lang.Class)
- cachedSerFactories.get(i);
- java.lang.Class df = (java.lang.Class)
- cachedDeserFactories.get(i);
- _call.registerTypeMapping(cls, qName, sf, df, false);
- }
- }
- }
- return _call;
- }
- catch (java.lang.Throwable _t) {
- throw new org.apache.axis.AxisFault("Failure trying to get the Call object", _t);
- }
- }
-
- public vamsas.objects.simple.WsJobId align(vamsas.objects.simple.SequenceSet seqSet) throws java.rmi.RemoteException {
- if (super.cachedEndpoint == null) {
- throw new org.apache.axis.NoEndPointException();
- }
- org.apache.axis.client.Call _call = createCall();
- _call.setOperation(_operations[0]);
- _call.setUseSOAPAction(true);
- _call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "align"));
-
- setRequestHeaders(_call);
- setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {seqSet});
-
- if (_resp instanceof java.rmi.RemoteException) {
- throw (java.rmi.RemoteException)_resp;
- }
- else {
- extractAttachments(_call);
- try {
- return (vamsas.objects.simple.WsJobId) _resp;
- } catch (java.lang.Exception _exception) {
- return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.WsJobId.class);
- }
- }
- }
-
- public vamsas.objects.simple.Alignment getalign(java.lang.String job_id) throws java.rmi.RemoteException {
- if (super.cachedEndpoint == null) {
- throw new org.apache.axis.NoEndPointException();
- }
- org.apache.axis.client.Call _call = createCall();
- _call.setOperation(_operations[1]);
- _call.setUseSOAPAction(true);
- _call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getalign"));
-
- setRequestHeaders(_call);
- setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {job_id});
-
- if (_resp instanceof java.rmi.RemoteException) {
- throw (java.rmi.RemoteException)_resp;
- }
- else {
- extractAttachments(_call);
- try {
- return (vamsas.objects.simple.Alignment) _resp;
- } catch (java.lang.Exception _exception) {
- return (vamsas.objects.simple.Alignment) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.Alignment.class);
- }
- }
- }
-
- public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id) throws java.rmi.RemoteException {
- if (super.cachedEndpoint == null) {
- throw new org.apache.axis.NoEndPointException();
- }
- org.apache.axis.client.Call _call = createCall();
- _call.setOperation(_operations[2]);
- _call.setUseSOAPAction(true);
- _call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getResult"));
-
- setRequestHeaders(_call);
- setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {job_id});
-
- if (_resp instanceof java.rmi.RemoteException) {
- throw (java.rmi.RemoteException)_resp;
- }
- else {
- extractAttachments(_call);
- try {
- return (vamsas.objects.simple.MsaResult) _resp;
- } catch (java.lang.Exception _exception) {
- return (vamsas.objects.simple.MsaResult) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.MsaResult.class);
- }
- }
- }
-
- public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId) throws java.rmi.RemoteException {
- if (super.cachedEndpoint == null) {
- throw new org.apache.axis.NoEndPointException();
- }
- org.apache.axis.client.Call _call = createCall();
- _call.setOperation(_operations[3]);
- _call.setUseSOAPAction(true);
- _call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));
-
- setRequestHeaders(_call);
- setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {jobId});
-
- if (_resp instanceof java.rmi.RemoteException) {
- throw (java.rmi.RemoteException)_resp;
- }
- else {
- extractAttachments(_call);
- try {
- return (vamsas.objects.simple.WsJobId) _resp;
- } catch (java.lang.Exception _exception) {
- return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.WsJobId.class);
- }
- }
- }
-
-}
+*/\r
+package ext.vamsas;\r
+\r
+public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub\r
+ implements ext.vamsas.MuscleWS {\r
+ static org.apache.axis.description.OperationDesc[] _operations;\r
+\r
+ static {\r
+ _operations = new org.apache.axis.description.OperationDesc[4];\r
+ _initOperationDesc1();\r
+ }\r
+\r
+ private java.util.Vector cachedSerClasses = new java.util.Vector();\r
+ private java.util.Vector cachedSerQNames = new java.util.Vector();\r
+ private java.util.Vector cachedSerFactories = new java.util.Vector();\r
+ private java.util.Vector cachedDeserFactories = new java.util.Vector();\r
+\r
+ public MuscleWSSoapBindingStub() throws org.apache.axis.AxisFault {\r
+ this(null);\r
+ }\r
+\r
+ public MuscleWSSoapBindingStub(java.net.URL endpointURL,\r
+ javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {\r
+ this(service);\r
+ super.cachedEndpoint = endpointURL;\r
+ }\r
+\r
+ public MuscleWSSoapBindingStub(javax.xml.rpc.Service service)\r
+ throws org.apache.axis.AxisFault {\r
+ if (service == null) {\r
+ super.service = new org.apache.axis.client.Service();\r
+ } else {\r
+ super.service = service;\r
+ }\r
+\r
+ java.lang.Class cls;\r
+ javax.xml.namespace.QName qName;\r
+ java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;\r
+ java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;\r
+ java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;\r
+ java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;\r
+ java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;\r
+ java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;\r
+ java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;\r
+ java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;\r
+ java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;\r
+ java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;\r
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas",\r
+ "Sequence");\r
+ cachedSerQNames.add(qName);\r
+ cls = vamsas.objects.simple.Sequence.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");\r
+ cachedSerQNames.add(qName);\r
+ cls = vamsas.objects.simple.Sequence[].class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(arraysf);\r
+ cachedDeserFactories.add(arraydf);\r
+\r
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas",\r
+ "MsaResult");\r
+ cachedSerQNames.add(qName);\r
+ cls = vamsas.objects.simple.MsaResult.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas",\r
+ "SequenceSet");\r
+ cachedSerQNames.add(qName);\r
+ cls = vamsas.objects.simple.SequenceSet.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",\r
+ "Object");\r
+ cachedSerQNames.add(qName);\r
+ cls = vamsas.objects.simple.Object.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas",\r
+ "Alignment");\r
+ cachedSerQNames.add(qName);\r
+ cls = vamsas.objects.simple.Alignment.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId");\r
+ cachedSerQNames.add(qName);\r
+ cls = vamsas.objects.simple.WsJobId.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+\r
+ qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");\r
+ cachedSerQNames.add(qName);\r
+ cls = java.lang.String[].class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(arraysf);\r
+ cachedDeserFactories.add(arraydf);\r
+\r
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");\r
+ cachedSerQNames.add(qName);\r
+ cls = vamsas.objects.simple.Result.class;\r
+ cachedSerClasses.add(cls);\r
+ cachedSerFactories.add(beansf);\r
+ cachedDeserFactories.add(beandf);\r
+ }\r
+\r
+ private static void _initOperationDesc1() {\r
+ org.apache.axis.description.OperationDesc oper;\r
+ oper = new org.apache.axis.description.OperationDesc();\r
+ oper.setName("align");\r
+ oper.addParameter(new javax.xml.namespace.QName("", "seqSet"),\r
+ new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"),\r
+ vamsas.objects.simple.SequenceSet.class,\r
+ org.apache.axis.description.ParameterDesc.IN, false, false);\r
+ oper.setReturnType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "WsJobId"));\r
+ oper.setReturnClass(vamsas.objects.simple.WsJobId.class);\r
+ oper.setReturnQName(new javax.xml.namespace.QName("", "alignReturn"));\r
+ oper.setStyle(org.apache.axis.constants.Style.RPC);\r
+ oper.setUse(org.apache.axis.constants.Use.ENCODED);\r
+ _operations[0] = oper;\r
+\r
+ oper = new org.apache.axis.description.OperationDesc();\r
+ oper.setName("getalign");\r
+ oper.addParameter(new javax.xml.namespace.QName("", "job_id"),\r
+ new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",\r
+ "string"), java.lang.String.class,\r
+ org.apache.axis.description.ParameterDesc.IN, false, false);\r
+ oper.setReturnType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "Alignment"));\r
+ oper.setReturnClass(vamsas.objects.simple.Alignment.class);\r
+ oper.setReturnQName(new javax.xml.namespace.QName("", "getalignReturn"));\r
+ oper.setStyle(org.apache.axis.constants.Style.RPC);\r
+ oper.setUse(org.apache.axis.constants.Use.ENCODED);\r
+ _operations[1] = oper;\r
+\r
+ oper = new org.apache.axis.description.OperationDesc();\r
+ oper.setName("getResult");\r
+ oper.addParameter(new javax.xml.namespace.QName("", "job_id"),\r
+ new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",\r
+ "string"), java.lang.String.class,\r
+ org.apache.axis.description.ParameterDesc.IN, false, false);\r
+ oper.setReturnType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "MsaResult"));\r
+ oper.setReturnClass(vamsas.objects.simple.MsaResult.class);\r
+ oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));\r
+ oper.setStyle(org.apache.axis.constants.Style.RPC);\r
+ oper.setUse(org.apache.axis.constants.Use.ENCODED);\r
+ _operations[2] = oper;\r
+\r
+ oper = new org.apache.axis.description.OperationDesc();\r
+ oper.setName("cancel");\r
+ oper.addParameter(new javax.xml.namespace.QName("", "jobId"),\r
+ new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",\r
+ "string"), java.lang.String.class,\r
+ org.apache.axis.description.ParameterDesc.IN, false, false);\r
+ oper.setReturnType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "WsJobId"));\r
+ oper.setReturnClass(vamsas.objects.simple.WsJobId.class);\r
+ oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));\r
+ oper.setStyle(org.apache.axis.constants.Style.RPC);\r
+ oper.setUse(org.apache.axis.constants.Use.ENCODED);\r
+ _operations[3] = oper;\r
+ }\r
+\r
+ protected org.apache.axis.client.Call createCall()\r
+ throws java.rmi.RemoteException {\r
+ try {\r
+ org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service.createCall();\r
+\r
+ if (super.maintainSessionSet) {\r
+ _call.setMaintainSession(super.maintainSession);\r
+ }\r
+\r
+ if (super.cachedUsername != null) {\r
+ _call.setUsername(super.cachedUsername);\r
+ }\r
+\r
+ if (super.cachedPassword != null) {\r
+ _call.setPassword(super.cachedPassword);\r
+ }\r
+\r
+ if (super.cachedEndpoint != null) {\r
+ _call.setTargetEndpointAddress(super.cachedEndpoint);\r
+ }\r
+\r
+ if (super.cachedTimeout != null) {\r
+ _call.setTimeout(super.cachedTimeout);\r
+ }\r
+\r
+ if (super.cachedPortName != null) {\r
+ _call.setPortName(super.cachedPortName);\r
+ }\r
+\r
+ java.util.Enumeration keys = super.cachedProperties.keys();\r
+\r
+ while (keys.hasMoreElements()) {\r
+ java.lang.String key = (java.lang.String) keys.nextElement();\r
+ _call.setProperty(key, super.cachedProperties.get(key));\r
+ }\r
+\r
+ // All the type mapping information is registered\r
+ // when the first call is made.\r
+ // The type mapping information is actually registered in\r
+ // the TypeMappingRegistry of the service, which\r
+ // is the reason why registration is only needed for the first call.\r
+ synchronized (this) {\r
+ if (firstCall()) {\r
+ // must set encoding style before registering serializers\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);\r
+\r
+ for (int i = 0; i < cachedSerFactories.size(); ++i) {\r
+ java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);\r
+ javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames.get(i);\r
+ java.lang.Class sf = (java.lang.Class) cachedSerFactories.get(i);\r
+ java.lang.Class df = (java.lang.Class) cachedDeserFactories.get(i);\r
+ _call.registerTypeMapping(cls, qName, sf, df, false);\r
+ }\r
+ }\r
+ }\r
+\r
+ return _call;\r
+ } catch (java.lang.Throwable _t) {\r
+ throw new org.apache.axis.AxisFault("Failure trying to get the Call object",\r
+ _t);\r
+ }\r
+ }\r
+\r
+ public vamsas.objects.simple.WsJobId align(\r
+ vamsas.objects.simple.SequenceSet seqSet)\r
+ throws java.rmi.RemoteException {\r
+ if (super.cachedEndpoint == null) {\r
+ throw new org.apache.axis.NoEndPointException();\r
+ }\r
+\r
+ org.apache.axis.client.Call _call = createCall();\r
+ _call.setOperation(_operations[0]);\r
+ _call.setUseSOAPAction(true);\r
+ _call.setSOAPActionURI("");\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setOperationName(new javax.xml.namespace.QName("vamsas", "align"));\r
+\r
+ setRequestHeaders(_call);\r
+ setAttachments(_call);\r
+\r
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { seqSet });\r
+\r
+ if (_resp instanceof java.rmi.RemoteException) {\r
+ throw (java.rmi.RemoteException) _resp;\r
+ } else {\r
+ extractAttachments(_call);\r
+\r
+ try {\r
+ return (vamsas.objects.simple.WsJobId) _resp;\r
+ } catch (java.lang.Exception _exception) {\r
+ return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp,\r
+ vamsas.objects.simple.WsJobId.class);\r
+ }\r
+ }\r
+ }\r
+\r
+ public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)\r
+ throws java.rmi.RemoteException {\r
+ if (super.cachedEndpoint == null) {\r
+ throw new org.apache.axis.NoEndPointException();\r
+ }\r
+\r
+ org.apache.axis.client.Call _call = createCall();\r
+ _call.setOperation(_operations[1]);\r
+ _call.setUseSOAPAction(true);\r
+ _call.setSOAPActionURI("");\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setOperationName(new javax.xml.namespace.QName("vamsas",\r
+ "getalign"));\r
+\r
+ setRequestHeaders(_call);\r
+ setAttachments(_call);\r
+\r
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { job_id });\r
+\r
+ if (_resp instanceof java.rmi.RemoteException) {\r
+ throw (java.rmi.RemoteException) _resp;\r
+ } else {\r
+ extractAttachments(_call);\r
+\r
+ try {\r
+ return (vamsas.objects.simple.Alignment) _resp;\r
+ } catch (java.lang.Exception _exception) {\r
+ return (vamsas.objects.simple.Alignment) org.apache.axis.utils.JavaUtils.convert(_resp,\r
+ vamsas.objects.simple.Alignment.class);\r
+ }\r
+ }\r
+ }\r
+\r
+ public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)\r
+ throws java.rmi.RemoteException {\r
+ if (super.cachedEndpoint == null) {\r
+ throw new org.apache.axis.NoEndPointException();\r
+ }\r
+\r
+ org.apache.axis.client.Call _call = createCall();\r
+ _call.setOperation(_operations[2]);\r
+ _call.setUseSOAPAction(true);\r
+ _call.setSOAPActionURI("");\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setOperationName(new javax.xml.namespace.QName("vamsas",\r
+ "getResult"));\r
+\r
+ setRequestHeaders(_call);\r
+ setAttachments(_call);\r
+\r
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { job_id });\r
+\r
+ if (_resp instanceof java.rmi.RemoteException) {\r
+ throw (java.rmi.RemoteException) _resp;\r
+ } else {\r
+ extractAttachments(_call);\r
+\r
+ try {\r
+ return (vamsas.objects.simple.MsaResult) _resp;\r
+ } catch (java.lang.Exception _exception) {\r
+ return (vamsas.objects.simple.MsaResult) org.apache.axis.utils.JavaUtils.convert(_resp,\r
+ vamsas.objects.simple.MsaResult.class);\r
+ }\r
+ }\r
+ }\r
+\r
+ public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)\r
+ throws java.rmi.RemoteException {\r
+ if (super.cachedEndpoint == null) {\r
+ throw new org.apache.axis.NoEndPointException();\r
+ }\r
+\r
+ org.apache.axis.client.Call _call = createCall();\r
+ _call.setOperation(_operations[3]);\r
+ _call.setUseSOAPAction(true);\r
+ _call.setSOAPActionURI("");\r
+ _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);\r
+ _call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));\r
+\r
+ setRequestHeaders(_call);\r
+ setAttachments(_call);\r
+\r
+ java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobId });\r
+\r
+ if (_resp instanceof java.rmi.RemoteException) {\r
+ throw (java.rmi.RemoteException) _resp;\r
+ } else {\r
+ extractAttachments(_call);\r
+\r
+ try {\r
+ return (vamsas.objects.simple.WsJobId) _resp;\r
+ } catch (java.lang.Exception _exception) {\r
+ return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp,\r
+ vamsas.objects.simple.WsJobId.class);\r
+ }\r
+ }\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class Result implements java.io.Serializable {
- private boolean broken;
- private boolean failed;
- private boolean finished;
- private boolean invalid;
- private boolean jobFailed;
- private boolean queued;
- private boolean running;
- private boolean serverError;
- private int state;
- private java.lang.String status;
- private boolean suspended;
-
- public Result() {
- }
-
- public Result(
- boolean broken,
- boolean failed,
- boolean finished,
- boolean invalid,
- boolean jobFailed,
- boolean queued,
- boolean running,
- boolean serverError,
- int state,
- java.lang.String status,
- boolean suspended) {
- this.broken = broken;
- this.failed = failed;
- this.finished = finished;
- this.invalid = invalid;
- this.jobFailed = jobFailed;
- this.queued = queued;
- this.running = running;
- this.serverError = serverError;
- this.state = state;
- this.status = status;
- this.suspended = suspended;
- }
-
-
+*/\r
+package ext.vamsas;\r
+\r
+public class Result implements java.io.Serializable {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Result.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "Result"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("broken");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "broken"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("failed");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "failed"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("finished");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "finished"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("invalid");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "invalid"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("jobFailed");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "jobFailed"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("queued");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "queued"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("running");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "running"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("serverError");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "serverError"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("state");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "state"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "int"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("status");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "status"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("suspended");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "suspended"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
+ private boolean broken;\r
+ private boolean failed;\r
+ private boolean finished;\r
+ private boolean invalid;\r
+ private boolean jobFailed;\r
+ private boolean queued;\r
+ private boolean running;\r
+ private boolean serverError;\r
+ private int state;\r
+ private java.lang.String status;\r
+ private boolean suspended;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Result() {\r
+ }\r
+\r
+ public Result(boolean broken, boolean failed, boolean finished,\r
+ boolean invalid, boolean jobFailed, boolean queued, boolean running,\r
+ boolean serverError, int state, java.lang.String status,\r
+ boolean suspended) {\r
+ this.broken = broken;\r
+ this.failed = failed;\r
+ this.finished = finished;\r
+ this.invalid = invalid;\r
+ this.jobFailed = jobFailed;\r
+ this.queued = queued;\r
+ this.running = running;\r
+ this.serverError = serverError;\r
+ this.state = state;\r
+ this.status = status;\r
+ this.suspended = suspended;\r
+ }\r
+\r
/**
- * Gets the broken value for this Result.
- *
- * @return broken
- */
- public boolean isBroken() {
- return broken;
- }
-
-
+ * Gets the broken value for this Result.
+ *
+ * @return broken
+ */\r
+ public boolean isBroken() {\r
+ return broken;\r
+ }\r
+\r
/**
- * Sets the broken value for this Result.
- *
- * @param broken
- */
- public void setBroken(boolean broken) {
- this.broken = broken;
- }
-
-
+ * Sets the broken value for this Result.
+ *
+ * @param broken
+ */\r
+ public void setBroken(boolean broken) {\r
+ this.broken = broken;\r
+ }\r
+\r
/**
- * Gets the failed value for this Result.
- *
- * @return failed
- */
- public boolean isFailed() {
- return failed;
- }
-
-
+ * Gets the failed value for this Result.
+ *
+ * @return failed
+ */\r
+ public boolean isFailed() {\r
+ return failed;\r
+ }\r
+\r
/**
- * Sets the failed value for this Result.
- *
- * @param failed
- */
- public void setFailed(boolean failed) {
- this.failed = failed;
- }
-
-
+ * Sets the failed value for this Result.
+ *
+ * @param failed
+ */\r
+ public void setFailed(boolean failed) {\r
+ this.failed = failed;\r
+ }\r
+\r
/**
- * Gets the finished value for this Result.
- *
- * @return finished
- */
- public boolean isFinished() {
- return finished;
- }
-
-
+ * Gets the finished value for this Result.
+ *
+ * @return finished
+ */\r
+ public boolean isFinished() {\r
+ return finished;\r
+ }\r
+\r
/**
- * Sets the finished value for this Result.
- *
- * @param finished
- */
- public void setFinished(boolean finished) {
- this.finished = finished;
- }
-
-
+ * Sets the finished value for this Result.
+ *
+ * @param finished
+ */\r
+ public void setFinished(boolean finished) {\r
+ this.finished = finished;\r
+ }\r
+\r
/**
- * Gets the invalid value for this Result.
- *
- * @return invalid
- */
- public boolean isInvalid() {
- return invalid;
- }
-
-
+ * Gets the invalid value for this Result.
+ *
+ * @return invalid
+ */\r
+ public boolean isInvalid() {\r
+ return invalid;\r
+ }\r
+\r
/**
- * Sets the invalid value for this Result.
- *
- * @param invalid
- */
- public void setInvalid(boolean invalid) {
- this.invalid = invalid;
- }
-
-
+ * Sets the invalid value for this Result.
+ *
+ * @param invalid
+ */\r
+ public void setInvalid(boolean invalid) {\r
+ this.invalid = invalid;\r
+ }\r
+\r
/**
- * Gets the jobFailed value for this Result.
- *
- * @return jobFailed
- */
- public boolean isJobFailed() {
- return jobFailed;
- }
-
-
+ * Gets the jobFailed value for this Result.
+ *
+ * @return jobFailed
+ */\r
+ public boolean isJobFailed() {\r
+ return jobFailed;\r
+ }\r
+\r
/**
- * Sets the jobFailed value for this Result.
- *
- * @param jobFailed
- */
- public void setJobFailed(boolean jobFailed) {
- this.jobFailed = jobFailed;
- }
-
-
+ * Sets the jobFailed value for this Result.
+ *
+ * @param jobFailed
+ */\r
+ public void setJobFailed(boolean jobFailed) {\r
+ this.jobFailed = jobFailed;\r
+ }\r
+\r
/**
- * Gets the queued value for this Result.
- *
- * @return queued
- */
- public boolean isQueued() {
- return queued;
- }
-
-
+ * Gets the queued value for this Result.
+ *
+ * @return queued
+ */\r
+ public boolean isQueued() {\r
+ return queued;\r
+ }\r
+\r
/**
- * Sets the queued value for this Result.
- *
- * @param queued
- */
- public void setQueued(boolean queued) {
- this.queued = queued;
- }
-
-
+ * Sets the queued value for this Result.
+ *
+ * @param queued
+ */\r
+ public void setQueued(boolean queued) {\r
+ this.queued = queued;\r
+ }\r
+\r
/**
- * Gets the running value for this Result.
- *
- * @return running
- */
- public boolean isRunning() {
- return running;
- }
-
-
+ * Gets the running value for this Result.
+ *
+ * @return running
+ */\r
+ public boolean isRunning() {\r
+ return running;\r
+ }\r
+\r
/**
- * Sets the running value for this Result.
- *
- * @param running
- */
- public void setRunning(boolean running) {
- this.running = running;
- }
-
-
+ * Sets the running value for this Result.
+ *
+ * @param running
+ */\r
+ public void setRunning(boolean running) {\r
+ this.running = running;\r
+ }\r
+\r
/**
- * Gets the serverError value for this Result.
- *
- * @return serverError
- */
- public boolean isServerError() {
- return serverError;
- }
-
-
+ * Gets the serverError value for this Result.
+ *
+ * @return serverError
+ */\r
+ public boolean isServerError() {\r
+ return serverError;\r
+ }\r
+\r
/**
- * Sets the serverError value for this Result.
- *
- * @param serverError
- */
- public void setServerError(boolean serverError) {
- this.serverError = serverError;
- }
-
-
+ * Sets the serverError value for this Result.
+ *
+ * @param serverError
+ */\r
+ public void setServerError(boolean serverError) {\r
+ this.serverError = serverError;\r
+ }\r
+\r
/**
- * Gets the state value for this Result.
- *
- * @return state
- */
- public int getState() {
- return state;
- }
-
-
+ * Gets the state value for this Result.
+ *
+ * @return state
+ */\r
+ public int getState() {\r
+ return state;\r
+ }\r
+\r
/**
- * Sets the state value for this Result.
- *
- * @param state
- */
- public void setState(int state) {
- this.state = state;
- }
-
-
+ * Sets the state value for this Result.
+ *
+ * @param state
+ */\r
+ public void setState(int state) {\r
+ this.state = state;\r
+ }\r
+\r
/**
- * Gets the status value for this Result.
- *
- * @return status
- */
- public java.lang.String getStatus() {
- return status;
- }
-
-
+ * Gets the status value for this Result.
+ *
+ * @return status
+ */\r
+ public java.lang.String getStatus() {\r
+ return status;\r
+ }\r
+\r
/**
- * Sets the status value for this Result.
- *
- * @param status
- */
- public void setStatus(java.lang.String status) {
- this.status = status;
- }
-
-
+ * Sets the status value for this Result.
+ *
+ * @param status
+ */\r
+ public void setStatus(java.lang.String status) {\r
+ this.status = status;\r
+ }\r
+\r
/**
- * Gets the suspended value for this Result.
- *
- * @return suspended
- */
- public boolean isSuspended() {
- return suspended;
- }
-
-
+ * Gets the suspended value for this Result.
+ *
+ * @return suspended
+ */\r
+ public boolean isSuspended() {\r
+ return suspended;\r
+ }\r
+\r
/**
- * Sets the suspended value for this Result.
- *
- * @param suspended
- */
- public void setSuspended(boolean suspended) {
- this.suspended = suspended;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof Result)) return false;
- Result other = (Result) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true &&
- this.broken == other.isBroken() &&
- this.failed == other.isFailed() &&
- this.finished == other.isFinished() &&
- this.invalid == other.isInvalid() &&
- this.jobFailed == other.isJobFailed() &&
- this.queued == other.isQueued() &&
- this.running == other.isRunning() &&
- this.serverError == other.isServerError() &&
- this.state == other.getState() &&
- ((this.status==null && other.getStatus()==null) ||
- (this.status!=null &&
- this.status.equals(other.getStatus()))) &&
- this.suspended == other.isSuspended();
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += getState();
- if (getStatus() != null) {
- _hashCode += getStatus().hashCode();
- }
- _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- __hashCodeCalc = false;
- return _hashCode;
- }
-
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(Result.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Result"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("broken");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "broken"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("failed");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "failed"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("finished");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "finished"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("invalid");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "invalid"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("jobFailed");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "jobFailed"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("queued");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "queued"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("running");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "running"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("serverError");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "serverError"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("state");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "state"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("status");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "status"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("suspended");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "suspended"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- }
-
+ * Sets the suspended value for this Result.
+ *
+ * @param suspended
+ */\r
+ public void setSuspended(boolean suspended) {\r
+ this.suspended = suspended;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof Result)) {\r
+ return false;\r
+ }\r
+\r
+ Result other = (Result) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true && (this.broken == other.isBroken()) &&\r
+ (this.failed == other.isFailed()) &&\r
+ (this.finished == other.isFinished()) &&\r
+ (this.invalid == other.isInvalid()) &&\r
+ (this.jobFailed == other.isJobFailed()) &&\r
+ (this.queued == other.isQueued()) &&\r
+ (this.running == other.isRunning()) &&\r
+ (this.serverError == other.isServerError()) &&\r
+ (this.state == other.getState()) &&\r
+ (((this.status == null) && (other.getStatus() == null)) ||\r
+ ((this.status != null) && this.status.equals(other.getStatus()))) &&\r
+ (this.suspended == other.isSuspended());\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+ _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += getState();\r
+\r
+ if (getStatus() != null) {\r
+ _hashCode += getStatus().hashCode();\r
+ }\r
+\r
+ _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class Secstructpred implements java.io.Serializable {
- private java.lang.String output;
-
- public Secstructpred() {
- }
-
- public Secstructpred(
- java.lang.String output) {
- this.output = output;
- }
-
-
+*/\r
+package ext.vamsas;\r
+\r
+public class Secstructpred implements java.io.Serializable {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Secstructpred.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "Secstructpred"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("output");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "output"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
+ private java.lang.String output;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Secstructpred() {\r
+ }\r
+\r
+ public Secstructpred(java.lang.String output) {\r
+ this.output = output;\r
+ }\r
+\r
/**
- * Gets the output value for this Secstructpred.
- *
- * @return output
- */
- public java.lang.String getOutput() {
- return output;
- }
-
-
+ * Gets the output value for this Secstructpred.
+ *
+ * @return output
+ */\r
+ public java.lang.String getOutput() {\r
+ return output;\r
+ }\r
+\r
/**
- * Sets the output value for this Secstructpred.
- *
- * @param output
- */
- public void setOutput(java.lang.String output) {
- this.output = output;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof Secstructpred)) return false;
- Secstructpred other = (Secstructpred) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true &&
- ((this.output==null && other.getOutput()==null) ||
- (this.output!=null &&
- this.output.equals(other.getOutput())));
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- if (getOutput() != null) {
- _hashCode += getOutput().hashCode();
- }
- __hashCodeCalc = false;
- return _hashCode;
- }
-
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(Secstructpred.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("output");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "output"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- typeDesc.addFieldDesc(elemField);
- }
-
+ * Sets the output value for this Secstructpred.
+ *
+ * @param output
+ */\r
+ public void setOutput(java.lang.String output) {\r
+ this.output = output;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof Secstructpred)) {\r
+ return false;\r
+ }\r
+\r
+ Secstructpred other = (Secstructpred) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true &&\r
+ (((this.output == null) && (other.getOutput() == null)) ||\r
+ ((this.output != null) && this.output.equals(other.getOutput())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+\r
+ if (getOutput() != null) {\r
+ _hashCode += getOutput().hashCode();\r
+ }\r
+\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package ext.vamsas;
-
-public class Sequence implements java.io.Serializable {
- private java.lang.String id;
- private java.lang.String seq;
-
- public Sequence() {
- }
-
- public Sequence(
- java.lang.String id,
- java.lang.String seq) {
- this.id = id;
- this.seq = seq;
- }
-
-
+*/\r
+package ext.vamsas;\r
+\r
+public class Sequence implements java.io.Serializable {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Sequence.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "Sequence"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("id");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "id"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("seq");\r
+ elemField.setXmlName(new javax.xml.namespace.QName(\r
+ "http://dataTypes.vamsas", "seq"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
+ private java.lang.String id;\r
+ private java.lang.String seq;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Sequence() {\r
+ }\r
+\r
+ public Sequence(java.lang.String id, java.lang.String seq) {\r
+ this.id = id;\r
+ this.seq = seq;\r
+ }\r
+\r
/**
- * Gets the id value for this Sequence.
- *
- * @return id
- */
- public java.lang.String getId() {
- return id;
- }
-
-
+ * Gets the id value for this Sequence.
+ *
+ * @return id
+ */\r
+ public java.lang.String getId() {\r
+ return id;\r
+ }\r
+\r
/**
- * Sets the id value for this Sequence.
- *
- * @param id
- */
- public void setId(java.lang.String id) {
- this.id = id;
- }
-
-
+ * Sets the id value for this Sequence.
+ *
+ * @param id
+ */\r
+ public void setId(java.lang.String id) {\r
+ this.id = id;\r
+ }\r
+\r
/**
- * Gets the seq value for this Sequence.
- *
- * @return seq
- */
- public java.lang.String getSeq() {
- return seq;
- }
-
-
+ * Gets the seq value for this Sequence.
+ *
+ * @return seq
+ */\r
+ public java.lang.String getSeq() {\r
+ return seq;\r
+ }\r
+\r
/**
- * Sets the seq value for this Sequence.
- *
- * @param seq
- */
- public void setSeq(java.lang.String seq) {
- this.seq = seq;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof Sequence)) return false;
- Sequence other = (Sequence) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true &&
- ((this.id==null && other.getId()==null) ||
- (this.id!=null &&
- this.id.equals(other.getId()))) &&
- ((this.seq==null && other.getSeq()==null) ||
- (this.seq!=null &&
- this.seq.equals(other.getSeq())));
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- if (getId() != null) {
- _hashCode += getId().hashCode();
- }
- if (getSeq() != null) {
- _hashCode += getSeq().hashCode();
- }
- __hashCodeCalc = false;
- return _hashCode;
- }
-
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(Sequence.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("id");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "id"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("seq");
- elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "seq"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
- typeDesc.addFieldDesc(elemField);
- }
-
+ * Sets the seq value for this Sequence.
+ *
+ * @param seq
+ */\r
+ public void setSeq(java.lang.String seq) {\r
+ this.seq = seq;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof Sequence)) {\r
+ return false;\r
+ }\r
+\r
+ Sequence other = (Sequence) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true &&\r
+ (((this.id == null) && (other.getId() == null)) ||\r
+ ((this.id != null) && this.id.equals(other.getId()))) &&\r
+ (((this.seq == null) && (other.getSeq() == null)) ||\r
+ ((this.seq != null) && this.seq.equals(other.getSeq())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+\r
+ if (getId() != null) {\r
+ _hashCode += getId().hashCode();\r
+ }\r
+\r
+ if (getSeq() != null) {\r
+ _hashCode += getSeq().hashCode();\r
+ }\r
+\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.analysis;\r
\r
-import jalview.jbgui.*;\r
+import jalview.analysis.*;\r
+\r
import jalview.datamodel.*;\r
+\r
import jalview.io.*;\r
-import jalview.analysis.*;\r
\r
-import java.awt.*;\r
+import jalview.jbgui.*;\r
+\r
import java.applet.Applet;\r
-import java.util.*;\r
-import java.net.*;\r
+\r
+import java.awt.*;\r
+\r
import java.io.*;\r
\r
-public class AAFrequency {\r
+import java.net.*;\r
\r
+import java.util.*;\r
+\r
+\r
+public class AAFrequency {\r
// Takes in a vector of sequences and column start and column end\r
// and returns a vector of size (end-start+1). Each element of the\r
// vector contains a hashtable with the keys being residues and\r
// the values being the count of each residue in that column.\r
// This class is used extensively in calculating alignment colourschemes\r
// that depend on the amount of conservation in each alignment column.\r
+ public static Vector calculate(Vector sequences, int start, int end) {\r
+ Vector result = new Vector();\r
+\r
+ for (int i = start; i <= end; i++) {\r
+ Hashtable residueHash = new Hashtable();\r
+ int maxCount = 0;\r
+ String maxResidue = "-";\r
+ int nongap = 0;\r
+\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ if (sequences.elementAt(j) instanceof Sequence) {\r
+ Sequence s = (Sequence) sequences.elementAt(j);\r
+\r
+ if (s.getSequence().length() > i) {\r
+ String res = s.getSequence().charAt(i) + "";\r
+\r
+ if (!jalview.util.Comparison.isGap(res.charAt(0))) {\r
+ nongap++;\r
+ } else {\r
+ res = "-"; // we always use this for gaps in the property vectors\r
+ }\r
+\r
+ if (residueHash.containsKey(res)) {\r
+ int count = ((Integer) residueHash.get(res)).intValue();\r
+ count++;\r
+\r
+ if (!jalview.util.Comparison.isGap(res.charAt(0)) &&\r
+ (count >= maxCount)) {\r
+ if (count > maxCount) {\r
+ maxResidue = res;\r
+ } else if (maxResidue.indexOf(res) == -1) {\r
+ maxResidue += res;\r
+ }\r
+\r
+ maxCount = count;\r
+ }\r
+\r
+ residueHash.put(res, new Integer(count));\r
+ } else {\r
+ residueHash.put(res, new Integer(1));\r
+ }\r
+ } else {\r
+ if (residueHash.containsKey("-")) {\r
+ int count = ((Integer) residueHash.get("-")).intValue();\r
+ count++;\r
+ residueHash.put("-", new Integer(count));\r
+ } else {\r
+ residueHash.put("-", new Integer(1));\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
+ residueHash.put("maxCount", new Integer(maxCount));\r
\r
- public static Vector calculate(Vector sequences,int start,int end) {\r
-\r
- Vector result = new Vector();\r
-\r
- for (int i = start;i <= end; i++)\r
- {\r
-\r
- Hashtable residueHash = new Hashtable();\r
- int maxCount = 0;\r
- String maxResidue = "-";\r
- int nongap = 0;\r
- for (int j=0; j < sequences.size(); j++)\r
- {\r
-\r
- if (sequences.elementAt(j) instanceof Sequence)\r
- {\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- if (s.getSequence().length() > i)\r
- {\r
-\r
- String res = s.getSequence().charAt(i)+"";\r
-\r
- if (!jalview.util.Comparison.isGap(res.charAt(0)))\r
- nongap++;\r
- else\r
- res = "-"; // we always use this for gaps in the property vectors\r
-\r
- if (residueHash.containsKey(res))\r
- {\r
-\r
- int count = ((Integer)residueHash.get(res)).intValue() ;\r
- count++;\r
-\r
- if (!jalview.util.Comparison.isGap(res.charAt(0)) && count >= maxCount)\r
- {\r
-\r
- if(count>maxCount)\r
- maxResidue = res;\r
- else if(maxResidue.indexOf(res)==-1)\r
- maxResidue += res;\r
-\r
- maxCount = count;\r
- }\r
-\r
- residueHash.put(res,new Integer(count));\r
+ if (maxCount < 0) {\r
+ System.out.println("asasa " + maxCount);\r
}\r
- else\r
- residueHash.put(res,new Integer(1));\r
-\r
-\r
- }\r
- else\r
- {\r
- if (residueHash.containsKey("-"))\r
- {\r
- int count = ((Integer)residueHash.get("-")).intValue() ;\r
- count++;\r
- residueHash.put("-",new Integer(count));\r
- }\r
- else\r
- residueHash.put("-",new Integer(1));\r
\r
- }\r
+ residueHash.put("maxResidue", maxResidue);\r
+ residueHash.put("size", new Integer(sequences.size()));\r
+ residueHash.put("nongap", new Integer(nongap));\r
+ result.addElement(residueHash);\r
}\r
- }\r
-\r
- residueHash.put("maxCount",new Integer(maxCount));\r
- if(maxCount<0)\r
- System.out.println("asasa "+maxCount);\r
- residueHash.put("maxResidue", maxResidue);\r
- residueHash.put("size", new Integer(sequences.size()));\r
- residueHash.put("nongap", new Integer(nongap));\r
- result.addElement(residueHash);\r
- }\r
-\r
- return result;\r
- }\r
\r
- public static Vector calculatePID(SequenceI refseq,Vector sequences,int window,int start,int end) {\r
-\r
- Vector result = new Vector();\r
-\r
- boolean init = true;\r
-\r
-\r
- Vector prev = null;\r
-\r
- for (int i = start;i <= end; i++) {\r
- Vector values = new Vector();\r
+ return result;\r
+ }\r
\r
- result.addElement(values);\r
+ public static Vector calculatePID(SequenceI refseq, Vector sequences,\r
+ int window, int start, int end) {\r
+ Vector result = new Vector();\r
\r
- // If start < window/2 then set value to zero.\r
+ boolean init = true;\r
\r
- if (i< window/2 || i >= refseq.getSequence().length()-window/2) {\r
- for (int j = 0; j < sequences.size(); j++) {\r
- values.addElement(new Integer(0));\r
- }\r
- } else if (init == true) {\r
- init = false;\r
+ Vector prev = null;\r
\r
- int winstart = i-window/2;\r
- int winend = i+window/2;\r
+ for (int i = start; i <= end; i++) {\r
+ Vector values = new Vector();\r
\r
- if (window%2 != 0) {\r
- winend++;\r
- }\r
+ result.addElement(values);\r
\r
- for (int j = 0; j < sequences.size(); j++) {\r
- values.addElement(new Integer(0));\r
- }\r
-\r
- for (int k = winstart; k <= winend; k++) {\r
- String refchar = refseq.getSequence().substring(k,k+1);\r
- if (jalview.util.Comparison.isGap(refchar.charAt(0)))\r
- refchar="-";\r
- else {\r
- for (int j = 0; j < sequences.size(); j++) {\r
+ // If start < window/2 then set value to zero.\r
+ if ((i < (window / 2)) ||\r
+ (i >= (refseq.getSequence().length() - (window / 2)))) {\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ values.addElement(new Integer(0));\r
+ }\r
+ } else if (init == true) {\r
+ init = false;\r
\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
+ int winstart = i - (window / 2);\r
+ int winend = i + (window / 2);\r
\r
- if (s.getSequence().length() > k) {\r
+ if ((window % 2) != 0) {\r
+ winend++;\r
+ }\r
\r
- String res = s.getSequence().substring(k,k+1); // no gapchar test needed\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ values.addElement(new Integer(0));\r
+ }\r
\r
- if (res.equals(refchar)) {\r
- int val = ((Integer)values.elementAt(j)).intValue();\r
- val++;\r
- values.setElementAt(new Integer(val),j);\r
- }\r
+ for (int k = winstart; k <= winend; k++) {\r
+ String refchar = refseq.getSequence().substring(k, k + 1);\r
+\r
+ if (jalview.util.Comparison.isGap(refchar.charAt(0))) {\r
+ refchar = "-";\r
+ } else {\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ Sequence s = (Sequence) sequences.elementAt(j);\r
+\r
+ if (s.getSequence().length() > k) {\r
+ String res = s.getSequence().substring(k, k +\r
+ 1); // no gapchar test needed\r
+\r
+ if (res.equals(refchar)) {\r
+ int val = ((Integer) values.elementAt(j)).intValue();\r
+ val++;\r
+ values.setElementAt(new Integer(val), j);\r
+ }\r
+ }\r
+ }\r
}\r
- }\r
}\r
\r
- }\r
-\r
- prev = values;\r
- } else {\r
- int winstart = i-window/2;\r
- int winend = i+window/2;\r
+ prev = values;\r
+ } else {\r
+ int winstart = i - (window / 2);\r
+ int winend = i + (window / 2);\r
\r
- if (window%2 != 0) {\r
- winend++;\r
- }\r
- // We need to take the previous set of values\r
- // subtract the pid at winstart-1\r
- // and add the pid at winend;\r
-\r
- String pre_refchar = refseq.getSequence().substring(winstart-1,winstart);\r
- String pos_refchar = "-";\r
-\r
- if (refseq.getSequence().length() > winend) {\r
- pos_refchar = refseq.getSequence().substring(winend,winend+1);\r
- }\r
-\r
- for (int j = 0; j < sequences.size(); j++) {\r
- // First copy the pid value from i-1\r
-\r
- int val = ((Integer)prev.elementAt(j)).intValue();\r
-\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- String pre_char = s.getSequence().substring(winstart-1,winstart);\r
-\r
- String pos_char = "-";\r
-\r
- if (s.getSequence().length() > winend) {\r
- pos_char = s.getSequence().substring(winend,winend+1);\r
+ if ((window % 2) != 0) {\r
+ winend++;\r
}\r
\r
- // Now substract 1 if the chars at winstart-1 match\r
-\r
- if (jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false\r
- && pre_char.equals(pre_refchar)) {\r
- val--;\r
- }\r
-\r
- if (jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false\r
- && pos_char.equals(pos_refchar)) {\r
- val++;\r
- }\r
-\r
- values.addElement(new Integer(val));\r
+ // We need to take the previous set of values\r
+ // subtract the pid at winstart-1\r
+ // and add the pid at winend;\r
+ String pre_refchar = refseq.getSequence().substring(winstart -\r
+ 1, winstart);\r
+ String pos_refchar = "-";\r
\r
+ if (refseq.getSequence().length() > winend) {\r
+ pos_refchar = refseq.getSequence().substring(winend,\r
+ winend + 1);\r
+ }\r
\r
- }\r
- prev = values;\r
- }\r
- }\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ // First copy the pid value from i-1\r
+ int val = ((Integer) prev.elementAt(j)).intValue();\r
\r
- return result;\r
- }\r
+ Sequence s = (Sequence) sequences.elementAt(j);\r
\r
- public static Hashtable findBlocks(Vector seqs, int start, int end,Vector exc) {\r
+ String pre_char = s.getSequence().substring(winstart - 1,\r
+ winstart);\r
\r
- // start and end are in real (not relative coords);\r
+ String pos_char = "-";\r
\r
- // The coords in the hashtable that is returned are in relative coords\r
- // i.e. start from 0\r
+ if (s.getSequence().length() > winend) {\r
+ pos_char = s.getSequence().substring(winend, winend +\r
+ 1);\r
+ }\r
\r
- Hashtable blocks = new Hashtable();\r
+ // Now substract 1 if the chars at winstart-1 match\r
+ if ((jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false) &&\r
+ pre_char.equals(pre_refchar)) {\r
+ val--;\r
+ }\r
\r
- boolean prev = false;\r
- int bstart = -1;\r
+ if ((jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false) &&\r
+ pos_char.equals(pos_refchar)) {\r
+ val++;\r
+ }\r
\r
- for (int i = start; i <= end ; i++) {\r
- SequenceI seq = (SequenceI)seqs.elementAt(0);\r
+ values.addElement(new Integer(val));\r
+ }\r
\r
- char c = seq.getCharAt(i);\r
+ prev = values;\r
+ }\r
+ }\r
\r
- boolean found = true;\r
+ return result;\r
+ }\r
\r
- int j = 1;\r
+ public static Hashtable findBlocks(Vector seqs, int start, int end,\r
+ Vector exc) {\r
+ // start and end are in real (not relative coords);\r
+ // The coords in the hashtable that is returned are in relative coords\r
+ // i.e. start from 0\r
+ Hashtable blocks = new Hashtable();\r
\r
- while (j < seqs.size() && found == true) {\r
+ boolean prev = false;\r
+ int bstart = -1;\r
\r
- SequenceI jseq = (SequenceI)seqs.elementAt(j);\r
+ for (int i = start; i <= end; i++) {\r
+ SequenceI seq = (SequenceI) seqs.elementAt(0);\r
\r
- if (!exc.contains(jseq)) {\r
+ char c = seq.getCharAt(i);\r
\r
- char cc = jseq.getCharAt(i);\r
+ boolean found = true;\r
\r
- if ( cc != c) {\r
- found = false;\r
- }\r
- }\r
- j++;\r
- }\r
+ int j = 1;\r
\r
+ while ((j < seqs.size()) && (found == true)) {\r
+ SequenceI jseq = (SequenceI) seqs.elementAt(j);\r
\r
- if (prev == false && found == true) {\r
- bstart = i;\r
- } else if (prev == true && found == false && bstart != -1) {\r
+ if (!exc.contains(jseq)) {\r
+ char cc = jseq.getCharAt(i);\r
\r
- int blockstart = bstart-start;\r
- int blocklen = i-bstart;\r
+ if (cc != c) {\r
+ found = false;\r
+ }\r
+ }\r
\r
- //System.out.println("Start len " + blockstart + " " + blocklen);\r
+ j++;\r
+ }\r
\r
- for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(jj),new Integer(blocklen));\r
- }\r
+ if ((prev == false) && (found == true)) {\r
+ bstart = i;\r
+ } else if ((prev == true) && (found == false) && (bstart != -1)) {\r
+ int blockstart = bstart - start;\r
+ int blocklen = i - bstart;\r
\r
- bstart = -1;\r
- }\r
- prev = found;\r
- }\r
+ //System.out.println("Start len " + blockstart + " " + blocklen);\r
+ for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {\r
+ blocks.put(new Integer(jj), new Integer(blocklen));\r
+ }\r
\r
- if (bstart != -1) {\r
+ bstart = -1;\r
+ }\r
\r
- int blockstart = bstart-start;\r
- int blocklen = end-bstart;\r
+ prev = found;\r
+ }\r
\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ if (bstart != -1) {\r
+ int blockstart = bstart - start;\r
+ int blocklen = end - bstart;\r
\r
- for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- }\r
+ // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {\r
+ blocks.put(new Integer(blockstart), new Integer(blocklen));\r
+ }\r
+ }\r
\r
- }\r
- return blocks;\r
+ return blocks;\r
}\r
\r
+ public static Hashtable findKmerCount(SequenceI seq, int start, int end,\r
+ int window, int step, Vector kmers) {\r
+ int tmpstart = start;\r
+ Hashtable vals = new Hashtable();\r
\r
+ while (tmpstart <= end) {\r
+ String tmpstr = seq.getSequence().substring(tmpstart -\r
+ (window / 2), tmpstart + (window / 2));\r
\r
- public static Hashtable findKmerCount(SequenceI seq, int start, int end,int window, int step,Vector kmers) {\r
-\r
- int tmpstart = start;\r
- Hashtable vals = new Hashtable();\r
+ int count = 0;\r
\r
- while (tmpstart <= end) {\r
+ //System.out.println("Str " + tmpstr);\r
+ for (int ii = 0; ii < kmers.size(); ii++) {\r
+ String kmer = ((SequenceI) kmers.elementAt(ii)).getSequence();\r
\r
- String tmpstr = seq.getSequence().substring(tmpstart-window/2,tmpstart+window/2);\r
+ int i = -1;\r
\r
- int count = 0;\r
+ while (tmpstr.indexOf(kmer, i) != -1) {\r
+ i = tmpstr.indexOf(kmer, i);\r
\r
- //System.out.println("Str " + tmpstr);\r
-\r
- for (int ii = 0; ii < kmers.size(); ii++) {\r
- String kmer = ((SequenceI)kmers.elementAt(ii)).getSequence();\r
+ i++;\r
+ count++;\r
+ }\r
\r
- int i = -1;\r
+ ii++;\r
+ }\r
\r
- while (tmpstr.indexOf(kmer,i) != -1) {\r
- i = tmpstr.indexOf(kmer,i);\r
+ vals.put(new Integer(tmpstart), new Integer(count));\r
+ tmpstart += step;\r
+ }\r
\r
- i++;\r
- count++;\r
- }\r
- ii++;\r
- }\r
- vals.put(new Integer(tmpstart),new Integer(count));\r
- tmpstart += step;\r
- }\r
- return vals;\r
+ return vals;\r
}\r
\r
- public static Hashtable findBlockStarts(Vector seqs, int start, int end,Vector exc) {\r
-\r
- // start and end are in real (not relative coords);\r
-\r
- // The coords in the hashtable that is returned are in relative coords\r
- // i.e. start from 0\r
+ public static Hashtable findBlockStarts(Vector seqs, int start, int end,\r
+ Vector exc) {\r
+ // start and end are in real (not relative coords);\r
+ // The coords in the hashtable that is returned are in relative coords\r
+ // i.e. start from 0\r
+ Hashtable blocks = new Hashtable();\r
\r
- Hashtable blocks = new Hashtable();\r
+ boolean prev = false;\r
+ int bstart = -1;\r
\r
- boolean prev = false;\r
- int bstart = -1;\r
+ for (int i = start; i <= end; i++) {\r
+ SequenceI seq = (SequenceI) seqs.elementAt(0);\r
\r
- for (int i = start; i <= end ; i++) {\r
- SequenceI seq = (SequenceI)seqs.elementAt(0);\r
+ char c = seq.getCharAt(i);\r
\r
- char c = seq.getCharAt(i);\r
+ boolean found = true;\r
\r
- boolean found = true;\r
+ int j = 1;\r
\r
- int j = 1;\r
+ while ((j < seqs.size()) && (found == true)) {\r
+ SequenceI jseq = (SequenceI) seqs.elementAt(j);\r
\r
- while (j < seqs.size() && found == true) {\r
+ if (!exc.contains(jseq)) {\r
+ char cc = jseq.getCharAt(i);\r
\r
- SequenceI jseq = (SequenceI)seqs.elementAt(j);\r
-\r
- if (!exc.contains(jseq)) {\r
-\r
- char cc = jseq.getCharAt(i);\r
-\r
- if ( cc != c) {\r
- found = false;\r
- }\r
- }\r
- j++;\r
- }\r
-\r
-\r
- if (prev == false && found == true) {\r
- bstart = i;\r
- } else if (prev == true && found == false && bstart != -1) {\r
+ if (cc != c) {\r
+ found = false;\r
+ }\r
+ }\r
\r
- int blockstart = bstart-start;\r
- int blocklen = i-bstart;\r
+ j++;\r
+ }\r
\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ if ((prev == false) && (found == true)) {\r
+ bstart = i;\r
+ } else if ((prev == true) && (found == false) && (bstart != -1)) {\r
+ int blockstart = bstart - start;\r
+ int blocklen = i - bstart;\r
\r
- //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- // }\r
+ // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
+ blocks.put(new Integer(blockstart), new Integer(blocklen));\r
\r
- bstart = -1;\r
- }\r
- prev = found;\r
- }\r
+ // }\r
+ bstart = -1;\r
+ }\r
\r
- if (bstart != -1) {\r
+ prev = found;\r
+ }\r
\r
- int blockstart = bstart-start;\r
- int blocklen = end-bstart;\r
+ if (bstart != -1) {\r
+ int blockstart = bstart - start;\r
+ int blocklen = end - bstart;\r
\r
- // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ // System.out.println("Start len " + blockstart + " " + blocklen);\r
+ //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
+ blocks.put(new Integer(blockstart), new Integer(blocklen));\r
\r
- //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {\r
- blocks.put(new Integer(blockstart),new Integer(blocklen));\r
- // }\r
+ // }\r
+ }\r
\r
- }\r
- return blocks;\r
+ return blocks;\r
}\r
-\r
}\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.analysis;\r
\r
-import jalview.schemes.*;\r
import jalview.datamodel.SequenceI;\r
-import jalview.util.*;\r
+\r
import jalview.io.*;\r
\r
-import java.util.*;\r
-import java.io.*;\r
+import jalview.schemes.*;\r
+\r
+import jalview.util.*;\r
+\r
import java.awt.*;\r
\r
+import java.io.*;\r
+\r
+import java.util.*;\r
+\r
+\r
public class AlignSeq {\r
+ public static java.util.Hashtable dnaHash = new java.util.Hashtable();\r
+\r
+ static {\r
+ dnaHash.put("C", new Integer(0));\r
+ dnaHash.put("T", new Integer(1));\r
+ dnaHash.put("A", new Integer(2));\r
+ dnaHash.put("G", new Integer(3));\r
+ dnaHash.put("-", new Integer(4));\r
+ }\r
+\r
+ static String[] dna = { "C", "T", "A", "G", "-" };\r
+ static String[] pep = {\r
+ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",\r
+ "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-"\r
+ };\r
+ int[][] score;\r
+ int[][] E;\r
+ int[][] F;\r
+ int[][] traceback;\r
+ int[] seq1;\r
+ int[] seq2;\r
+ SequenceI s1;\r
+ SequenceI s2;\r
+ String s1str;\r
+ String s2str;\r
+ int maxi;\r
+ int maxj;\r
+ int[] aseq1;\r
+ int[] aseq2;\r
+ String astr1 = "";\r
+ String astr2 = "";\r
+ public int seq1start;\r
+ public int seq1end;\r
+ public int seq2start;\r
+ public int seq2end;\r
+ int count;\r
+ public int maxscore;\r
+ float pid;\r
+ int prev = 0;\r
+ int gapOpen = 120;\r
+ int gapExtend = 20;\r
+ int[][] lookup = ResidueProperties.getBLOSUM62();\r
+ String[] intToStr = pep;\r
+ int defInt = 23;\r
+ String output = "";\r
+ String type;\r
+ Runtime rt;\r
+\r
+ public AlignSeq() {\r
+ }\r
+\r
+ public AlignSeq(SequenceI s1, SequenceI s2, String type) {\r
+ rt = Runtime.getRuntime();\r
+ SeqInit(s1, s2, type);\r
+ }\r
+\r
+ public int getMaxScore() {\r
+ return maxscore;\r
+ }\r
\r
- int[][] score;\r
- int[][] E;\r
- int[][] F;\r
- int[][] traceback;\r
-\r
- int[] seq1;\r
- int[] seq2;\r
-\r
- SequenceI s1;\r
- SequenceI s2;\r
-\r
- String s1str;\r
- String s2str;\r
-\r
- int maxi;\r
- int maxj;\r
-\r
- int[] aseq1;\r
- int[] aseq2;\r
-\r
- String astr1 = "";\r
- String astr2 = "";\r
-\r
- public int seq1start;\r
- public int seq1end;\r
- public int seq2start;\r
- public int seq2end;\r
-\r
- int count;\r
-\r
- public int maxscore;\r
- float pid;\r
- int prev = 0;\r
-\r
- public static java.util.Hashtable dnaHash = new java.util.Hashtable();\r
-\r
- static {\r
- dnaHash.put("C", new Integer(0));\r
- dnaHash.put("T", new Integer(1));\r
- dnaHash.put("A", new Integer(2));\r
- dnaHash.put("G", new Integer(3));\r
- dnaHash.put("-", new Integer(4));\r
- }\r
-\r
- static String dna[] = {"C","T","A","G","-"};\r
- static String pep[] = {"A","R","N","D","C","Q","E","G","H","I","L","K","M","F","P","S","T","W","Y","V","B","Z","X","-"};\r
-\r
- int gapOpen = 120;\r
- int gapExtend = 20;\r
-\r
- int lookup[][] = ResidueProperties.getBLOSUM62();\r
- String intToStr[] = pep;\r
- int defInt = 23;\r
-\r
- String output = "";\r
-\r
- String type;\r
- Runtime rt;\r
- public AlignSeq() {}\r
-\r
- public AlignSeq(SequenceI s1, SequenceI s2,String type) {\r
- rt = Runtime.getRuntime();\r
- SeqInit(s1,s2,type);\r
- }\r
-\r
- public int getMaxScore() {\r
- return maxscore;\r
- }\r
-\r
- public int getSeq2Start() {\r
- return seq2start;\r
- }\r
-\r
- public int getSeq2End() {\r
- return seq2end;\r
- }\r
-\r
- public int getSeq1Start() {\r
- return seq1start;\r
- }\r
-\r
- public int getSeq1End() {\r
- return seq1end;\r
- }\r
-\r
- public String getOutput() {\r
- return output;\r
- }\r
-\r
- public String getAStr1() {\r
- return astr1;\r
- }\r
- public String getAStr2() {\r
- return astr2;\r
- }\r
- public int [] getASeq1() {\r
- return aseq1;\r
- }\r
- public int [] getASeq2() {\r
- return aseq2;\r
- }\r
- public SequenceI getS1() {\r
- return s1;\r
- }\r
- public SequenceI getS2() {\r
- return s2;\r
- }\r
-\r
- public void SeqInit(SequenceI s1, SequenceI s2,String type) {\r
- s1str = extractGaps(".",s1.getSequence());\r
- s2str = extractGaps(".",s2.getSequence());\r
- s1str = extractGaps("-",s1str);\r
- s2str = extractGaps("-",s2str);\r
- s1str = extractGaps(" ",s1str);\r
- s2str = extractGaps(" ",s2str);\r
-\r
- this.s1 = s1;\r
- this.s2 = s2;\r
-\r
- this.type = type;\r
-\r
- if (type.equals("pep")) {\r
- lookup = ResidueProperties.getBLOSUM62();\r
- intToStr = pep;\r
- defInt = 23;\r
- } else if (type.equals("dna")) {\r
- lookup = ResidueProperties.getDNA();\r
- intToStr = dna;\r
- defInt = 4;\r
- } else {\r
- output = output + ("Wrong type = dna or pep only");\r
- System.exit(0);\r
+ public int getSeq2Start() {\r
+ return seq2start;\r
}\r
\r
+ public int getSeq2End() {\r
+ return seq2end;\r
+ }\r
\r
- //System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());\r
- seq1 = new int[s1str.length()];\r
- //System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());\r
- seq2 = new int[s2str.length()];\r
- //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());\r
- score = new int[s1str.length()][s2str.length()];\r
- //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());\r
- E = new int[s1str.length()][s2str.length()];\r
- //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());\r
- F = new int[s1str.length()][s2str.length()];\r
- traceback = new int[s1str.length()][s2str.length()];\r
- //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());\r
- seq1 = stringToInt(s1str,type);\r
- //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());\r
- seq2 = stringToInt(s2str,type);\r
- //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());\r
-\r
- // long tstart = System.currentTimeMillis();\r
- // calcScoreMatrix();\r
- //long tend = System.currentTimeMillis();\r
-\r
- //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");\r
-\r
-\r
- // printScoreMatrix(score);\r
- //System.out.println();\r
-\r
- //printScoreMatrix(traceback);\r
- //System.out.println();\r
-\r
- // printScoreMatrix(E);\r
- //System.out.println();\r
-\r
- ///printScoreMatrix(F);\r
- //System.out.println();\r
- // tstart = System.currentTimeMillis();\r
- //traceAlignment();\r
- //tend = System.currentTimeMillis();\r
- //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");\r
- }\r
-\r
- public void traceAlignment() {\r
-\r
- // Find the maximum score along the rhs or bottom row\r
- int max = -9999;\r
- for (int i = 0; i < seq1.length; i++) {\r
- if (score[i][seq2.length - 1] > max ) {\r
- max = score[i][seq2.length - 1];\r
- maxi = i;\r
- maxj = seq2.length-1;\r
- }\r
+ public int getSeq1Start() {\r
+ return seq1start;\r
}\r
- for (int j = 0; j < seq2.length; j++) {\r
- if (score[seq1.length - 1][j] > max ) {\r
- max = score[seq1.length - 1][j];\r
- maxi = seq1.length-1;\r
- maxj = j;\r
- }\r
+\r
+ public int getSeq1End() {\r
+ return seq1end;\r
}\r
\r
- // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);\r
-\r
- int i = maxi;\r
- int j = maxj;\r
- int trace;\r
- maxscore = score[i][j] / 10;\r
-\r
- seq1end = maxi+1;\r
- seq2end = maxj+1;\r
-\r
- aseq1 = new int[seq1.length + seq2.length];\r
- aseq2 = new int[seq1.length + seq2.length];\r
-\r
- count = seq1.length + seq2.length - 1;\r
-\r
- while (i>0 && j >0) {\r
-\r
- if (aseq1[count] != defInt && i >=0) {\r
- aseq1[count] = seq1[i];\r
- astr1 = intToStr[seq1[i]] + astr1;\r
- }\r
-\r
- if (aseq2[count] != defInt && j > 0) {\r
- aseq2[count] = seq2[j];\r
- astr2 = intToStr[seq2[j]] + astr2;\r
- }\r
- trace = findTrace(i,j);\r
- if (trace == 0) {\r
- i--;\r
- j--;\r
-\r
- } else if (trace == 1) {\r
- j--;\r
- aseq1[count] = defInt;\r
- astr1 = "-" + astr1.substring(1);\r
- } else if (trace == -1) {\r
- i--;\r
- aseq2[count] = defInt;\r
- astr2 = "-" + astr2.substring(1);\r
- }\r
- count--;\r
+ public String getOutput() {\r
+ return output;\r
}\r
\r
- seq1start = i+1;\r
- seq2start = j+1;\r
+ public String getAStr1() {\r
+ return astr1;\r
+ }\r
\r
- if (aseq1[count] != defInt) {\r
- aseq1[count] = seq1[i];\r
- astr1 = intToStr[seq1[i]] + astr1;\r
+ public String getAStr2() {\r
+ return astr2;\r
}\r
\r
- if (aseq2[count] != defInt) {\r
- aseq2[count] = seq2[j];\r
- astr2 = intToStr[seq2[j]] + astr2;\r
+ public int[] getASeq1() {\r
+ return aseq1;\r
}\r
- }\r
\r
- public void printAlignment() {\r
- // Find the biggest id length for formatting purposes\r
- int maxid = s1.getName().length();\r
+ public int[] getASeq2() {\r
+ return aseq2;\r
+ }\r
\r
- if (s2.getName().length() > maxid) {\r
- maxid = s2.getName().length();\r
+ public SequenceI getS1() {\r
+ return s1;\r
}\r
\r
- int len = 72 - maxid - 1;\r
- int nochunks = ((aseq1.length - count) / len) + 1;\r
- pid = 0;\r
- int overlap = 0;\r
-\r
- output = output + ("Score = " + score[maxi][maxj] + "\n");\r
- output = output + ("Length of alignment = " + (aseq1.length-count) + "\n");\r
- output = output + ("Sequence ");\r
- output = output + (new Format("%" + maxid + "s").form(s1.getName()));\r
- output = output + (" : " + seq1start + " - " + seq1end + " (Sequence length = " + s1str.length() + ")\n");\r
- output = output + ("Sequence ");\r
- output = output + (new Format("%" + maxid + "s").form(s2.getName()));\r
- output = output + (" : " + seq2start + " - " + seq2end + " (Sequence length = " + s2str.length() + ")\n\n");\r
-\r
- for (int j = 0; j < nochunks; j++) {\r
- // Print the first aligned sequence\r
- output = output + (new Format("%" + (maxid) + "s").form(s1.getName()) + " ");\r
- for (int i = 0; i < len ; i++) {\r
-\r
- if ((count + i + j*len) < aseq1.length) {\r
- output = output + (new Format("%s").form(intToStr[aseq1[count + i + j*len]]));\r
+ public SequenceI getS2() {\r
+ return s2;\r
+ }\r
+\r
+ public void SeqInit(SequenceI s1, SequenceI s2, String type) {\r
+ s1str = extractGaps(".", s1.getSequence());\r
+ s2str = extractGaps(".", s2.getSequence());\r
+ s1str = extractGaps("-", s1str);\r
+ s2str = extractGaps("-", s2str);\r
+ s1str = extractGaps(" ", s1str);\r
+ s2str = extractGaps(" ", s2str);\r
+\r
+ this.s1 = s1;\r
+ this.s2 = s2;\r
+\r
+ this.type = type;\r
+\r
+ if (type.equals("pep")) {\r
+ lookup = ResidueProperties.getBLOSUM62();\r
+ intToStr = pep;\r
+ defInt = 23;\r
+ } else if (type.equals("dna")) {\r
+ lookup = ResidueProperties.getDNA();\r
+ intToStr = dna;\r
+ defInt = 4;\r
+ } else {\r
+ output = output + ("Wrong type = dna or pep only");\r
+ System.exit(0);\r
}\r
- }\r
-\r
- output = output + ("\n");\r
- output = output + (new Format("%" + (maxid) + "s").form(" ") + " ");\r
- // Print out the matching chars\r
- for (int i = 0; i < len ; i++) {\r
-\r
- if ((count + i + j*len) < aseq1.length) {\r
- if ( intToStr[aseq1[count+i+j*len]].equals(intToStr[aseq2[count+i+j*len]]) && !intToStr[aseq1[count+i+j*len]].equals("-")) {\r
- pid++;\r
- output = output + ("|");\r
- } else if (type.equals("pep")) {\r
- if (ResidueProperties.getPAM250(intToStr[aseq1[count+i+j*len]],intToStr[aseq2[count+i+j*len]]) > 0) {\r
- output = output + (".");\r
- } else {\r
- output = output + (" ");\r
+\r
+ //System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());\r
+ seq1 = new int[s1str.length()];\r
+\r
+ //System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());\r
+ seq2 = new int[s2str.length()];\r
+\r
+ //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());\r
+ score = new int[s1str.length()][s2str.length()];\r
+\r
+ //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());\r
+ E = new int[s1str.length()][s2str.length()];\r
+\r
+ //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());\r
+ F = new int[s1str.length()][s2str.length()];\r
+ traceback = new int[s1str.length()][s2str.length()];\r
+\r
+ //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());\r
+ seq1 = stringToInt(s1str, type);\r
+\r
+ //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());\r
+ seq2 = stringToInt(s2str, type);\r
+\r
+ //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());\r
+ // long tstart = System.currentTimeMillis();\r
+ // calcScoreMatrix();\r
+ //long tend = System.currentTimeMillis();\r
+ //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");\r
+ // printScoreMatrix(score);\r
+ //System.out.println();\r
+ //printScoreMatrix(traceback);\r
+ //System.out.println();\r
+ // printScoreMatrix(E);\r
+ //System.out.println();\r
+ ///printScoreMatrix(F);\r
+ //System.out.println();\r
+ // tstart = System.currentTimeMillis();\r
+ //traceAlignment();\r
+ //tend = System.currentTimeMillis();\r
+ //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");\r
+ }\r
+\r
+ public void traceAlignment() {\r
+ // Find the maximum score along the rhs or bottom row\r
+ int max = -9999;\r
+\r
+ for (int i = 0; i < seq1.length; i++) {\r
+ if (score[i][seq2.length - 1] > max) {\r
+ max = score[i][seq2.length - 1];\r
+ maxi = i;\r
+ maxj = seq2.length - 1;\r
}\r
- } else {\r
- output = output + (" ");\r
- }\r
+ }\r
\r
+ for (int j = 0; j < seq2.length; j++) {\r
+ if (score[seq1.length - 1][j] > max) {\r
+ max = score[seq1.length - 1][j];\r
+ maxi = seq1.length - 1;\r
+ maxj = j;\r
+ }\r
}\r
- }\r
- // Now print the second aligned sequence\r
- output = output + ("\n");\r
- output = output + (new Format("%" + (maxid) + "s").form(s2.getName()) + " " );\r
- for (int i = 0; i < len ; i++) {\r
- if ((count + i + j*len) < aseq1.length) {\r
- output = output + (new Format("%s").form(intToStr[aseq2[count + i + j*len]]));\r
+\r
+ // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);\r
+ int i = maxi;\r
+ int j = maxj;\r
+ int trace;\r
+ maxscore = score[i][j] / 10;\r
+\r
+ seq1end = maxi + 1;\r
+ seq2end = maxj + 1;\r
+\r
+ aseq1 = new int[seq1.length + seq2.length];\r
+ aseq2 = new int[seq1.length + seq2.length];\r
+\r
+ count = (seq1.length + seq2.length) - 1;\r
+\r
+ while ((i > 0) && (j > 0)) {\r
+ if ((aseq1[count] != defInt) && (i >= 0)) {\r
+ aseq1[count] = seq1[i];\r
+ astr1 = intToStr[seq1[i]] + astr1;\r
+ }\r
+\r
+ if ((aseq2[count] != defInt) && (j > 0)) {\r
+ aseq2[count] = seq2[j];\r
+ astr2 = intToStr[seq2[j]] + astr2;\r
+ }\r
+\r
+ trace = findTrace(i, j);\r
+\r
+ if (trace == 0) {\r
+ i--;\r
+ j--;\r
+ } else if (trace == 1) {\r
+ j--;\r
+ aseq1[count] = defInt;\r
+ astr1 = "-" + astr1.substring(1);\r
+ } else if (trace == -1) {\r
+ i--;\r
+ aseq2[count] = defInt;\r
+ astr2 = "-" + astr2.substring(1);\r
+ }\r
+\r
+ count--;\r
}\r
- }\r
- output = output + ("\n\n");\r
- }\r
- pid = pid/(float)(aseq1.length-count)*100;\r
- output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));\r
\r
- }\r
+ seq1start = i + 1;\r
+ seq2start = j + 1;\r
\r
- public void printScoreMatrix(int[][] mat) {\r
- int n = seq1.length;\r
- int m = seq2.length;\r
+ if (aseq1[count] != defInt) {\r
+ aseq1[count] = seq1[i];\r
+ astr1 = intToStr[seq1[i]] + astr1;\r
+ }\r
\r
- for (int i = 0; i < n;i++) {\r
- // Print the top sequence\r
- if (i == 0) {\r
- Format.print(System.out,"%8s",s2str.substring(0,1));\r
- for (int jj = 1;jj < m; jj++) {\r
- Format.print(System.out,"%5s",s2str.substring(jj,jj+1));\r
+ if (aseq2[count] != defInt) {\r
+ aseq2[count] = seq2[j];\r
+ astr2 = intToStr[seq2[j]] + astr2;\r
}\r
- System.out.println();\r
- }\r
+ }\r
\r
- for (int j = 0;j < m; j++) {\r
- if (j == 0) {\r
- Format.print(System.out,"%3s",s1str.substring(i,i+1));\r
+ public void printAlignment() {\r
+ // Find the biggest id length for formatting purposes\r
+ int maxid = s1.getName().length();\r
+\r
+ if (s2.getName().length() > maxid) {\r
+ maxid = s2.getName().length();\r
}\r
- Format.print(System.out,"%3d ",mat[i][j]/10);\r
- }\r
- System.out.println();\r
+\r
+ int len = 72 - maxid - 1;\r
+ int nochunks = ((aseq1.length - count) / len) + 1;\r
+ pid = 0;\r
+\r
+ int overlap = 0;\r
+\r
+ output = output + ("Score = " + score[maxi][maxj] + "\n");\r
+ output = output +\r
+ ("Length of alignment = " + (aseq1.length - count) + "\n");\r
+ output = output + ("Sequence ");\r
+ output = output + (new Format("%" + maxid + "s").form(s1.getName()));\r
+ output = output +\r
+ (" : " + seq1start + " - " + seq1end + " (Sequence length = " +\r
+ s1str.length() + ")\n");\r
+ output = output + ("Sequence ");\r
+ output = output + (new Format("%" + maxid + "s").form(s2.getName()));\r
+ output = output +\r
+ (" : " + seq2start + " - " + seq2end + " (Sequence length = " +\r
+ s2str.length() + ")\n\n");\r
+\r
+ for (int j = 0; j < nochunks; j++) {\r
+ // Print the first aligned sequence\r
+ output = output +\r
+ (new Format("%" + (maxid) + "s").form(s1.getName()) + " ");\r
+\r
+ for (int i = 0; i < len; i++) {\r
+ if ((count + i + (j * len)) < aseq1.length) {\r
+ output = output +\r
+ (new Format("%s").form(intToStr[aseq1[count + i +\r
+ (j * len)]]));\r
+ }\r
+ }\r
+\r
+ output = output + ("\n");\r
+ output = output +\r
+ (new Format("%" + (maxid) + "s").form(" ") + " ");\r
+\r
+ // Print out the matching chars\r
+ for (int i = 0; i < len; i++) {\r
+ if ((count + i + (j * len)) < aseq1.length) {\r
+ if (intToStr[aseq1[count + i + (j * len)]].equals(\r
+ intToStr[aseq2[count + i + (j * len)]]) &&\r
+ !intToStr[aseq1[count + i + (j * len)]].equals("-")) {\r
+ pid++;\r
+ output = output + ("|");\r
+ } else if (type.equals("pep")) {\r
+ if (ResidueProperties.getPAM250(\r
+ intToStr[aseq1[count + i + (j * len)]],\r
+ intToStr[aseq2[count + i + (j * len)]]) > 0) {\r
+ output = output + (".");\r
+ } else {\r
+ output = output + (" ");\r
+ }\r
+ } else {\r
+ output = output + (" ");\r
+ }\r
+ }\r
+ }\r
+\r
+ // Now print the second aligned sequence\r
+ output = output + ("\n");\r
+ output = output +\r
+ (new Format("%" + (maxid) + "s").form(s2.getName()) + " ");\r
+\r
+ for (int i = 0; i < len; i++) {\r
+ if ((count + i + (j * len)) < aseq1.length) {\r
+ output = output +\r
+ (new Format("%s").form(intToStr[aseq2[count + i +\r
+ (j * len)]]));\r
+ }\r
+ }\r
+\r
+ output = output + ("\n\n");\r
+ }\r
+\r
+ pid = pid / (float) (aseq1.length - count) * 100;\r
+ output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));\r
}\r
- }\r
-\r
- public int findTrace(int i,int j) {\r
- int t = 0;\r
- int max = score[i-1][j-1] + lookup[seq1[i]][seq2[j]] * 10;\r
-\r
- if (F[i][j] > max) {\r
- max = F[i][j];\r
- t = -1;\r
- } else if (F[i][j] == max) {\r
- if (prev == -1) {\r
- max = F[i][j];\r
- t = -1;\r
- }\r
+\r
+ public void printScoreMatrix(int[][] mat) {\r
+ int n = seq1.length;\r
+ int m = seq2.length;\r
+\r
+ for (int i = 0; i < n; i++) {\r
+ // Print the top sequence\r
+ if (i == 0) {\r
+ Format.print(System.out, "%8s", s2str.substring(0, 1));\r
+\r
+ for (int jj = 1; jj < m; jj++) {\r
+ Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));\r
+ }\r
+\r
+ System.out.println();\r
+ }\r
+\r
+ for (int j = 0; j < m; j++) {\r
+ if (j == 0) {\r
+ Format.print(System.out, "%3s", s1str.substring(i, i + 1));\r
+ }\r
+\r
+ Format.print(System.out, "%3d ", mat[i][j] / 10);\r
+ }\r
+\r
+ System.out.println();\r
+ }\r
}\r
- if (E[i][j] >= max) {\r
- max = E[i][j];\r
- t = 1;\r
- } else if (E[i][j] == max) {\r
- if (prev == 1) {\r
- max = E[i][j];\r
- t = 1;\r
- }\r
+\r
+ public int findTrace(int i, int j) {\r
+ int t = 0;\r
+ int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);\r
+\r
+ if (F[i][j] > max) {\r
+ max = F[i][j];\r
+ t = -1;\r
+ } else if (F[i][j] == max) {\r
+ if (prev == -1) {\r
+ max = F[i][j];\r
+ t = -1;\r
+ }\r
+ }\r
+\r
+ if (E[i][j] >= max) {\r
+ max = E[i][j];\r
+ t = 1;\r
+ } else if (E[i][j] == max) {\r
+ if (prev == 1) {\r
+ max = E[i][j];\r
+ t = 1;\r
+ }\r
+ }\r
+\r
+ prev = t;\r
+\r
+ return t;\r
}\r
- prev = t;\r
- return t;\r
- }\r
\r
- public void calcScoreMatrix() {\r
+ public void calcScoreMatrix() {\r
+ int n = seq1.length;\r
+ int m = seq2.length;\r
\r
+ // top left hand element\r
+ score[0][0] = lookup[seq1[0]][seq2[0]] * 10;\r
+ E[0][0] = -gapExtend;\r
+ F[0][0] = 0;\r
\r
- int n = seq1.length;\r
- int m = seq2.length;\r
+ // Calculate the top row first\r
+ for (int j = 1; j < m; j++) {\r
+ // What should these values be? 0 maybe\r
+ E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);\r
+ F[0][j] = -gapExtend;\r
\r
+ score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,\r
+ -gapExtend);\r
\r
- // top left hand element\r
- score[0][0] = lookup[seq1[0]][seq2[0]] * 10;\r
- E[0][0] = -gapExtend;\r
- F[0][0] = 0;\r
+ traceback[0][j] = 1;\r
+ }\r
\r
- // Calculate the top row first\r
- for (int j=1; j < m; j++) {\r
- // What should these values be? 0 maybe\r
- E[0][j] = max(score[0][j-1] - gapOpen,E[0][j-1] - gapExtend);\r
- F[0][j] = -gapExtend;\r
+ // Now do the left hand column\r
+ for (int i = 1; i < n; i++) {\r
+ E[i][0] = -gapOpen;\r
+ F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);\r
\r
- score[0][j] = max( lookup[seq1[0]][seq2[j]] * 10 ,-gapOpen,-gapExtend);\r
+ score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);\r
+ traceback[i][0] = -1;\r
+ }\r
\r
- traceback[0][j] = 1;\r
+ // Now do all the other rows\r
+ for (int i = 1; i < n; i++) {\r
+ for (int j = 1; j < m; j++) {\r
+ E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] -\r
+ gapExtend);\r
+ F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] -\r
+ gapExtend);\r
+\r
+ score[i][j] = max(score[i - 1][j - 1] +\r
+ (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]);\r
+ traceback[i][j] = findTrace(i, j);\r
+ }\r
+ }\r
}\r
\r
- // Now do the left hand column\r
- for (int i=1; i < n; i++) {\r
- E[i][0] = -gapOpen;\r
- F[i][0] = max(score[i-1][0]-gapOpen,F[i-1][0]-gapExtend);\r
+ public static String extractChars(String chars, String seq) {\r
+ String out = seq;\r
+\r
+ for (int i = 0; i < chars.length(); i++) {\r
+ String gap = chars.substring(i, i + 1);\r
+ out = extractGaps(gap, out);\r
+ }\r
\r
- score[i][0] = max( lookup[seq1[i]][seq2[0]] * 10 ,E[i][0],F[i][0]);\r
- traceback[i][0] = -1;\r
+ return out;\r
}\r
\r
- // Now do all the other rows\r
- for (int i = 1; i < n; i++) {\r
- for (int j = 1; j < m; j++) {\r
+ public static String extractGaps(String gapChar, String seq) {\r
+ StringTokenizer str = new StringTokenizer(seq, gapChar);\r
+ String newString = "";\r
\r
- E[i][j] = max(score[i][j-1] - gapOpen, E[i][j-1] - gapExtend);\r
- F[i][j] = max(score[i-1][j] - gapOpen, F[i-1][j] - gapExtend);\r
+ while (str.hasMoreTokens()) {\r
+ newString = newString + str.nextToken();\r
+ }\r
\r
- score[i][j] = max(score[i-1][j-1] + lookup[seq1[i]][seq2[j]]*10,\r
- E[i][j],\r
- F[i][j]);\r
- traceback[i][j] = findTrace(i,j);\r
- }\r
+ return newString;\r
}\r
\r
- }\r
- public static String extractChars(String chars, String seq) {\r
- String out = seq;\r
- for (int i=0; i < chars.length(); i++) {\r
- String gap = chars.substring(i,i+1);\r
- out = extractGaps(gap,out);\r
- }\r
- return out;\r
- }\r
- public static String extractGaps(String gapChar, String seq) {\r
- StringTokenizer str = new StringTokenizer(seq,gapChar);\r
- String newString = "";\r
-\r
- while (str.hasMoreTokens()) {\r
- newString = newString + str.nextToken();\r
- }\r
- return newString;\r
- }\r
+ public int max(int i1, int i2, int i3) {\r
+ int max = i1;\r
\r
+ if (i2 > i1) {\r
+ max = i2;\r
+ }\r
\r
- public int max(int i1, int i2, int i3) {\r
- int max = i1;\r
- if (i2 > i1) {\r
- max = i2;\r
- }\r
- if (i3 > max) {\r
- max = i3;\r
- }\r
- return max;\r
- }\r
+ if (i3 > max) {\r
+ max = i3;\r
+ }\r
\r
- public int max(int i1, int i2) {\r
- int max = i1;\r
- if (i2 > i1) {\r
- max = i2;\r
+ return max;\r
}\r
- return max;\r
- }\r
\r
- public int[] stringToInt(String s,String type) {\r
- int[] seq1 = new int[s.length()];\r
+ public int max(int i1, int i2) {\r
+ int max = i1;\r
\r
- for (int i = 0;i < s.length(); i++) {\r
- String ss = s.substring(i,i+1).toUpperCase();\r
- try {\r
- if (type.equals("pep")) {\r
- seq1[i] = ((Integer)ResidueProperties.aaHash.get(ss)).intValue();\r
- } else if (type.equals("dna")) {\r
- seq1[i] = ((Integer)dnaHash.get(ss)).intValue();\r
- }\r
- if (seq1[i] > 23) {\r
- seq1[i] = 23;\r
+ if (i2 > i1) {\r
+ max = i2;\r
}\r
- } catch (Exception e) {\r
- if (type.equals("dna")) {\r
- seq1[i] = 4;\r
- } else {\r
- seq1[i] = 23;\r
+\r
+ return max;\r
+ }\r
+\r
+ public int[] stringToInt(String s, String type) {\r
+ int[] seq1 = new int[s.length()];\r
+\r
+ for (int i = 0; i < s.length(); i++) {\r
+ String ss = s.substring(i, i + 1).toUpperCase();\r
+\r
+ try {\r
+ if (type.equals("pep")) {\r
+ seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();\r
+ } else if (type.equals("dna")) {\r
+ seq1[i] = ((Integer) dnaHash.get(ss)).intValue();\r
+ }\r
+\r
+ if (seq1[i] > 23) {\r
+ seq1[i] = 23;\r
+ }\r
+ } catch (Exception e) {\r
+ if (type.equals("dna")) {\r
+ seq1[i] = 4;\r
+ } else {\r
+ seq1[i] = 23;\r
+ }\r
+ }\r
}\r
- }\r
+\r
+ return seq1;\r
}\r
- return seq1;\r
- }\r
\r
- public static void displayMatrix(Graphics g, int[][] mat, int n, int m,int psize) {\r
+ public static void displayMatrix(Graphics g, int[][] mat, int n, int m,\r
+ int psize) {\r
+ int max = -1000;\r
+ int min = 1000;\r
\r
- int max = -1000;\r
- int min = 1000;\r
+ for (int i = 0; i < n; i++) {\r
+ for (int j = 0; j < m; j++) {\r
+ if (mat[i][j] >= max) {\r
+ max = mat[i][j];\r
+ }\r
\r
- for (int i=0; i < n; i++) {\r
- for (int j=0; j < m; j++) {\r
- if (mat[i][j] >= max) {\r
- max = mat[i][j];\r
- }\r
- if (mat[i][j] <= min) {\r
- min = mat[i][j];\r
+ if (mat[i][j] <= min) {\r
+ min = mat[i][j];\r
+ }\r
+ }\r
}\r
- }\r
- }\r
- System.out.println(max + " " + min);\r
- for (int i=0; i < n; i++) {\r
- for (int j=0; j < m; j++) {\r
- int x = psize*i;\r
- int y = psize*j;\r
- // System.out.println(mat[i][j]);\r
- float score = (float)(mat[i][j] - min)/(float)(max-min);\r
- g.setColor(new Color(score,0,0));\r
- g.fillRect(x,y,psize,psize);\r
- // System.out.println(x + " " + y + " " + score);\r
- }\r
\r
- }\r
- }\r
+ System.out.println(max + " " + min);\r
+\r
+ for (int i = 0; i < n; i++) {\r
+ for (int j = 0; j < m; j++) {\r
+ int x = psize * i;\r
+ int y = psize * j;\r
+\r
+ // System.out.println(mat[i][j]);\r
+ float score = (float) (mat[i][j] - min) / (float) (max - min);\r
+ g.setColor(new Color(score, 0, 0));\r
+ g.fillRect(x, y, psize, psize);\r
\r
+ // System.out.println(x + " " + y + " " + score);\r
+ }\r
+ }\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
-import jalview.util.*;\r
+\r
import jalview.io.*;\r
\r
+import jalview.util.*;\r
+\r
import java.util.*;\r
\r
+\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
*/\r
public class AlignmentSorter {\r
-\r
- private AlignmentSorter() {\r
- try\r
- {\r
- jbInit();\r
+ /** */\r
+ static boolean sortIdAscending = true;\r
+ static int lastGroupHash = 0;\r
+ static boolean sortGroupAscending = true;\r
+ static AlignmentOrder lastOrder = null;\r
+ static boolean sortOrderAscending = true;\r
+ static NJTree lastTree = null;\r
+ static boolean sortTreeAscending = true;\r
+\r
+ private AlignmentSorter() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
}\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
\r
- public static void sortGroups(AlignmentI align) {\r
- Vector groups = align.getGroups();\r
- int nGroup = groups.size();\r
+ public static void sortGroups(AlignmentI align) {\r
+ Vector groups = align.getGroups();\r
+ int nGroup = groups.size();\r
+\r
+ float[] arr = new float[nGroup];\r
+ Object[] s = new Object[nGroup];\r
\r
- float[] arr = new float [nGroup];\r
- Object[] s = new Object[nGroup];\r
+ for (int i = 0; i < nGroup; i++) {\r
+ arr[i] = ((SequenceGroup) groups.elementAt(i)).getSize();\r
+ s[i] = groups.elementAt(i);\r
+ }\r
\r
- for (int i=0; i < nGroup; i++) {\r
- arr[i] = ((SequenceGroup)groups.elementAt(i)).getSize();\r
- s[i] = groups.elementAt(i);\r
+ QuickSort.sort(arr, s);\r
+\r
+ // align..setGroups(newg);\r
}\r
\r
- QuickSort.sort(arr,s);\r
+ /**\r
+ * Sort by Percentage Identity\r
+ *\r
+ * @param align AlignmentI\r
+ * @param s SequenceI\r
+ */\r
+ public static void sortByPID(AlignmentI align, SequenceI s) {\r
+ int nSeq = align.getHeight();\r
\r
- // align..setGroups(newg);\r
- }\r
+ float[] scores = new float[nSeq];\r
+ SequenceI[] seqs = new SequenceI[nSeq];\r
\r
- /**\r
- * Sort by Percentage Identity\r
- *\r
- * @param align AlignmentI\r
- * @param s SequenceI\r
- */\r
- public static void sortByPID(AlignmentI align, SequenceI s) {\r
- int nSeq = align.getHeight();\r
+ for (int i = 0; i < nSeq; i++) {\r
+ scores[i] = Comparison.PID(align.getSequenceAt(i), s);\r
+ seqs[i] = align.getSequenceAt(i);\r
+ }\r
\r
- float scores[] = new float[nSeq];\r
- SequenceI seqs[] = new SequenceI[nSeq];\r
+ QuickSort.sort(scores, 0, scores.length - 1, seqs);\r
\r
- for (int i = 0; i < nSeq; i++) {\r
- scores[i] = Comparison.PID(align.getSequenceAt(i),s);\r
- seqs[i] = align.getSequenceAt(i);\r
+ setReverseOrder(align, seqs);\r
}\r
\r
- QuickSort.sort(scores,0,scores.length-1,seqs);\r
+ private static void setReverseOrder(AlignmentI align, SequenceI[] seqs) {\r
+ int nSeq = seqs.length;\r
+\r
+ int len = 0;\r
\r
- setReverseOrder(align,seqs);\r
- }\r
+ if ((nSeq % 2) == 0) {\r
+ len = nSeq / 2;\r
+ } else {\r
+ len = (nSeq + 1) / 2;\r
+ }\r
\r
- private static void setReverseOrder(AlignmentI align, SequenceI [] seqs) {\r
- int nSeq = seqs.length;\r
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
+ for (int i = 0; i < len; i++) {\r
+ //SequenceI tmp = seqs[i];\r
+ align.getSequences().setElementAt(seqs[nSeq - i - 1], i);\r
+ align.getSequences().setElementAt(seqs[i], nSeq - i - 1);\r
+ }\r
+ }\r
\r
- int len = 0;\r
- if (nSeq%2 == 0) {\r
- len = nSeq/2;\r
- } else {\r
- len = (nSeq+1)/2;\r
+ private static void setOrder(AlignmentI align, Vector tmp) {\r
+ setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\r
}\r
\r
-// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
- for (int i = 0; i < len; i++) {\r
- //SequenceI tmp = seqs[i];\r
- align.getSequences().setElementAt(seqs[nSeq-i-1],i);\r
- align.getSequences().setElementAt(seqs[i],nSeq-i-1);\r
+ private static void setOrder(AlignmentI align, SequenceI[] seqs) {\r
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
+ Vector algn = align.getSequences();\r
+\r
+ for (int i = 0, p = 0; i < seqs.length; i++)\r
+ algn.setElementAt(seqs[i], p++);\r
}\r
- }\r
\r
- private static void setOrder(AlignmentI align, Vector tmp) {\r
- setOrder(align,vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
+ public static void sortByID(AlignmentI align) {\r
+ int nSeq = align.getHeight();\r
\r
- private static void setOrder(AlignmentI align, SequenceI [] seqs) {\r
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
+ String[] ids = new String[nSeq];\r
+ SequenceI[] seqs = new SequenceI[nSeq];\r
\r
- Vector algn = align.getSequences();\r
+ for (int i = 0; i < nSeq; i++) {\r
+ ids[i] = align.getSequenceAt(i).getName();\r
+ seqs[i] = align.getSequenceAt(i);\r
+ }\r
\r
- for (int i = 0, p = 0; i < seqs.length; i++)\r
- algn.setElementAt(seqs[i], p++);\r
- }\r
- /** */\r
- static boolean sortIdAscending = true;\r
- public static void sortByID(AlignmentI align) {\r
- int nSeq = align.getHeight();\r
+ QuickSort.sort(ids, seqs);\r
\r
- String ids[] = new String[nSeq];\r
- SequenceI seqs[] = new SequenceI[nSeq];\r
+ if (sortIdAscending) {\r
+ setReverseOrder(align, seqs);\r
+ } else {\r
+ setOrder(align, seqs);\r
+ }\r
\r
- for (int i = 0; i < nSeq; i++) {\r
- ids[i] = align.getSequenceAt(i).getName();\r
- seqs[i] = align.getSequenceAt(i);\r
+ sortIdAscending = !sortIdAscending;\r
}\r
\r
- QuickSort.sort(ids,seqs);\r
+ public static void sortByGroup(AlignmentI align) {\r
+ Vector groups = align.getGroups();\r
+\r
+ if (groups.hashCode() != lastGroupHash) {\r
+ sortGroupAscending = true;\r
+ lastGroupHash = groups.hashCode();\r
+ } else {\r
+ sortGroupAscending = !sortGroupAscending;\r
+ }\r
+\r
+ Vector seqs = new Vector();\r
+\r
+ for (int i = 0; i < groups.size(); i++) {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ for (int j = 0; j < sg.getSize(); j++) {\r
+ seqs.addElement(sg.getSequenceAt(j));\r
+ }\r
+ }\r
+\r
+ // Deletions can happen so this check may fail\r
+\r
+ /*\r
+ if (seqs.size() != nSeq) {\r
+ System.err.println("ERROR: tmp.size() != nseq in sortByGroups");\r
+ if (seqs.size() < nSeq) {\r
+ addStrays(align,seqs);\r
+ }\r
+ }\r
+ */\r
+ if (sortGroupAscending) {\r
+ setOrder(align, seqs);\r
+ } else {\r
+ setReverseOrder(align,\r
+ vectorSubsetToArray(seqs, align.getSequences()));\r
+ }\r
+ }\r
+\r
+ private static SequenceI[] vectorToArray(Vector tmp) {\r
+ SequenceI[] seqs = new SequenceI[tmp.size()];\r
\r
- if(sortIdAscending)\r
- setReverseOrder(align,seqs);\r
- else\r
- setOrder(align, seqs);\r
+ for (int i = 0; i < tmp.size(); i++) {\r
+ seqs[i] = (SequenceI) tmp.elementAt(i);\r
+ }\r
+\r
+ return seqs;\r
+ }\r
\r
- sortIdAscending = !sortIdAscending;\r
- }\r
- static int lastGroupHash = 0;\r
- static boolean sortGroupAscending = true;\r
+ private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask) {\r
+ Vector seqs = new Vector();\r
+ int i;\r
+ int m;\r
+ int p;\r
+ boolean[] tmask = new boolean[m = mask.size()];\r
\r
- public static void sortByGroup(AlignmentI align) {\r
- Vector groups = align.getGroups();\r
- if (groups.hashCode()!=lastGroupHash) {\r
- sortGroupAscending=true;\r
- lastGroupHash = groups.hashCode();\r
- } else\r
- sortGroupAscending = ! sortGroupAscending;\r
+ for (i = 0; i < m; i++)\r
+ tmask[i] = true;\r
\r
- Vector seqs = new Vector();\r
+ for (i = 0; i < tmp.size(); i++) {\r
+ Object sq;\r
\r
- for (int i=0; i < groups.size(); i++) {\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ if (mask.contains(sq = tmp.elementAt(i))) {\r
+ tmask[mask.indexOf(sq)] = false;\r
+ seqs.addElement(sq);\r
+ m--;\r
+ }\r
+ }\r
\r
- for (int j = 0; j < sg.getSize(); j++) {\r
- seqs.addElement(sg.getSequenceAt(j));\r
- }\r
+ for (i = 0; i < tmask.length; i++)\r
+ if (tmask[i]) {\r
+ seqs.addElement(mask.elementAt(i));\r
+ }\r
+\r
+ return vectorToArray(seqs);\r
}\r
\r
- // Deletions can happen so this check may fail\r
- /*\r
- if (seqs.size() != nSeq) {\r
- System.err.println("ERROR: tmp.size() != nseq in sortByGroups");\r
- if (seqs.size() < nSeq) {\r
- addStrays(align,seqs);\r
- }\r
+ public static void sortBy(AlignmentI align, AlignmentOrder order) {\r
+ // Get an ordered vector of sequences which may also be present in align\r
+ Vector tmp = order.getOrder();\r
+\r
+ // if (tmp.size()<align.getHeight())\r
+ // addStrays(align, tmp);\r
+ if (lastOrder == order) {\r
+ sortOrderAscending = !sortOrderAscending;\r
+ } else {\r
+ sortOrderAscending = true;\r
+ }\r
+\r
+ if (sortOrderAscending) {\r
+ setOrder(align, tmp);\r
+ } else {\r
+ setReverseOrder(align,\r
+ vectorSubsetToArray(tmp, align.getSequences()));\r
+ }\r
}\r
-*/\r
- if(sortGroupAscending)\r
- setOrder(align,seqs);\r
- else\r
- setReverseOrder( align, vectorSubsetToArray(seqs, align.getSequences()));\r
\r
- }\r
+ public static Vector getOrderByTree(AlignmentI align, NJTree tree) {\r
+ int nSeq = align.getHeight();\r
\r
- private static SequenceI [] vectorToArray(Vector tmp) {\r
- SequenceI[] seqs = new SequenceI[tmp.size()];\r
+ Vector tmp = new Vector();\r
\r
- for (int i=0; i < tmp.size(); i++) {\r
- seqs[i] = (SequenceI)tmp.elementAt(i);\r
- }\r
- return seqs;\r
- }\r
-\r
- private static SequenceI [] vectorSubsetToArray(Vector tmp, Vector mask) {\r
- Vector seqs = new Vector();\r
- int i,m, p;\r
- boolean[] tmask = new boolean[m=mask.size()];\r
- for (i=0; i<m; i++)\r
- tmask[i] = true;\r
- for (i=0; i < tmp.size(); i++) {\r
- Object sq;\r
- if (mask.contains(sq=tmp.elementAt(i))) {\r
- tmask[mask.indexOf(sq)] = false;\r
- seqs.addElement(sq);\r
- m--;\r
- }\r
- }\r
- for (i=0; i<tmask.length; i++)\r
- if (tmask[i])\r
- seqs.addElement(mask.elementAt(i));\r
- return vectorToArray(seqs);\r
- }\r
-\r
- static AlignmentOrder lastOrder = null;\r
- static boolean sortOrderAscending = true;\r
-\r
- public static void sortBy(AlignmentI align, AlignmentOrder order) {\r
- // Get an ordered vector of sequences which may also be present in align\r
- Vector tmp = order.getOrder();\r
-// if (tmp.size()<align.getHeight())\r
-// addStrays(align, tmp);\r
- if (lastOrder==order)\r
- sortOrderAscending=!sortOrderAscending;\r
- else\r
- sortOrderAscending=true;\r
-\r
- if (sortOrderAscending)\r
- setOrder(align, tmp);\r
- else\r
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
- static NJTree lastTree = null;\r
- static boolean sortTreeAscending = true;\r
-\r
- public static Vector getOrderByTree(AlignmentI align, NJTree tree) {\r
- int nSeq = align.getHeight();\r
-\r
- Vector tmp = new Vector();\r
-\r
- tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());\r
-\r
- if (tmp.size() != nSeq)\r
- {\r
- // TODO: JBPNote - decide if this is always an error\r
- // (eg. not when a tree is associated to another alignment which has more\r
- // sequences)\r
-\r
- if (tmp.size() < nSeq)\r
- {\r
- addStrays(align, tmp);\r
- }\r
- if (tmp.size() != nSeq)\r
- System.err.println("ERROR: tmp.size()="+tmp.size()+" != nseq="+nSeq+" in getOrderByTree");\r
+ tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());\r
\r
+ if (tmp.size() != nSeq) {\r
+ // TODO: JBPNote - decide if this is always an error\r
+ // (eg. not when a tree is associated to another alignment which has more\r
+ // sequences)\r
+ if (tmp.size() < nSeq) {\r
+ addStrays(align, tmp);\r
+ }\r
+\r
+ if (tmp.size() != nSeq) {\r
+ System.err.println("ERROR: tmp.size()=" + tmp.size() +\r
+ " != nseq=" + nSeq + " in getOrderByTree");\r
+ }\r
+ }\r
+\r
+ return tmp;\r
}\r
- return tmp;\r
- }\r
-\r
- public static void sortByTree(AlignmentI align, NJTree tree) {\r
- Vector tmp = getOrderByTree(align, tree);\r
- // tmp should properly permute align with tree.\r
- if(lastTree!=tree) {\r
- sortTreeAscending = true;\r
- lastTree = tree;\r
- } else {\r
- sortTreeAscending = !sortTreeAscending;\r
+\r
+ public static void sortByTree(AlignmentI align, NJTree tree) {\r
+ Vector tmp = getOrderByTree(align, tree);\r
+\r
+ // tmp should properly permute align with tree.\r
+ if (lastTree != tree) {\r
+ sortTreeAscending = true;\r
+ lastTree = tree;\r
+ } else {\r
+ sortTreeAscending = !sortTreeAscending;\r
+ }\r
+\r
+ if (sortTreeAscending) {\r
+ setOrder(align, tmp);\r
+ } else {\r
+ setReverseOrder(align,\r
+ vectorSubsetToArray(tmp, align.getSequences()));\r
+ }\r
}\r
- if(sortTreeAscending)\r
- setOrder(align,tmp);\r
- else\r
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
-\r
- private static void addStrays(AlignmentI align, Vector seqs) {\r
- int nSeq = align.getHeight();\r
- for (int i=0;i<nSeq;i++) {\r
- if (!seqs.contains(align.getSequenceAt(i))) {\r
- seqs.addElement(align.getSequenceAt(i));\r
- }\r
+\r
+ private static void addStrays(AlignmentI align, Vector seqs) {\r
+ int nSeq = align.getHeight();\r
+\r
+ for (int i = 0; i < nSeq; i++) {\r
+ if (!seqs.contains(align.getSequenceAt(i))) {\r
+ seqs.addElement(align.getSequenceAt(i));\r
+ }\r
+ }\r
+\r
+ if (nSeq != seqs.size()) {\r
+ System.err.println(\r
+ "ERROR: Size still not right even after addStrays");\r
+ }\r
}\r
- if (nSeq != seqs.size()) {\r
- System.err.println("ERROR: Size still not right even after addStrays");\r
+\r
+ public static Vector _sortByTree(SequenceNode node, Vector tmp,\r
+ Vector seqset) {\r
+ if (node == null) {\r
+ return tmp;\r
+ }\r
+\r
+ SequenceNode left = (SequenceNode) node.left();\r
+ SequenceNode right = (SequenceNode) node.right();\r
+\r
+ if ((left == null) && (right == null)) {\r
+ if (!node.isPlaceholder() && (node.element() != null)) {\r
+ if (node.element() instanceof SequenceI) {\r
+ if (!tmp.contains(node.element())) {\r
+ tmp.addElement((SequenceI) node.element());\r
+ }\r
+ }\r
+ }\r
+\r
+ return tmp;\r
+ } else {\r
+ _sortByTree(left, tmp, seqset);\r
+ _sortByTree(right, tmp, seqset);\r
+ }\r
+\r
+ return tmp;\r
}\r
- }\r
\r
- public static Vector _sortByTree(SequenceNode node, Vector tmp, Vector seqset) {\r
- if (node == null) {return tmp;}\r
+ // Ordering Objects\r
+ // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order\r
+ //\r
\r
- SequenceNode left = (SequenceNode)node.left();\r
- SequenceNode right = (SequenceNode)node.right();\r
+ /**\r
+ * recover the order of sequences given by the safe numbering scheme introducd\r
+ * SeqsetUtils.uniquify.\r
+ */\r
+ public static void recoverOrder(SequenceI[] alignment) {\r
+ float[] ids = new float[alignment.length];\r
\r
- if (left == null && right == null) {\r
- if (!node.isPlaceholder() && node.element()!=null)\r
- if (node.element() instanceof SequenceI)\r
- if (!tmp.contains(node.element()))\r
- tmp.addElement((SequenceI)node.element());\r
- return tmp;\r
+ for (int i = 0; i < alignment.length; i++)\r
+ ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();\r
\r
- } else {\r
- _sortByTree(left,tmp, seqset);\r
- _sortByTree(right,tmp, seqset);\r
+ jalview.util.QuickSort.sort(ids, alignment);\r
}\r
- return tmp;\r
- }\r
- // Ordering Objects\r
- // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order\r
- //\r
-\r
- /**\r
- * recover the order of sequences given by the safe numbering scheme introducd\r
- * SeqsetUtils.uniquify.\r
- */\r
- public static void recoverOrder(SequenceI[] alignment) {\r
- float[] ids = new float[alignment.length];\r
- for (int i=0; i<alignment.length; i++)\r
- ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();\r
- jalview.util.QuickSort.sort(ids, alignment);\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- }\r
\r
+ private void jbInit() throws Exception {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
-import jalview.util.*;\r
-import java.util.*;\r
\r
-public class AlignmentUtil {\r
+import jalview.util.*;\r
\r
- private AlignmentUtil() {\r
- }\r
+import java.util.*;\r
\r
- public static int[][] percentIdentity2(AlignmentI align) {\r
- return percentIdentity2(align,0,align.getWidth()-1);\r
- }\r
\r
- public static int[][] percentIdentity2(AlignmentI align, int start, int end) {\r
- int [][] cons2 = new int[align.getWidth()][24];\r
- // Initialize the array\r
- for (int j=0;j<24;j++) {\r
- for (int i=0; i < align.getWidth();i++) {\r
- cons2[i][j] = 0;\r
- }\r
+public class AlignmentUtil {\r
+ private AlignmentUtil() {\r
}\r
\r
- return cons2;\r
- }\r
- public static int getPixelHeight(int i, int j,int charHeight) {\r
- int h=0;\r
- while (i < j) {\r
- h += charHeight;\r
- i++;\r
+ public static int[][] percentIdentity2(AlignmentI align) {\r
+ return percentIdentity2(align, 0, align.getWidth() - 1);\r
}\r
- return h;\r
- }\r
-\r
-\r
- public static Vector substitution_rates (AlignmentI align, int start, int end) {\r
-\r
- Vector rates = new Vector();\r
-\r
- int len = (end-start+1);\r
-\r
- // Turn seqs into char arrays\r
-\r
- int[][] seqint = new int[align.getHeight()][len];\r
-\r
-\r
- for (int j = 0; j < align.getHeight(); j++) {\r
-\r
- SequenceI seq = align.getSequenceAt(j);\r
-\r
- for (int i = 0 ; i < len; i++) {\r
- char c = seq.getCharAt(start + i - 1);\r
-\r
- if (c == 'A') {\r
- seqint[j][i] = 0;\r
- } else if (c == 'C') {\r
- seqint[j][i] = 1;\r
- } else if (c == 'T') {\r
- seqint[j][i] = 2;\r
- } else if (c == 'G') {\r
- seqint[j][i] = 3;\r
- } else {\r
- seqint[j][i] = -1;\r
- }\r
-\r
- }\r
-\r
- }\r
-\r
-\r
- // print_matrix(seqint,2,len); for (int j = 0; j < align.getHeight(); j++) {\r
-\r
- for (int j = 0; j < align.getHeight(); j++) {\r
-\r
- for (int k = 0; k < align.getHeight(); k++) {\r
-\r
- int counts[][] = new int[4][4];\r
- int tot = 0;\r
- int tots[] = new int[4];\r
- int fulltot = 0;\r
- int fulltots[] = new int[4];\r
-\r
- for (int i = 0 ; i < len; i++) {\r
-\r
- if (k != j) {\r
\r
- // System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);\r
- if (seqint[j][i] >= 0 &&\r
- seqint[k][i] >= 0) {\r
- counts[seqint[k][i]][seqint[j][i]]++;\r
+ public static int[][] percentIdentity2(AlignmentI align, int start, int end) {\r
+ int[][] cons2 = new int[align.getWidth()][24];\r
\r
- // print_matrix(counts,4,4);\r
- tots[seqint[j][i]]++;\r
- tot++;\r
- }\r
- if (seqint[j][i] != -1) {\r
- fulltots[seqint[j][i]]++;\r
- fulltot++;\r
- }\r
- }\r
- }\r
+ // Initialize the array\r
+ for (int j = 0; j < 24; j++) {\r
+ for (int i = 0; i < align.getWidth(); i++) {\r
+ cons2[i][j] = 0;\r
+ }\r
+ }\r
\r
- if (k != j) {\r
-\r
- System.out.println();\r
-\r
- System.out.println("Sequence " + align.getSequenceAt(j).getName() + " " + align.getSequenceAt(k).getName());\r
-\r
- System.out.println();\r
- print_matrix(counts,4,4);\r
- System.out.println();\r
-\r
-\r
-\r
- double[][] out = new double[4][4];// = constant_multiply_matrix(counts,1.0/tot,4,4);\r
-\r
- for (int i = 0; i < 4; i++) {\r
- for (int jj = 0; jj < 4; jj++) {\r
- out[i][jj] = (double)counts[i][jj]/tots[jj];\r
- }\r
- }\r
-\r
- print_matrix(out,4,4);\r
- System.out.println();\r
-\r
-\r
- System.out.print("RATES\t");\r
- System.out.print(align.getSequenceAt(j).getName() + "\t" + align.getSequenceAt(k).getName() + "\t");\r
-\r
- for (int i = 0; i < 4; i++) {\r
- for (int jj = 0; jj < 4; jj++) {\r
- Format.print(System.out,"%4.3f\t",out[i][jj]);\r
- }\r
- }\r
- System.out.println();\r
-\r
- for (int i = 0; i < 4; i++) {\r
- Format.print(System.out,"%4.3f\t",(double)fulltots[i]*1.0/fulltot);\r
- }\r
-\r
- System.out.println();\r
- System.out.print("\nGC ");\r
-\r
- Format.print(System.out,"%4.3f\t",(double)(100*fulltots[1]+fulltots[3])/fulltot);\r
-\r
- System.out.print((fulltots[1]+fulltots[3]) + "\t" + fulltot);\r
+ return cons2;\r
+ }\r
\r
+ public static int getPixelHeight(int i, int j, int charHeight) {\r
+ int h = 0;\r
\r
- System.out.println();\r
+ while (i < j) {\r
+ h += charHeight;\r
+ i++;\r
+ }\r
\r
- rates.addElement(out);\r
- }\r
+ return h;\r
+ }\r
\r
- }\r
- }\r
- return rates;\r
+ public static Vector substitution_rates(AlignmentI align, int start, int end) {\r
+ Vector rates = new Vector();\r
+\r
+ int len = (end - start + 1);\r
+\r
+ // Turn seqs into char arrays\r
+ int[][] seqint = new int[align.getHeight()][len];\r
+\r
+ for (int j = 0; j < align.getHeight(); j++) {\r
+ SequenceI seq = align.getSequenceAt(j);\r
+\r
+ for (int i = 0; i < len; i++) {\r
+ char c = seq.getCharAt((start + i) - 1);\r
+\r
+ if (c == 'A') {\r
+ seqint[j][i] = 0;\r
+ } else if (c == 'C') {\r
+ seqint[j][i] = 1;\r
+ } else if (c == 'T') {\r
+ seqint[j][i] = 2;\r
+ } else if (c == 'G') {\r
+ seqint[j][i] = 3;\r
+ } else {\r
+ seqint[j][i] = -1;\r
+ }\r
+ }\r
+ }\r
+\r
+ // print_matrix(seqint,2,len); for (int j = 0; j < align.getHeight(); j++) {\r
+ for (int j = 0; j < align.getHeight(); j++) {\r
+ for (int k = 0; k < align.getHeight(); k++) {\r
+ int[][] counts = new int[4][4];\r
+ int tot = 0;\r
+ int[] tots = new int[4];\r
+ int fulltot = 0;\r
+ int[] fulltots = new int[4];\r
+\r
+ for (int i = 0; i < len; i++) {\r
+ if (k != j) {\r
+ // System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);\r
+ if ((seqint[j][i] >= 0) && (seqint[k][i] >= 0)) {\r
+ counts[seqint[k][i]][seqint[j][i]]++;\r
+\r
+ // print_matrix(counts,4,4);\r
+ tots[seqint[j][i]]++;\r
+ tot++;\r
+ }\r
+\r
+ if (seqint[j][i] != -1) {\r
+ fulltots[seqint[j][i]]++;\r
+ fulltot++;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (k != j) {\r
+ System.out.println();\r
+\r
+ System.out.println("Sequence " +\r
+ align.getSequenceAt(j).getName() + " " +\r
+ align.getSequenceAt(k).getName());\r
+\r
+ System.out.println();\r
+ print_matrix(counts, 4, 4);\r
+ System.out.println();\r
+\r
+ double[][] out = new double[4][4]; // = constant_multiply_matrix(counts,1.0/tot,4,4);\r
+\r
+ for (int i = 0; i < 4; i++) {\r
+ for (int jj = 0; jj < 4; jj++) {\r
+ out[i][jj] = (double) counts[i][jj] / tots[jj];\r
+ }\r
+ }\r
+\r
+ print_matrix(out, 4, 4);\r
+ System.out.println();\r
+\r
+ System.out.print("RATES\t");\r
+ System.out.print(align.getSequenceAt(j).getName() + "\t" +\r
+ align.getSequenceAt(k).getName() + "\t");\r
+\r
+ for (int i = 0; i < 4; i++) {\r
+ for (int jj = 0; jj < 4; jj++) {\r
+ Format.print(System.out, "%4.3f\t", out[i][jj]);\r
+ }\r
+ }\r
+\r
+ System.out.println();\r
+\r
+ for (int i = 0; i < 4; i++) {\r
+ Format.print(System.out, "%4.3f\t",\r
+ ((double) fulltots[i] * 1.0) / fulltot);\r
+ }\r
+\r
+ System.out.println();\r
+ System.out.print("\nGC ");\r
+\r
+ Format.print(System.out, "%4.3f\t",\r
+ (double) ((100 * fulltots[1]) + fulltots[3]) / fulltot);\r
+\r
+ System.out.print((fulltots[1] + fulltots[3]) + "\t" +\r
+ fulltot);\r
+\r
+ System.out.println();\r
+\r
+ rates.addElement(out);\r
+ }\r
+ }\r
+ }\r
+\r
+ return rates;\r
}\r
\r
- public static double[][] constant_multiply_matrix(int[][] matrix, double c,int n, int m) {\r
- double[][] out = new double[n][m];\r
+ public static double[][] constant_multiply_matrix(int[][] matrix, double c,\r
+ int n, int m) {\r
+ double[][] out = new double[n][m];\r
\r
- for (int i = 0; i < n; i++) {\r
- for (int j = 0; j < m; j++) {\r
+ for (int i = 0; i < n; i++) {\r
+ for (int j = 0; j < m; j++) {\r
+ out[i][j] = matrix[i][j] * c;\r
+ }\r
+ }\r
\r
- out[i][j] = matrix[i][j]*c;\r
- }\r
- }\r
- return out;\r
+ return out;\r
}\r
\r
-\r
public static void print_matrix(int[][] matrix, int n, int m) {\r
+ for (int i = 0; i < n; i++) {\r
+ for (int j = 0; j < m; j++) {\r
+ System.out.print(matrix[i][j] + "\t");\r
+ }\r
\r
-\r
- for (int i = 0; i < n; i++) {\r
- for (int j = 0; j < m; j++) {\r
-\r
- System.out.print(matrix[i][j] + "\t");\r
- }\r
- System.out.println();\r
- }\r
+ System.out.println();\r
+ }\r
}\r
- public static void print_matrix(double[][] matrix, int n, int m) {\r
-\r
-\r
- for (int i = 0; i < n; i++) {\r
- for (int j = 0; j < m; j++) {\r
\r
- Format.print(System.out,"%4.3f\t",matrix[i][j]);\r
+ public static void print_matrix(double[][] matrix, int n, int m) {\r
+ for (int i = 0; i < n; i++) {\r
+ for (int j = 0; j < m; j++) {\r
+ Format.print(System.out, "%4.3f\t", matrix[i][j]);\r
+ }\r
\r
- }\r
- System.out.println();\r
- }\r
+ System.out.println();\r
+ }\r
}\r
-\r
-\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
+\r
import jalview.io.*;\r
\r
import java.util.*;\r
\r
-public class CompareAlignments {\r
\r
+public class CompareAlignments {\r
Vector align;\r
String refId;\r
Vector ids;\r
\r
public CompareAlignments(Vector align) {\r
+ this.align = align;\r
\r
- this.align = align;\r
-\r
- ids = new Vector();\r
+ ids = new Vector();\r
\r
- Alignment al0 = (Alignment)align.elementAt(0);\r
+ Alignment al0 = (Alignment) align.elementAt(0);\r
\r
- for (int i = 0; i < al0.getHeight(); i++) {\r
- SequenceI seq = al0.getSequenceAt(i);\r
+ for (int i = 0; i < al0.getHeight(); i++) {\r
+ SequenceI seq = al0.getSequenceAt(i);\r
\r
- ids.addElement(seq.getName());\r
-\r
- if (i == 0) {\r
- setReferenceId(seq.getName());\r
- }\r
- }\r
+ ids.addElement(seq.getName());\r
\r
+ if (i == 0) {\r
+ setReferenceId(seq.getName());\r
+ }\r
+ }\r
}\r
\r
public void compare() {\r
+ Hashtable positions = new Hashtable();\r
\r
- Hashtable positions = new Hashtable();\r
-\r
- for (int k = 0; k < ids.size(); k++) {\r
-\r
- String id = (String)ids.elementAt(k);\r
-\r
- System.out.println("Ids " + id + " " + refId);\r
+ for (int k = 0; k < ids.size(); k++) {\r
+ String id = (String) ids.elementAt(k);\r
\r
- if (!id.equals(refId)) {\r
+ System.out.println("Ids " + id + " " + refId);\r
\r
- Hashtable fullhash = new Hashtable();\r
+ if (!id.equals(refId)) {\r
+ Hashtable fullhash = new Hashtable();\r
\r
- for (int i = 0; i < align.size(); i++) {\r
- System.out.println("Alignment " + i);\r
+ for (int i = 0; i < align.size(); i++) {\r
+ System.out.println("Alignment " + i);\r
\r
- Alignment al = (Alignment)align.elementAt(i);\r
+ Alignment al = (Alignment) align.elementAt(i);\r
\r
- SequenceI refseq = null;\r
+ SequenceI refseq = null;\r
\r
- for (int j = 0; j < al.getHeight(); j++) {\r
- if (((SequenceI)al.getSequenceAt(j)).getName().equals(refId)) {\r
- refseq = (SequenceI)al.getSequenceAt(j);\r
- }\r
- }\r
+ for (int j = 0; j < al.getHeight(); j++) {\r
+ if (((SequenceI) al.getSequenceAt(j)).getName().equals(refId)) {\r
+ refseq = (SequenceI) al.getSequenceAt(j);\r
+ }\r
+ }\r
\r
- if (refseq != null) {\r
+ if (refseq != null) {\r
+ System.out.println("Refseq " + refseq.getName());\r
\r
- System.out.println("Refseq " + refseq.getName());\r
+ for (int jj = 0; jj < al.getHeight(); jj++) {\r
+ SequenceI seq = (SequenceI) al.getSequenceAt(jj);\r
\r
- for (int jj = 0; jj < al.getHeight(); jj++) {\r
- SequenceI seq = (SequenceI)al.getSequenceAt(jj);\r
+ if (seq.getName().equals(id)) {\r
+ Hashtable hash = getAlignPositions(seq, refseq);\r
\r
- if (seq.getName().equals(id)) {\r
- Hashtable hash = getAlignPositions(seq,refseq);\r
+ Enumeration keys = hash.keys();\r
\r
- Enumeration keys = hash.keys();\r
+ while (keys.hasMoreElements()) {\r
+ Integer key = (Integer) keys.nextElement();\r
\r
- while (keys.hasMoreElements()) {\r
- Integer key = (Integer)keys.nextElement();\r
- // System.out.println(key + " " + hash.get(key));\r
- if (fullhash.get(key) == null) {\r
- fullhash.put(key,new Vector());\r
- }\r
+ // System.out.println(key + " " + hash.get(key));\r
+ if (fullhash.get(key) == null) {\r
+ fullhash.put(key, new Vector());\r
+ }\r
\r
- Vector tmp = (Vector)fullhash.get(key);\r
+ Vector tmp = (Vector) fullhash.get(key);\r
\r
- tmp.addElement(hash.get(key));\r
- }\r
- }\r
+ tmp.addElement(hash.get(key));\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- }\r
- }\r
- }\r
+ System.out.println("\nId " + id);\r
\r
- System.out.println ("\nId " + id);\r
+ Enumeration keys = fullhash.keys();\r
\r
- Enumeration keys = fullhash.keys();\r
+ int totdiff = 0;\r
\r
+ while (keys.hasMoreElements()) {\r
+ Integer key = (Integer) keys.nextElement();\r
\r
- int totdiff = 0;\r
- while (keys.hasMoreElements()) {\r
- Integer key = (Integer)keys.nextElement();\r
+ Vector tmp = (Vector) fullhash.get(key);\r
\r
- Vector tmp = (Vector)fullhash.get(key);\r
+ int diff0 = ((Integer) tmp.elementAt(0)).intValue();\r
+ ;\r
\r
+ int diff = 0;\r
\r
+ for (int l = 1; l < tmp.size(); l++) {\r
+ diff += Math.abs(diff0 -\r
+ ((Integer) tmp.elementAt(l)).intValue());\r
+ }\r
\r
- int diff0 = ((Integer)tmp.elementAt(0)).intValue();;\r
- int diff = 0;\r
+ if (diff > 0) {\r
+ totdiff++;\r
+ System.out.print(id + " Ref pos " + key + " : " +\r
+ diff0 + " " + diff + " : ");\r
\r
- for (int l = 1; l < tmp.size(); l++) {\r
- diff += Math.abs(diff0 - ((Integer)tmp.elementAt(l)).intValue());\r
+ for (int l = 1; l < tmp.size(); l++) {\r
+ System.out.print(diff0 -\r
+ ((Integer) tmp.elementAt(l)).intValue() + " ");\r
+ }\r
\r
- }\r
+ System.out.println();\r
+ }\r
+ }\r
\r
- if (diff > 0) {\r
- totdiff++;\r
- System.out.print(id + " Ref pos " + key + " : " + diff0 + " " + diff + " : ");\r
-\r
- for (int l = 1; l < tmp.size(); l++) {\r
- System.out.print(diff0 - ((Integer)tmp.elementAt(l)).intValue() + " ");\r
- }\r
- System.out.println();\r
- }\r
- }\r
-\r
- System.out.println("Total " + id + " " + totdiff);\r
-\r
- }\r
- }\r
+ System.out.println("Total " + id + " " + totdiff);\r
+ }\r
+ }\r
}\r
\r
-\r
public void setReferenceId(String id) {\r
- this.refId = id;\r
+ this.refId = id;\r
}\r
\r
public Hashtable getAlignPositions(SequenceI seq1, SequenceI seq2) {\r
+ Hashtable hash = new Hashtable();\r
\r
- Hashtable hash = new Hashtable();\r
+ int i = 0;\r
\r
- int i = 0;\r
+ int pos1 = 0;\r
+ int pos2 = 0;\r
\r
- int pos1 = 0;\r
- int pos2 = 0;\r
+ while (i < seq1.getLength()) {\r
+ char c1 = seq1.getCharAt(i);\r
+ char c2 = seq2.getCharAt(i);\r
\r
- while (i < seq1.getLength()) {\r
+ if (c1 != '-') {\r
+ pos1++;\r
+ }\r
\r
- char c1 = seq1.getCharAt(i);\r
- char c2 = seq2.getCharAt(i);\r
+ if (c2 != '-') {\r
+ pos2++;\r
+ }\r
\r
- if (c1 != '-') {\r
- pos1++;\r
- }\r
+ if (c1 != '-') {\r
+ hash.put(new Integer(pos1), new Integer(pos2));\r
+ }\r
\r
- if (c2 != '-') {\r
- pos2++;\r
- }\r
+ i++;\r
+ }\r
\r
- if (c1 != '-') {\r
- hash.put(new Integer(pos1),new Integer(pos2));\r
- }\r
-\r
- i++;\r
- }\r
- return hash;\r
+ return hash;\r
}\r
-\r
-\r
-\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.analysis;\r
\r
+import jalview.datamodel.*;\r
\r
-import java.util.*;\r
import jalview.gui.*;\r
-import jalview.datamodel.*;\r
+\r
+import java.util.*;\r
\r
\r
public class Conservation {\r
- Vector sequences;\r
- int start;\r
- int end;\r
- Vector seqNums; // vector of int vectors where first is sequence checksum\r
- int maxLength=0; // used by quality calcs\r
- boolean seqNumsChanged = false; // updated after any change via calcSeqNum;\r
- private void calcSeqNums() {\r
- for (int i=0; i<sequences.size(); i++) {\r
- calcSeqNum(i);\r
+ Vector sequences;\r
+ int start;\r
+ int end;\r
+ Vector seqNums; // vector of int vectors where first is sequence checksum\r
+ int maxLength = 0; // used by quality calcs\r
+ boolean seqNumsChanged = false; // updated after any change via calcSeqNum;\r
+ Vector total = new Vector();\r
+ public Vector quality;\r
+ public Double[] qualityRange = new Double[2];\r
+ String consString = "";\r
+ Sequence consSequence;\r
+ Hashtable propHash;\r
+ int threshold;\r
+ String name = "";\r
+ int[][] cons2;\r
+\r
+ public Conservation(String name, Hashtable propHash, int threshold,\r
+ Vector sequences, int start, int end) {\r
+ this.name = name;\r
+ this.propHash = propHash;\r
+ this.threshold = threshold;\r
+ this.sequences = sequences;\r
+ this.start = start;\r
+ this.end = end;\r
+ seqNums = new Vector(sequences.size());\r
+ calcSeqNums();\r
}\r
- }\r
- private void calcSeqNum(int i) {\r
- String sq=null; // for dumb jbuilder not-inited exception warning\r
- int[] sqnum = null;\r
- if (i>-1 && i<sequences.size()) {\r
- sq = ((SequenceI)sequences.elementAt(i)).getSequence();\r
- if (seqNums.size()<=i) {\r
- seqNums.addElement(new int[sq.length()+1]);\r
- }\r
- if (sq.hashCode()!=((int[])seqNums.elementAt(i))[0])\r
- {\r
- int j, len;\r
- seqNumsChanged = true;\r
- sq = ((SequenceI) sequences.elementAt(i)).getSequence();\r
- len = sq.length();\r
- if (maxLength < len)\r
- maxLength = len;\r
- sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length\r
- sqnum[0] = sq.hashCode();\r
- for (j = 1; j <= len; j++)\r
- {\r
- sqnum[j] = ( (Integer) jalview.schemes.ResidueProperties.aaHash.get(new\r
- String(sq.substring(j - 1, j)))).intValue(); // yuk\r
- }\r
- seqNums.setElementAt(sqnum, i);\r
- }\r
- } else {\r
- // JBPNote INFO level debug\r
- System.err.println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");\r
- }\r
- }\r
- Vector total = new Vector();\r
- public Vector quality;\r
- public Double[] qualityRange = new Double[2];\r
- String consString = "";\r
-\r
- Sequence consSequence;\r
- Hashtable propHash;\r
- int threshold;\r
-\r
- String name = "";\r
-\r
- public Conservation(String name,Hashtable propHash, int threshold, Vector sequences, int start, int end) {\r
- this.name = name;\r
- this.propHash = propHash;\r
- this.threshold = threshold;\r
- this.sequences = sequences;\r
- this.start = start;\r
- this.end = end;\r
- seqNums = new Vector(sequences.size());\r
- calcSeqNums();\r
- }\r
-\r
-\r
- public void calculate() {\r
-\r
- for (int i = start;i <= end; i++) {\r
- Hashtable resultHash = null;\r
- Hashtable residueHash = null;\r
-\r
- resultHash = new Hashtable();\r
- residueHash = new Hashtable();\r
-\r
- for (int j=0; j < sequences.size(); j++) {\r
- // JBPNote - have to make sure elements of the sequences vector\r
- // are tested like this everywhere...\r
- if (sequences.elementAt(j) instanceof Sequence) {\r
- Sequence s = (Sequence)sequences.elementAt(j);\r
-\r
- if (s.getLength() > i) {\r
- String res = s.getSequence().substring(i,i+1);\r
-\r
- if (residueHash.containsKey(res)) {\r
- int count = ((Integer)residueHash.get(res)).intValue() ;\r
- count++;\r
- residueHash.put(res,new Integer(count));\r
- } else {\r
- residueHash.put(res,new Integer(1));\r
+\r
+ private void calcSeqNums() {\r
+ for (int i = 0; i < sequences.size(); i++) {\r
+ calcSeqNum(i);\r
+ }\r
+ }\r
+\r
+ private void calcSeqNum(int i) {\r
+ String sq = null; // for dumb jbuilder not-inited exception warning\r
+ int[] sqnum = null;\r
+\r
+ if ((i > -1) && (i < sequences.size())) {\r
+ sq = ((SequenceI) sequences.elementAt(i)).getSequence();\r
+\r
+ if (seqNums.size() <= i) {\r
+ seqNums.addElement(new int[sq.length() + 1]);\r
}\r
- } else {\r
- if (residueHash.containsKey("-")) {\r
- int count = ((Integer)residueHash.get("-")).intValue() ;\r
- count++;\r
- residueHash.put("-",new Integer(count));\r
- } else {\r
- residueHash.put("-",new Integer(1));\r
+\r
+ if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0]) {\r
+ int j;\r
+ int len;\r
+ seqNumsChanged = true;\r
+ sq = ((SequenceI) sequences.elementAt(i)).getSequence();\r
+ len = sq.length();\r
+\r
+ if (maxLength < len) {\r
+ maxLength = len;\r
+ }\r
+\r
+ sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length\r
+ sqnum[0] = sq.hashCode();\r
+\r
+ for (j = 1; j <= len; j++) {\r
+ sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(\r
+ sq.substring(j - 1, j)))).intValue(); // yuk\r
+ }\r
+\r
+ seqNums.setElementAt(sqnum, i);\r
}\r
- }\r
+ } else {\r
+ // JBPNote INFO level debug\r
+ System.err.println(\r
+ "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");\r
}\r
- }\r
+ }\r
\r
- //What is the count threshold to count the residues in residueHash()\r
- int thresh = threshold*(sequences.size())/100;\r
+ public void calculate() {\r
+ for (int i = start; i <= end; i++) {\r
+ Hashtable resultHash = null;\r
+ Hashtable residueHash = null;\r
+\r
+ resultHash = new Hashtable();\r
+ residueHash = new Hashtable();\r
+\r
+ for (int j = 0; j < sequences.size(); j++) {\r
+ // JBPNote - have to make sure elements of the sequences vector\r
+ // are tested like this everywhere...\r
+ if (sequences.elementAt(j) instanceof Sequence) {\r
+ Sequence s = (Sequence) sequences.elementAt(j);\r
+\r
+ if (s.getLength() > i) {\r
+ String res = s.getSequence().substring(i, i + 1);\r
+\r
+ if (residueHash.containsKey(res)) {\r
+ int count = ((Integer) residueHash.get(res)).intValue();\r
+ count++;\r
+ residueHash.put(res, new Integer(count));\r
+ } else {\r
+ residueHash.put(res, new Integer(1));\r
+ }\r
+ } else {\r
+ if (residueHash.containsKey("-")) {\r
+ int count = ((Integer) residueHash.get("-")).intValue();\r
+ count++;\r
+ residueHash.put("-", new Integer(count));\r
+ } else {\r
+ residueHash.put("-", new Integer(1));\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- //loop over all the found residues\r
- Enumeration e = residueHash.keys();\r
+ //What is the count threshold to count the residues in residueHash()\r
+ int thresh = (threshold * (sequences.size())) / 100;\r
+\r
+ //loop over all the found residues\r
+ Enumeration e = residueHash.keys();\r
+\r
+ while (e.hasMoreElements()) {\r
+ String res = (String) e.nextElement();\r
+\r
+ if (((Integer) residueHash.get(res)).intValue() > thresh) {\r
+ //Now loop over the properties\r
+ Enumeration e2 = propHash.keys();\r
+\r
+ while (e2.hasMoreElements()) {\r
+ String type = (String) e2.nextElement();\r
+ Hashtable ht = (Hashtable) propHash.get(type);\r
+\r
+ //Have we ticked this before?\r
+ if (!resultHash.containsKey(type)) {\r
+ if (ht.containsKey(res)) {\r
+ resultHash.put(type, ht.get(res));\r
+ } else {\r
+ resultHash.put(type, ht.get("-"));\r
+ }\r
+ } else if (((Integer) resultHash.get(type)).equals(\r
+ (Integer) ht.get(res)) == false) {\r
+ resultHash.put(type, new Integer(-1));\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ total.addElement(resultHash);\r
+ }\r
+ }\r
\r
- while (e.hasMoreElements()) {\r
+ public int countGaps(int j) {\r
+ int count = 0;\r
\r
- String res = (String)e.nextElement();\r
- if (((Integer)residueHash.get(res)).intValue() > thresh) {\r
+ for (int i = 0; i < sequences.size(); i++) {\r
+ if ((j + 1) > ((Sequence) sequences.elementAt(i)).getSequence()\r
+ .length()) {\r
+ count++;\r
\r
- //Now loop over the properties\r
- Enumeration e2 = propHash.keys();\r
+ continue;\r
+ }\r
\r
- while (e2.hasMoreElements()) {\r
- String type = (String)e2.nextElement();\r
- Hashtable ht = (Hashtable)propHash.get(type);\r
+ char c = ((Sequence) sequences.elementAt(i)).getSequence().charAt(j);\r
\r
- //Have we ticked this before?\r
- if (! resultHash.containsKey(type)) {\r
- if (ht.containsKey(res)) {\r
- resultHash.put(type,ht.get(res));\r
- } else {\r
- resultHash.put(type,ht.get("-"));\r
- }\r
- } else if ( ((Integer)resultHash.get(type)).equals((Integer)ht.get(res)) == false) {\r
- resultHash.put(type,new Integer(-1));\r
+ if (jalview.util.Comparison.isGap((c))) {\r
+ count++;\r
}\r
- }\r
}\r
- }\r
\r
- total.addElement(resultHash);\r
+ return count;\r
}\r
- }\r
\r
- public int countGaps(int j)\r
- {\r
- int count = 0;\r
+ /***\r
+ * countConsNGaps\r
+ * returns gap count in int[0], and conserved residue count in int[1]\r
+ */\r
+ public int[] countConsNGaps(int j) {\r
+ int count = 0;\r
+ int cons = 0;\r
+ int nres = 0;\r
+ int[] r = new int[2];\r
+ char f = '$';\r
+\r
+ for (int i = 0; i < sequences.size(); i++) {\r
+ if (j >= ((Sequence) sequences.elementAt(i)).getSequence().length()) {\r
+ count++;\r
+\r
+ continue;\r
+ }\r
\r
- for (int i = 0; i < sequences.size();i++)\r
- {\r
- if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())\r
- { count++; continue;}\r
+ char c = ((Sequence) sequences.elementAt(i)).getSequence().charAt(j);\r
+\r
+ if (jalview.util.Comparison.isGap((c))) {\r
+ count++;\r
+ } else {\r
+ nres++;\r
+\r
+ if (nres == 1) {\r
+ f = c;\r
+ cons++;\r
+ } else if (f == c) {\r
+ cons++;\r
+ }\r
+ }\r
+ }\r
\r
- char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);\r
- if (jalview.util.Comparison.isGap((c)))\r
- count++;\r
+ r[0] = (nres == cons) ? 1 : 0;\r
+ r[1] = count;\r
\r
+ return r;\r
}\r
- return count;\r
- }\r
- /***\r
- * countConsNGaps\r
- * returns gap count in int[0], and conserved residue count in int[1]\r
- */\r
- public int[] countConsNGaps(int j)\r
- {\r
- int count = 0;\r
- int cons=0;\r
- int nres = 0;\r
- int[] r = new int[2];\r
- char f='$';\r
- for (int i = 0; i < sequences.size();i++)\r
- {\r
- if( j >= ((Sequence)sequences.elementAt(i)).getSequence().length())\r
- { count++;\r
- continue;}\r
-\r
- char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);\r
- if (jalview.util.Comparison.isGap((c)))\r
- count++;\r
- else {\r
- nres++;\r
- if (nres==1) {\r
- f = c;\r
- cons++;\r
- } else\r
- if (f == c) {\r
- cons++;\r
- }\r
- }\r
+\r
+ public void verdict(boolean consflag, float percentageGaps) {\r
+ String consString = "";\r
+\r
+ for (int i = start; i <= end; i++) {\r
+ int[] gapcons = countConsNGaps(i);\r
+ boolean cons = (gapcons[0] == 1) ? true : false;\r
+ int totGaps = gapcons[1];\r
+ float pgaps = ((float) totGaps * 100) / (float) sequences.size();\r
+\r
+ // System.out.println("percentage gaps = "+pgaps+"\n");\r
+ if (percentageGaps > pgaps) {\r
+ Hashtable resultHash = (Hashtable) total.elementAt(i - start);\r
+\r
+ //Now find the verdict\r
+ int count = 0;\r
+ Enumeration e3 = resultHash.keys();\r
+\r
+ while (e3.hasMoreElements()) {\r
+ String type = (String) e3.nextElement();\r
+ Integer result = (Integer) resultHash.get(type);\r
+\r
+ //Do we want to count +ve conservation or +ve and -ve cons.?\r
+ if (consflag) {\r
+ if (result.intValue() == 1) {\r
+ count++;\r
+ }\r
+ } else {\r
+ if (result.intValue() != -1) {\r
+ count++;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (count < 10) {\r
+ consString = consString + String.valueOf(count); // Conserved props!=Identity\r
+ } else {\r
+ consString = consString + ((gapcons[0] == 1) ? "*" : "+");\r
+ }\r
+ } else {\r
+ consString = consString + "-";\r
+ }\r
+ }\r
+\r
+ consSequence = new Sequence(name, consString, start, end);\r
}\r
- r[0] = (nres==cons) ? 1 : 0;\r
- r[1] = count;\r
\r
+ public Sequence getConsSequence() {\r
+ return consSequence;\r
+ }\r
\r
- return r;\r
- }\r
+ // From Alignment.java in jalview118\r
+ public void findQuality() {\r
+ findQuality(0, maxLength - 1);\r
+ }\r
\r
- public void verdict(boolean consflag, float percentageGaps) {\r
- String consString = "";\r
+ private void percentIdentity2() {\r
+ calcSeqNums(); // updates maxLength, too.\r
\r
- for (int i=start; i <= end; i++) {\r
- int[] gapcons = countConsNGaps(i);\r
- boolean cons = (gapcons[0]==1) ? true : false;\r
- int totGaps = gapcons[1];\r
- float pgaps = (float)totGaps*100/(float)sequences.size();\r
- // System.out.println("percentage gaps = "+pgaps+"\n");\r
- if (percentageGaps > pgaps)\r
- {\r
- Hashtable resultHash = (Hashtable)total.elementAt(i-start);\r
-\r
- //Now find the verdict\r
- int count = 0;\r
- Enumeration e3 = resultHash.keys();\r
-\r
- while (e3.hasMoreElements())\r
- {\r
- String type = (String)e3.nextElement();\r
- Integer result = (Integer)resultHash.get(type);\r
-\r
- //Do we want to count +ve conservation or +ve and -ve cons.?\r
-\r
- if (consflag)\r
- {\r
- if (result.intValue() == 1)\r
- count++;\r
- }\r
- else\r
- {\r
- if (result.intValue() != -1)\r
- count++;\r
- }\r
- }\r
+ if ((cons2 == null) || seqNumsChanged) {\r
+ cons2 = new int[maxLength][24];\r
\r
- if (count < 10)\r
- consString = consString + String.valueOf(count);// Conserved props!=Identity\r
- else\r
- consString = consString + ((gapcons[0]==1) ? "*" : "+");\r
+ // Initialize the array\r
+ for (int j = 0; j < 24; j++) {\r
+ for (int i = 0; i < maxLength; i++) {\r
+ cons2[i][j] = 0;\r
+ }\r
+ }\r
\r
- }\r
- else\r
- {\r
- consString = consString + "-";\r
- }\r
- }\r
+ int[] sqnum;\r
+ int j = 0;\r
\r
- consSequence = new Sequence(name,consString,start,end);\r
- }\r
+ while (j < sequences.size()) {\r
+ sqnum = (int[]) seqNums.elementAt(j);\r
\r
- public Sequence getConsSequence() {\r
- return consSequence;\r
- }\r
+ for (int i = 1; i < sqnum.length; i++) {\r
+ cons2[i - 1][sqnum[i]]++;\r
+ }\r
\r
- // From Alignment.java in jalview118\r
+ for (int i = sqnum.length - 1; i < maxLength; i++) {\r
+ cons2[i][23]++; // gap count\r
+ }\r
\r
- public void findQuality() {\r
- findQuality(0,maxLength-1);\r
- }\r
+ j++;\r
+ }\r
\r
- int[][] cons2;\r
+ // unnecessary ?\r
\r
- private void percentIdentity2() {\r
- calcSeqNums(); // updates maxLength, too.\r
- if (cons2==null || seqNumsChanged) {\r
- cons2 = new int[maxLength][24];\r
- // Initialize the array\r
- for (int j=0;j<24;j++) {\r
- for (int i=0; i < maxLength;i++) {\r
- cons2[i][j] = 0;\r
- }\r
- }\r
-\r
- int sqnum[];\r
- int j = 0;\r
- while(j < sequences.size()) {\r
- sqnum=(int[])seqNums.elementAt(j);\r
- for (int i = 1; i < sqnum.length; i++) {\r
- cons2[i-1][sqnum[i]]++;\r
- }\r
- for (int i=sqnum.length-1; i<maxLength; i++) {\r
- cons2[i][23]++; // gap count\r
- }\r
- j++;\r
- }\r
-\r
- // unnecessary ?\r
- /* for (int i=start; i <= end; i++) {\r
- int max = -1000;\r
- int maxi = -1;\r
- int maxj = -1;\r
-\r
- for (int j=0;j<24;j++) {\r
- if (cons2[i][j] > max) {\r
- max = cons2[i][j];\r
- maxi = i;\r
- maxj = j;\r
- }\r
+ /* for (int i=start; i <= end; i++) {\r
+ int max = -1000;\r
+ int maxi = -1;\r
+ int maxj = -1;\r
\r
- }\r
- } */\r
+ for (int j=0;j<24;j++) {\r
+ if (cons2[i][j] > max) {\r
+ max = cons2[i][j];\r
+ maxi = i;\r
+ maxj = j;\r
+ }\r
+\r
+ }\r
+ } */\r
+ }\r
}\r
\r
-}\r
+ public void findQuality(int start, int end) {\r
+ quality = new Vector();\r
+\r
+ double max = -10000;\r
+ String s = "";\r
+ int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();\r
+\r
+ //Loop over columns // JBPNote Profiling info\r
+ // long ts = System.currentTimeMillis();\r
+ //long te = System.currentTimeMillis();\r
+ percentIdentity2();\r
+\r
+ int size = seqNums.size();\r
+ int[] lengths = new int[size];\r
+\r
+ for (int l = 0; l < size; l++)\r
+ lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;\r
+\r
+ for (int j = start; j <= end; j++) {\r
+ double bigtot = 0;\r
+\r
+ // First Xr = depends on column only\r
+ double[] x = new double[24];\r
+\r
+ for (int ii = 0; ii < 24; ii++) {\r
+ x[ii] = 0;\r
\r
+ try {\r
+ for (int i2 = 0; i2 < 24; i2++) {\r
+ x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) +\r
+ 4);\r
+ }\r
+ } catch (Exception e) {\r
+ System.err.println("Exception during quality calculation.");\r
+ e.printStackTrace();\r
+ }\r
\r
-public void findQuality(int start, int end) {\r
- quality = new Vector();\r
- double max = -10000;\r
- String s = "";\r
- int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();\r
- //Loop over columns // JBPNote Profiling info\r
- // long ts = System.currentTimeMillis();\r
- //long te = System.currentTimeMillis();\r
- percentIdentity2();\r
-\r
- int size = seqNums.size();\r
- int[] lengths = new int[size];\r
-\r
- for (int l = 0; l < size; l++)\r
- lengths[l] = ((int[]) seqNums.elementAt(l)).length-1;\r
-\r
- for (int j=start; j <= end; j++) {\r
- double bigtot = 0;\r
-\r
- // First Xr = depends on column only\r
- double x[] = new double[24];\r
-\r
- for (int ii=0; ii < 24; ii++) {\r
- x[ii] = 0;\r
- try {\r
- for (int i2=0; i2 < 24; i2++) {\r
- x[ii] += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4;\r
- }\r
- } catch (Exception e) {\r
- System.err.println("Exception during quality calculation.");\r
- e.printStackTrace();\r
- }\r
- //System.out.println("X " + ii + " " + x[ii]);\r
- x[ii] /= (size);\r
- //System.out.println("X " + ii + " " + x[ii]);\r
- }\r
- // Now calculate D for each position and sum\r
- for (int k=0; k < size; k++) {\r
- double tot = 0;\r
- double[] xx = new double[24];\r
- int seqNum =\r
- (j<lengths[k])\r
- ? ((int[]) seqNums.elementAt(k))[j+1]\r
- : 23; // Sequence, or gap at the end\r
-\r
- // This is a loop over r\r
- for (int i=0; i < 23; i++) {\r
- double sr = 0;\r
- try {\r
- sr = (double)BLOSUM62[i][seqNum]+4;\r
- } catch (Exception e) {\r
- System.out.println("Exception in sr: " + e);\r
- e.printStackTrace();\r
- }\r
- //Calculate X with another loop over residues\r
-\r
- // System.out.println("Xi " + i + " " + x[i] + " " + sr);\r
- xx[i] = x[i] - sr;\r
-\r
- tot += xx[i]*xx[i];\r
+ //System.out.println("X " + ii + " " + x[ii]);\r
+ x[ii] /= (size);\r
+\r
+ //System.out.println("X " + ii + " " + x[ii]);\r
+ }\r
+\r
+ // Now calculate D for each position and sum\r
+ for (int k = 0; k < size; k++) {\r
+ double tot = 0;\r
+ double[] xx = new double[24];\r
+ int seqNum = (j < lengths[k])\r
+ ? ((int[]) seqNums.elementAt(k))[j + 1] : 23; // Sequence, or gap at the end\r
+\r
+ // This is a loop over r\r
+ for (int i = 0; i < 23; i++) {\r
+ double sr = 0;\r
+\r
+ try {\r
+ sr = (double) BLOSUM62[i][seqNum] + 4;\r
+ } catch (Exception e) {\r
+ System.out.println("Exception in sr: " + e);\r
+ e.printStackTrace();\r
+ }\r
+\r
+ //Calculate X with another loop over residues\r
+ // System.out.println("Xi " + i + " " + x[i] + " " + sr);\r
+ xx[i] = x[i] - sr;\r
+\r
+ tot += (xx[i] * xx[i]);\r
+ }\r
+\r
+ bigtot += Math.sqrt(tot);\r
+ }\r
+\r
+ // This is the quality for one column\r
+ if (max < bigtot) {\r
+ max = bigtot;\r
+ }\r
+\r
+ // bigtot = bigtot * (size-cons2[j][23])/size;\r
+ quality.addElement(new Double(bigtot));\r
+\r
+ s += "-";\r
+\r
+ // Need to normalize by gaps\r
}\r
- bigtot += Math.sqrt(tot);\r
- }\r
- // This is the quality for one column\r
- if (max < bigtot) {max = bigtot;}\r
- // bigtot = bigtot * (size-cons2[j][23])/size;\r
\r
- quality.addElement(new Double(bigtot));\r
+ double newmax = -10000;\r
\r
- s += "-";\r
+ for (int j = start; j <= end; j++) {\r
+ double tmp = ((Double) quality.elementAt(j)).doubleValue();\r
+ tmp = ((max - tmp) * (size - cons2[j][23])) / size;\r
\r
- // Need to normalize by gaps\r
- }\r
- double newmax=-10000;\r
- for (int j=start; j <= end; j++) {\r
- double tmp = ((Double)quality.elementAt(j)).doubleValue();\r
- tmp = (max - tmp)*(size-cons2[j][23])/size;\r
- // System.out.println(tmp+ " " + j);\r
- quality.setElementAt(new Double(tmp),j);\r
- if (tmp>newmax)\r
- newmax = tmp;\r
- }\r
- // System.out.println("Quality " + s);\r
- qualityRange[0] = new Double(0);\r
- qualityRange[1] = new Double(newmax);\r
- }\r
+ // System.out.println(tmp+ " " + j);\r
+ quality.setElementAt(new Double(tmp), j);\r
\r
+ if (tmp > newmax) {\r
+ newmax = tmp;\r
+ }\r
+ }\r
\r
+ // System.out.println("Quality " + s);\r
+ qualityRange[0] = new Double(0);\r
+ qualityRange[1] = new Double(newmax);\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
-import jalview.util.*;\r
-import jalview.schemes.ResidueProperties;\r
-import java.util.*;\r
\r
import jalview.io.NewickFile;\r
\r
-public class NJTree {\r
-\r
- Vector cluster;\r
- SequenceI[] sequence;\r
-\r
- int done[];\r
- int noseqs;\r
- int noClus;\r
-\r
- float distance[][];\r
-\r
- int mini;\r
- int minj;\r
- float ri;\r
- float rj;\r
-\r
- Vector groups = new Vector();\r
- SequenceNode maxdist;\r
- SequenceNode top;\r
-\r
- float maxDistValue;\r
- float maxheight;\r
-\r
- int ycount;\r
-\r
- Vector node;\r
-\r
- String type;\r
- String pwtype;\r
-\r
- Object found = null;\r
- Object leaves = null;\r
-\r
- int start;\r
- int end;\r
-\r
- public NJTree(SequenceNode node) {\r
- top = node;\r
- maxheight = findHeight(top);\r
- }\r
-\r
- public String toString()\r
- {\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());\r
- return fout.print(false,true); // distances only\r
- }\r
-\r
- public NJTree(SequenceI[] seqs, NewickFile treefile) {\r
- top = treefile.getTree();\r
- maxheight = findHeight(top);\r
- SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);\r
-\r
- Vector leaves = new Vector();\r
- findLeaves(top, leaves);\r
-\r
- int i = 0;\r
- int namesleft = seqs.length;\r
-\r
- SequenceNode j;\r
- SequenceI nam;\r
- String realnam;\r
- while (i < leaves.size())\r
- {\r
- j = (SequenceNode) leaves.elementAt(i++);\r
- realnam = j.getName();\r
- nam = null;\r
- if (namesleft>-1)\r
- nam = algnIds.findIdMatch(realnam);\r
- if (nam != null) {\r
- j.setElement(nam);\r
- namesleft--;\r
- } else {\r
- j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));\r
- j.setPlaceholder(true);\r
-\r
- }\r
- }\r
- }\r
-\r
- /**\r
- *\r
- * used when the alignment associated to a tree has changed.\r
- *\r
- * @param alignment Vector\r
- */\r
- public void UpdatePlaceHolders(Vector alignment) {\r
- Vector leaves = new Vector();\r
- findLeaves(top, leaves);\r
- int sz = leaves.size();\r
- SequenceIdMatcher seqmatcher=null;\r
- int i=0;\r
- while (i<sz) {\r
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
- if (alignment.contains(leaf.element()))\r
- leaf.setPlaceholder(false);\r
- else {\r
- if (seqmatcher==null) {\r
- // Only create this the first time we need it\r
- SequenceI[] seqs = new SequenceI[alignment.size()];\r
- for (int j=0; j<seqs.length; j++)\r
- seqs[j] = (SequenceI) alignment.elementAt(j);\r
- seqmatcher = new SequenceIdMatcher(seqs);\r
- }\r
- SequenceI nam = seqmatcher.findIdMatch(leaf.getName());\r
- if (nam!=null) {\r
- leaf.setPlaceholder(false);\r
- leaf.setElement(nam);\r
- } else {\r
- leaf.setPlaceholder(true);\r
- }\r
- }\r
- }\r
- }\r
+import jalview.schemes.ResidueProperties;\r
\r
- public NJTree(SequenceI[] sequence,int start, int end) {\r
- this(sequence,"NJ","BL",start,end);\r
- }\r
+import jalview.util.*;\r
\r
- public NJTree(SequenceI[] sequence,String type,String pwtype,int start, int end ) {\r
+import java.util.*;\r
\r
- this.sequence = sequence;\r
- this.node = new Vector();\r
- this.type = type;\r
- this.pwtype = pwtype;\r
- this.start = start;\r
- this.end = end;\r
\r
- if (!(type.equals("NJ"))) {\r
- type = "AV";\r
+public class NJTree {\r
+ Vector cluster;\r
+ SequenceI[] sequence;\r
+ int[] done;\r
+ int noseqs;\r
+ int noClus;\r
+ float[][] distance;\r
+ int mini;\r
+ int minj;\r
+ float ri;\r
+ float rj;\r
+ Vector groups = new Vector();\r
+ SequenceNode maxdist;\r
+ SequenceNode top;\r
+ float maxDistValue;\r
+ float maxheight;\r
+ int ycount;\r
+ Vector node;\r
+ String type;\r
+ String pwtype;\r
+ Object found = null;\r
+ Object leaves = null;\r
+ int start;\r
+ int end;\r
+\r
+ public NJTree(SequenceNode node) {\r
+ top = node;\r
+ maxheight = findHeight(top);\r
+ }\r
+\r
+ public NJTree(SequenceI[] seqs, NewickFile treefile) {\r
+ top = treefile.getTree();\r
+ maxheight = findHeight(top);\r
+\r
+ SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);\r
+\r
+ Vector leaves = new Vector();\r
+ findLeaves(top, leaves);\r
+\r
+ int i = 0;\r
+ int namesleft = seqs.length;\r
+\r
+ SequenceNode j;\r
+ SequenceI nam;\r
+ String realnam;\r
+\r
+ while (i < leaves.size()) {\r
+ j = (SequenceNode) leaves.elementAt(i++);\r
+ realnam = j.getName();\r
+ nam = null;\r
+\r
+ if (namesleft > -1) {\r
+ nam = algnIds.findIdMatch(realnam);\r
+ }\r
+\r
+ if (nam != null) {\r
+ j.setElement(nam);\r
+ namesleft--;\r
+ } else {\r
+ j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));\r
+ j.setPlaceholder(true);\r
+ }\r
+ }\r
}\r
\r
- if (!(pwtype.equals("PID"))) {\r
- type = "BL";\r
+ public NJTree(SequenceI[] sequence, int start, int end) {\r
+ this(sequence, "NJ", "BL", start, end);\r
}\r
\r
- int i=0;\r
+ public NJTree(SequenceI[] sequence, String type, String pwtype, int start,\r
+ int end) {\r
+ this.sequence = sequence;\r
+ this.node = new Vector();\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
+ this.start = start;\r
+ this.end = end;\r
\r
- done = new int[sequence.length];\r
+ if (!(type.equals("NJ"))) {\r
+ type = "AV";\r
+ }\r
\r
+ if (!(pwtype.equals("PID"))) {\r
+ type = "BL";\r
+ }\r
\r
- while (i < sequence.length && sequence[i] != null) {\r
- done[i] = 0;\r
- i++;\r
- }\r
+ int i = 0;\r
\r
- noseqs = i++;\r
+ done = new int[sequence.length];\r
\r
- distance = findDistances();\r
+ while ((i < sequence.length) && (sequence[i] != null)) {\r
+ done[i] = 0;\r
+ i++;\r
+ }\r
\r
- makeLeaves();\r
+ noseqs = i++;\r
\r
- noClus = cluster.size();\r
+ distance = findDistances();\r
\r
- cluster();\r
+ makeLeaves();\r
\r
- }\r
+ noClus = cluster.size();\r
\r
+ cluster();\r
+ }\r
\r
- public void cluster() {\r
+ public String toString() {\r
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());\r
\r
- while (noClus > 2) {\r
- if (type.equals("NJ")) {\r
- float mind = findMinNJDistance();\r
- } else {\r
- float mind = findMinDistance();\r
- }\r
+ return fout.print(false, true); // distances only\r
+ }\r
\r
- Cluster c = joinClusters(mini,minj);\r
+ /**\r
+ *\r
+ * used when the alignment associated to a tree has changed.\r
+ *\r
+ * @param alignment Vector\r
+ */\r
+ public void UpdatePlaceHolders(Vector alignment) {\r
+ Vector leaves = new Vector();\r
+ findLeaves(top, leaves);\r
\r
+ int sz = leaves.size();\r
+ SequenceIdMatcher seqmatcher = null;\r
+ int i = 0;\r
\r
- done[minj] = 1;\r
+ while (i < sz) {\r
+ SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
\r
- cluster.setElementAt(null,minj);\r
- cluster.setElementAt(c,mini);\r
+ if (alignment.contains(leaf.element())) {\r
+ leaf.setPlaceholder(false);\r
+ } else {\r
+ if (seqmatcher == null) {\r
+ // Only create this the first time we need it\r
+ SequenceI[] seqs = new SequenceI[alignment.size()];\r
\r
- noClus--;\r
- }\r
+ for (int j = 0; j < seqs.length; j++)\r
+ seqs[j] = (SequenceI) alignment.elementAt(j);\r
\r
- boolean onefound = false;\r
+ seqmatcher = new SequenceIdMatcher(seqs);\r
+ }\r
\r
- int one = -1;\r
- int two = -1;\r
+ SequenceI nam = seqmatcher.findIdMatch(leaf.getName());\r
\r
- for (int i=0; i < noseqs; i++) {\r
- if (done[i] != 1) {\r
- if (onefound == false) {\r
- two = i;\r
- onefound = true;\r
- } else {\r
- one = i;\r
+ if (nam != null) {\r
+ leaf.setPlaceholder(false);\r
+ leaf.setElement(nam);\r
+ } else {\r
+ leaf.setPlaceholder(true);\r
+ }\r
+ }\r
}\r
- }\r
}\r
\r
- Cluster c = joinClusters(one,two);\r
- top = (SequenceNode)(node.elementAt(one));\r
+ public void cluster() {\r
+ while (noClus > 2) {\r
+ if (type.equals("NJ")) {\r
+ float mind = findMinNJDistance();\r
+ } else {\r
+ float mind = findMinDistance();\r
+ }\r
\r
- reCount(top);\r
- findHeight(top);\r
- findMaxDist(top);\r
+ Cluster c = joinClusters(mini, minj);\r
\r
- }\r
+ done[minj] = 1;\r
\r
- public Cluster joinClusters(int i, int j) {\r
+ cluster.setElementAt(null, minj);\r
+ cluster.setElementAt(c, mini);\r
\r
- float dist = distance[i][j];\r
+ noClus--;\r
+ }\r
\r
- int noi = ((Cluster)cluster.elementAt(i)).value.length;\r
- int noj = ((Cluster)cluster.elementAt(j)).value.length;\r
+ boolean onefound = false;\r
\r
- int[] value = new int[noi + noj];\r
+ int one = -1;\r
+ int two = -1;\r
\r
- for (int ii = 0; ii < noi;ii++) {\r
- value[ii] = ((Cluster)cluster.elementAt(i)).value[ii];\r
- }\r
+ for (int i = 0; i < noseqs; i++) {\r
+ if (done[i] != 1) {\r
+ if (onefound == false) {\r
+ two = i;\r
+ onefound = true;\r
+ } else {\r
+ one = i;\r
+ }\r
+ }\r
+ }\r
+\r
+ Cluster c = joinClusters(one, two);\r
+ top = (SequenceNode) (node.elementAt(one));\r
\r
- for (int ii = noi; ii < noi+ noj;ii++) {\r
- value[ii] = ((Cluster)cluster.elementAt(j)).value[ii-noi];\r
+ reCount(top);\r
+ findHeight(top);\r
+ findMaxDist(top);\r
}\r
\r
- Cluster c = new Cluster(value);\r
+ public Cluster joinClusters(int i, int j) {\r
+ float dist = distance[i][j];\r
\r
- ri = findr(i,j);\r
- rj = findr(j,i);\r
+ int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
+ int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
\r
- if (type.equals("NJ")) {\r
- findClusterNJDistance(i,j);\r
- } else {\r
- findClusterDistance(i,j);\r
- }\r
+ int[] value = new int[noi + noj];\r
+\r
+ for (int ii = 0; ii < noi; ii++) {\r
+ value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];\r
+ }\r
\r
- SequenceNode sn = new SequenceNode();\r
+ for (int ii = noi; ii < (noi + noj); ii++) {\r
+ value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];\r
+ }\r
\r
- sn.setLeft((SequenceNode)(node.elementAt(i)));\r
- sn.setRight((SequenceNode)(node.elementAt(j)));\r
+ Cluster c = new Cluster(value);\r
\r
- SequenceNode tmpi = (SequenceNode)(node.elementAt(i));\r
- SequenceNode tmpj = (SequenceNode)(node.elementAt(j));\r
+ ri = findr(i, j);\r
+ rj = findr(j, i);\r
\r
- if (type.equals("NJ")) {\r
- findNewNJDistances(tmpi,tmpj,dist);\r
- } else {\r
- findNewDistances(tmpi,tmpj,dist);\r
- }\r
+ if (type.equals("NJ")) {\r
+ findClusterNJDistance(i, j);\r
+ } else {\r
+ findClusterDistance(i, j);\r
+ }\r
\r
- tmpi.setParent(sn);\r
- tmpj.setParent(sn);\r
+ SequenceNode sn = new SequenceNode();\r
\r
- node.setElementAt(sn,i);\r
- return c;\r
- }\r
+ sn.setLeft((SequenceNode) (node.elementAt(i)));\r
+ sn.setRight((SequenceNode) (node.elementAt(j)));\r
\r
- public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, float dist) {\r
+ SequenceNode tmpi = (SequenceNode) (node.elementAt(i));\r
+ SequenceNode tmpj = (SequenceNode) (node.elementAt(j));\r
\r
- float ih = 0;\r
- float jh = 0;\r
+ if (type.equals("NJ")) {\r
+ findNewNJDistances(tmpi, tmpj, dist);\r
+ } else {\r
+ findNewDistances(tmpi, tmpj, dist);\r
+ }\r
\r
- SequenceNode sni = tmpi;\r
- SequenceNode snj = tmpj;\r
+ tmpi.setParent(sn);\r
+ tmpj.setParent(sn);\r
\r
- tmpi.dist = (dist + ri - rj)/2;\r
- tmpj.dist = (dist - tmpi.dist);\r
+ node.setElementAt(sn, i);\r
\r
- if (tmpi.dist < 0) {\r
- tmpi.dist = 0;\r
+ return c;\r
}\r
- if (tmpj.dist < 0) {\r
- tmpj.dist = 0;\r
- }\r
- }\r
\r
- public void findNewDistances(SequenceNode tmpi,SequenceNode tmpj,float dist) {\r
+ public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,\r
+ float dist) {\r
+ float ih = 0;\r
+ float jh = 0;\r
\r
- float ih = 0;\r
- float jh = 0;\r
+ SequenceNode sni = tmpi;\r
+ SequenceNode snj = tmpj;\r
\r
- SequenceNode sni = tmpi;\r
- SequenceNode snj = tmpj;\r
+ tmpi.dist = ((dist + ri) - rj) / 2;\r
+ tmpj.dist = (dist - tmpi.dist);\r
\r
- while (sni != null) {\r
- ih = ih + sni.dist;\r
- sni = (SequenceNode)sni.left();\r
- }\r
+ if (tmpi.dist < 0) {\r
+ tmpi.dist = 0;\r
+ }\r
\r
- while (snj != null) {\r
- jh = jh + snj.dist;\r
- snj = (SequenceNode)snj.left();\r
+ if (tmpj.dist < 0) {\r
+ tmpj.dist = 0;\r
+ }\r
}\r
\r
- tmpi.dist = (dist/2 - ih);\r
- tmpj.dist = (dist/2 - jh);\r
- }\r
+ public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,\r
+ float dist) {\r
+ float ih = 0;\r
+ float jh = 0;\r
\r
+ SequenceNode sni = tmpi;\r
+ SequenceNode snj = tmpj;\r
\r
+ while (sni != null) {\r
+ ih = ih + sni.dist;\r
+ sni = (SequenceNode) sni.left();\r
+ }\r
\r
- public void findClusterDistance(int i, int j) {\r
+ while (snj != null) {\r
+ jh = jh + snj.dist;\r
+ snj = (SequenceNode) snj.left();\r
+ }\r
\r
- int noi = ((Cluster)cluster.elementAt(i)).value.length;\r
- int noj = ((Cluster)cluster.elementAt(j)).value.length;\r
+ tmpi.dist = ((dist / 2) - ih);\r
+ tmpj.dist = ((dist / 2) - jh);\r
+ }\r
\r
- // New distances from cluster to others\r
- float[] newdist = new float[noseqs];\r
+ public void findClusterDistance(int i, int j) {\r
+ int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
+ int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
\r
- for (int l = 0; l < noseqs; l++) {\r
- if ( l != i && l != j) {\r
- newdist[l] = (distance[i][l] * noi + distance[j][l] * noj)/(noi + noj);\r
- } else {\r
- newdist[l] = 0;\r
- }\r
- }\r
+ // New distances from cluster to others\r
+ float[] newdist = new float[noseqs];\r
+\r
+ for (int l = 0; l < noseqs; l++) {\r
+ if ((l != i) && (l != j)) {\r
+ newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +\r
+ noj);\r
+ } else {\r
+ newdist[l] = 0;\r
+ }\r
+ }\r
\r
- for (int ii=0; ii < noseqs;ii++) {\r
- distance[i][ii] = newdist[ii];\r
- distance[ii][i] = newdist[ii];\r
+ for (int ii = 0; ii < noseqs; ii++) {\r
+ distance[i][ii] = newdist[ii];\r
+ distance[ii][i] = newdist[ii];\r
+ }\r
}\r
- }\r
\r
- public void findClusterNJDistance(int i, int j) {\r
+ public void findClusterNJDistance(int i, int j) {\r
+ int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
+ int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
\r
- int noi = ((Cluster)cluster.elementAt(i)).value.length;\r
- int noj = ((Cluster)cluster.elementAt(j)).value.length;\r
+ // New distances from cluster to others\r
+ float[] newdist = new float[noseqs];\r
\r
- // New distances from cluster to others\r
- float[] newdist = new float[noseqs];\r
+ for (int l = 0; l < noseqs; l++) {\r
+ if ((l != i) && (l != j)) {\r
+ newdist[l] = ((distance[i][l] + distance[j][l]) -\r
+ distance[i][j]) / 2;\r
+ } else {\r
+ newdist[l] = 0;\r
+ }\r
+ }\r
\r
- for (int l = 0; l < noseqs; l++) {\r
- if ( l != i && l != j) {\r
- newdist[l] = (distance[i][l] + distance[j][l] - distance[i][j])/2;\r
- } else {\r
- newdist[l] = 0;\r
- }\r
+ for (int ii = 0; ii < noseqs; ii++) {\r
+ distance[i][ii] = newdist[ii];\r
+ distance[ii][i] = newdist[ii];\r
+ }\r
}\r
\r
- for (int ii=0; ii < noseqs;ii++) {\r
- distance[i][ii] = newdist[ii];\r
- distance[ii][i] = newdist[ii];\r
+ public float findr(int i, int j) {\r
+ float tmp = 1;\r
+\r
+ for (int k = 0; k < noseqs; k++) {\r
+ if ((k != i) && (k != j) && (done[k] != 1)) {\r
+ tmp = tmp + distance[i][k];\r
+ }\r
+ }\r
+\r
+ if (noClus > 2) {\r
+ tmp = tmp / (noClus - 2);\r
+ }\r
+\r
+ return tmp;\r
}\r
- }\r
\r
- public float findr(int i, int j) {\r
+ public float findMinNJDistance() {\r
+ float min = 100000;\r
+\r
+ for (int i = 0; i < (noseqs - 1); i++) {\r
+ for (int j = i + 1; j < noseqs; j++) {\r
+ if ((done[i] != 1) && (done[j] != 1)) {\r
+ float tmp = distance[i][j] - (findr(i, j) + findr(j, i));\r
+\r
+ if (tmp < min) {\r
+ mini = i;\r
+ minj = j;\r
\r
- float tmp = 1;\r
- for (int k=0; k < noseqs;k++) {\r
- if (k!= i && k!= j && done[k] != 1) {\r
- tmp = tmp + distance[i][k];\r
- }\r
+ min = tmp;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ return min;\r
}\r
\r
- if (noClus > 2) {\r
- tmp = tmp/(noClus - 2);\r
+ public float findMinDistance() {\r
+ float min = 100000;\r
+\r
+ for (int i = 0; i < (noseqs - 1); i++) {\r
+ for (int j = i + 1; j < noseqs; j++) {\r
+ if ((done[i] != 1) && (done[j] != 1)) {\r
+ if (distance[i][j] < min) {\r
+ mini = i;\r
+ minj = j;\r
+\r
+ min = distance[i][j];\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ return min;\r
+ }\r
+\r
+ public float[][] findDistances() {\r
+ float[][] distance = new float[noseqs][noseqs];\r
+\r
+ if (pwtype.equals("PID")) {\r
+ for (int i = 0; i < (noseqs - 1); i++) {\r
+ for (int j = i; j < noseqs; j++) {\r
+ if (j == i) {\r
+ distance[i][i] = 0;\r
+ } else {\r
+ distance[i][j] = 100 -\r
+ Comparison.PID(sequence[i], sequence[j], start, end);\r
+ distance[j][i] = distance[i][j];\r
+ }\r
+ }\r
+ }\r
+ } else if (pwtype.equals("BL")) {\r
+ int maxscore = 0;\r
+\r
+ for (int i = 0; i < (noseqs - 1); i++) {\r
+ for (int j = i; j < noseqs; j++) {\r
+ int score = 0;\r
+\r
+ for (int k = start; k < end; k++) {\r
+ try {\r
+ score += ResidueProperties.getBLOSUM62(sequence[i].getSequence(\r
+ k, k + 1), sequence[j].getSequence(k, k +\r
+ 1));\r
+ } catch (Exception ex) {\r
+ System.err.println("err creating BLOSUM62 tree");\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ distance[i][j] = (float) score;\r
+\r
+ if (score > maxscore) {\r
+ maxscore = score;\r
+ }\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < (noseqs - 1); i++) {\r
+ for (int j = i; j < noseqs; j++) {\r
+ distance[i][j] = (float) maxscore - distance[i][j];\r
+ distance[j][i] = distance[i][j];\r
+ }\r
+ }\r
+ } else if (pwtype.equals("SW")) {\r
+ float max = -1;\r
+\r
+ for (int i = 0; i < (noseqs - 1); i++) {\r
+ for (int j = i; j < noseqs; j++) {\r
+ AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");\r
+ as.calcScoreMatrix();\r
+ as.traceAlignment();\r
+ as.printAlignment();\r
+ distance[i][j] = (float) as.maxscore;\r
+\r
+ if (max < distance[i][j]) {\r
+ max = distance[i][j];\r
+ }\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < (noseqs - 1); i++) {\r
+ for (int j = i; j < noseqs; j++) {\r
+ distance[i][j] = max - distance[i][j];\r
+ distance[j][i] = distance[i][j];\r
+ }\r
+ }\r
+ }\r
+\r
+ return distance;\r
}\r
\r
- return tmp;\r
- }\r
+ public void makeLeaves() {\r
+ cluster = new Vector();\r
+\r
+ for (int i = 0; i < noseqs; i++) {\r
+ SequenceNode sn = new SequenceNode();\r
\r
- public float findMinNJDistance() {\r
+ sn.setElement(sequence[i]);\r
+ sn.setName(sequence[i].getName());\r
+ node.addElement(sn);\r
\r
- float min = 100000;\r
+ int[] value = new int[1];\r
+ value[0] = i;\r
\r
- for (int i=0; i < noseqs-1; i++) {\r
- for (int j=i+1;j < noseqs;j++) {\r
- if (done[i] != 1 && done[j] != 1) {\r
- float tmp = distance[i][j] - (findr(i,j) + findr(j,i));\r
- if (tmp < min) {\r
+ Cluster c = new Cluster(value);\r
+ cluster.addElement(c);\r
+ }\r
+ }\r
\r
- mini = i;\r
- minj = j;\r
+ public Vector findLeaves(SequenceNode node, Vector leaves) {\r
+ if (node == null) {\r
+ return leaves;\r
+ }\r
\r
- min = tmp;\r
+ if ((node.left() == null) && (node.right() == null)) {\r
+ leaves.addElement(node);\r
\r
- }\r
+ return leaves;\r
+ } else {\r
+ findLeaves((SequenceNode) node.left(), leaves);\r
+ findLeaves((SequenceNode) node.right(), leaves);\r
}\r
- }\r
+\r
+ return leaves;\r
}\r
- return min;\r
- }\r
\r
- public float findMinDistance() {\r
+ public Object findLeaf(SequenceNode node, int count) {\r
+ found = _findLeaf(node, count);\r
\r
- float min = 100000;\r
+ return found;\r
+ }\r
\r
- for (int i=0; i < noseqs-1;i++) {\r
- for (int j = i+1; j < noseqs;j++) {\r
- if (done[i] != 1 && done[j] != 1) {\r
- if (distance[i][j] < min) {\r
- mini = i;\r
- minj = j;\r
+ public Object _findLeaf(SequenceNode node, int count) {\r
+ if (node == null) {\r
+ return null;\r
+ }\r
\r
- min = distance[i][j];\r
- }\r
+ if (node.ycount == count) {\r
+ found = node.element();\r
+\r
+ return found;\r
+ } else {\r
+ _findLeaf((SequenceNode) node.left(), count);\r
+ _findLeaf((SequenceNode) node.right(), count);\r
}\r
- }\r
+\r
+ return found;\r
}\r
- return min;\r
- }\r
\r
- public float[][] findDistances() {\r
+ /**\r
+ * printNode is mainly for debugging purposes.\r
+ *\r
+ * @param node SequenceNode\r
+ */\r
+ public void printNode(SequenceNode node) {\r
+ if (node == null) {\r
+ return;\r
+ }\r
+\r
+ if ((node.left() == null) && (node.right() == null)) {\r
+ System.out.println("Leaf = " +\r
+ ((SequenceI) node.element()).getName());\r
+ System.out.println("Dist " + ((SequenceNode) node).dist);\r
+ System.out.println("Boot " + node.getBootstrap());\r
+ } else {\r
+ System.out.println("Dist " + ((SequenceNode) node).dist);\r
+ printNode((SequenceNode) node.left());\r
+ printNode((SequenceNode) node.right());\r
+ }\r
+ }\r
\r
- float[][] distance = new float[noseqs][noseqs];\r
- if (pwtype.equals("PID")) {\r
- for (int i = 0; i < noseqs-1; i++) {\r
- for (int j = i; j < noseqs; j++) {\r
- if (j==i) {\r
- distance[i][i] = 0;\r
- } else {\r
- distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j], start, end);\r
- distance[j][i] = distance[i][j];\r
- }\r
+ public void findMaxDist(SequenceNode node) {\r
+ if (node == null) {\r
+ return;\r
}\r
- }\r
- } else if (pwtype.equals("BL")) {\r
- int maxscore = 0;\r
\r
- for (int i = 0; i < noseqs-1; i++) {\r
- for (int j = i; j < noseqs; j++) {\r
- int score = 0;\r
- for (int k=start; k < end; k++) {\r
- try{\r
- score +=\r
- ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,\r
- k + 1),\r
- sequence[j].getSequence(k,\r
- k + 1));\r
- }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();}\r
- }\r
- distance[i][j] = (float)score;\r
- if (score > maxscore) {\r
- maxscore = score;\r
- }\r
+ if ((node.left() == null) && (node.right() == null)) {\r
+ float dist = ((SequenceNode) node).dist;\r
+\r
+ if (dist > maxDistValue) {\r
+ maxdist = (SequenceNode) node;\r
+ maxDistValue = dist;\r
+ }\r
+ } else {\r
+ findMaxDist((SequenceNode) node.left());\r
+ findMaxDist((SequenceNode) node.right());\r
}\r
- }\r
- for (int i = 0; i < noseqs-1; i++) {\r
- for (int j = i; j < noseqs; j++) {\r
- distance[i][j] = (float)maxscore - distance[i][j];\r
- distance[j][i] = distance[i][j];\r
- }\r
- }\r
- } else if (pwtype.equals("SW")) {\r
- float max = -1;\r
- for (int i = 0; i < noseqs-1; i++) {\r
- for (int j = i; j < noseqs; j++) {\r
- AlignSeq as = new AlignSeq(sequence[i],sequence[j],"pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
- distance[i][j] = (float)as.maxscore;\r
- if (max < distance[i][j]) {\r
- max = distance[i][j];\r
- }\r
- }\r
- }\r
- for (int i = 0; i < noseqs-1; i++) {\r
- for (int j = i; j < noseqs; j++) {\r
- distance[i][j] = max - distance[i][j];\r
- distance[j][i] = distance[i][j];\r
- }\r
- }\r
- }\r
-\r
- return distance;\r
- }\r
-\r
- public void makeLeaves() {\r
- cluster = new Vector();\r
-\r
- for (int i=0; i < noseqs; i++) {\r
- SequenceNode sn = new SequenceNode();\r
-\r
- sn.setElement(sequence[i]);\r
- sn.setName(sequence[i].getName());\r
- node.addElement(sn);\r
-\r
- int[] value = new int[1];\r
- value[0] = i;\r
-\r
- Cluster c = new Cluster(value);\r
- cluster.addElement(c);\r
- }\r
- }\r
-\r
- public Vector findLeaves(SequenceNode node, Vector leaves) {\r
- if (node == null) {\r
- return leaves;\r
- }\r
-\r
- if (node.left() == null && node.right() == null) {\r
- leaves.addElement(node);\r
- return leaves;\r
- } else {\r
- findLeaves((SequenceNode)node.left(),leaves);\r
- findLeaves((SequenceNode)node.right(),leaves);\r
- }\r
- return leaves;\r
- }\r
-\r
- public Object findLeaf(SequenceNode node, int count) {\r
- found = _findLeaf(node,count);\r
-\r
- return found;\r
- }\r
- public Object _findLeaf(SequenceNode node,int count) {\r
- if (node == null) {\r
- return null;\r
- }\r
- if (node.ycount == count) {\r
- found = node.element();\r
- return found;\r
- } else {\r
- _findLeaf((SequenceNode)node.left(),count);\r
- _findLeaf((SequenceNode)node.right(),count);\r
- }\r
-\r
- return found;\r
- }\r
-\r
- /**\r
- * printNode is mainly for debugging purposes.\r
- *\r
- * @param node SequenceNode\r
- */\r
- public void printNode(SequenceNode node) {\r
- if (node == null) {\r
- return;\r
- }\r
- if (node.left() == null && node.right() == null) {\r
- System.out.println("Leaf = " + ((SequenceI)node.element()).getName());\r
- System.out.println("Dist " + ((SequenceNode)node).dist);\r
- System.out.println("Boot " + node.getBootstrap());\r
- } else {\r
- System.out.println("Dist " + ((SequenceNode)node).dist);\r
- printNode((SequenceNode)node.left());\r
- printNode((SequenceNode)node.right());\r
- }\r
- }\r
- public void findMaxDist(SequenceNode node) {\r
- if (node == null) {\r
- return;\r
- }\r
- if (node.left() == null && node.right() == null) {\r
-\r
- float dist = ((SequenceNode)node).dist;\r
- if (dist > maxDistValue) {\r
- maxdist = (SequenceNode)node;\r
- maxDistValue = dist;\r
- }\r
- } else {\r
- findMaxDist((SequenceNode)node.left());\r
- findMaxDist((SequenceNode)node.right());\r
}\r
- }\r
+\r
public Vector getGroups() {\r
return groups;\r
}\r
+\r
public float getMaxHeight() {\r
return maxheight;\r
}\r
- public void groupNodes(SequenceNode node, float threshold) {\r
- if (node == null) {\r
- return;\r
+\r
+ public void groupNodes(SequenceNode node, float threshold) {\r
+ if (node == null) {\r
+ return;\r
+ }\r
+\r
+ if ((node.height / maxheight) > threshold) {\r
+ groups.addElement(node);\r
+ } else {\r
+ groupNodes((SequenceNode) node.left(), threshold);\r
+ groupNodes((SequenceNode) node.right(), threshold);\r
+ }\r
}\r
\r
- if (node.height/maxheight > threshold) {\r
- groups.addElement(node);\r
- } else {\r
- groupNodes((SequenceNode)node.left(),threshold);\r
- groupNodes((SequenceNode)node.right(),threshold);\r
+ public float findHeight(SequenceNode node) {\r
+ if (node == null) {\r
+ return maxheight;\r
+ }\r
+\r
+ if ((node.left() == null) && (node.right() == null)) {\r
+ node.height = ((SequenceNode) node.parent()).height + node.dist;\r
+\r
+ if (node.height > maxheight) {\r
+ return node.height;\r
+ } else {\r
+ return maxheight;\r
+ }\r
+ } else {\r
+ if (node.parent() != null) {\r
+ node.height = ((SequenceNode) node.parent()).height +\r
+ node.dist;\r
+ } else {\r
+ maxheight = 0;\r
+ node.height = (float) 0.0;\r
+ }\r
+\r
+ maxheight = findHeight((SequenceNode) (node.left()));\r
+ maxheight = findHeight((SequenceNode) (node.right()));\r
+ }\r
+\r
+ return maxheight;\r
}\r
- }\r
\r
- public float findHeight(SequenceNode node) {\r
+ public SequenceNode reRoot() {\r
+ if (maxdist != null) {\r
+ ycount = 0;\r
+\r
+ float tmpdist = maxdist.dist;\r
+\r
+ // New top\r
+ SequenceNode sn = new SequenceNode();\r
+ sn.setParent(null);\r
+\r
+ // New right hand of top\r
+ SequenceNode snr = (SequenceNode) maxdist.parent();\r
+ changeDirection(snr, maxdist);\r
+ System.out.println("Printing reversed tree");\r
+ printN(snr);\r
+ snr.dist = tmpdist / 2;\r
+ maxdist.dist = tmpdist / 2;\r
+\r
+ snr.setParent(sn);\r
+ maxdist.setParent(sn);\r
+\r
+ sn.setRight(snr);\r
+ sn.setLeft(maxdist);\r
\r
- if (node == null) {\r
- return maxheight;\r
+ top = sn;\r
+\r
+ ycount = 0;\r
+ reCount(top);\r
+ findHeight(top);\r
+ }\r
+\r
+ return top;\r
}\r
\r
- if (node.left() == null && node.right() == null) {\r
- node.height = ((SequenceNode)node.parent()).height + node.dist;\r
+ public static void printN(SequenceNode node) {\r
+ if (node == null) {\r
+ return;\r
+ }\r
\r
- if (node.height > maxheight) {\r
- return node.height;\r
- } else {\r
- return maxheight;\r
- }\r
- } else {\r
- if (node.parent() != null) {\r
- node.height = ((SequenceNode)node.parent()).height + node.dist;\r
- } else {\r
- maxheight = 0;\r
- node.height = (float)0.0;\r
- }\r
-\r
- maxheight = findHeight((SequenceNode)(node.left()));\r
- maxheight = findHeight((SequenceNode)(node.right()));\r
- }\r
- return maxheight;\r
- }\r
- public SequenceNode reRoot() {\r
- if (maxdist != null) {\r
- ycount = 0;\r
- float tmpdist = maxdist.dist;\r
-\r
- // New top\r
- SequenceNode sn = new SequenceNode();\r
- sn.setParent(null);\r
-\r
- // New right hand of top\r
- SequenceNode snr = (SequenceNode)maxdist.parent();\r
- changeDirection(snr,maxdist);\r
- System.out.println("Printing reversed tree");\r
- printN(snr);\r
- snr.dist = tmpdist/2;\r
- maxdist.dist = tmpdist/2;\r
-\r
- snr.setParent(sn);\r
- maxdist.setParent(sn);\r
-\r
- sn.setRight(snr);\r
- sn.setLeft(maxdist);\r
-\r
- top = sn;\r
-\r
- ycount = 0;\r
- reCount(top);\r
- findHeight(top);\r
-\r
- }\r
- return top;\r
- }\r
- public static void printN(SequenceNode node) {\r
- if (node == null) {\r
- return;\r
- }\r
-\r
- if (node.left() != null && node.right() != null) {\r
- printN((SequenceNode)node.left());\r
- printN((SequenceNode)node.right());\r
- } else {\r
- System.out.println(" name = " + ((SequenceI)node.element()).getName());\r
- }\r
- System.out.println(" dist = " + ((SequenceNode)node).dist + " " + ((SequenceNode)node).count + " " + ((SequenceNode)node).height);\r
- }\r
+ if ((node.left() != null) && (node.right() != null)) {\r
+ printN((SequenceNode) node.left());\r
+ printN((SequenceNode) node.right());\r
+ } else {\r
+ System.out.println(" name = " +\r
+ ((SequenceI) node.element()).getName());\r
+ }\r
+\r
+ System.out.println(" dist = " + ((SequenceNode) node).dist + " " +\r
+ ((SequenceNode) node).count + " " + ((SequenceNode) node).height);\r
+ }\r
\r
public void reCount(SequenceNode node) {\r
ycount = 0;\r
_reCount(node);\r
}\r
- public void _reCount(SequenceNode node) {\r
- if (node == null) {\r
- return;\r
- }\r
\r
- if (node.left() != null && node.right() != null) {\r
- _reCount((SequenceNode)node.left());\r
- _reCount((SequenceNode)node.right());\r
+ public void _reCount(SequenceNode node) {\r
+ if (node == null) {\r
+ return;\r
+ }\r
\r
- SequenceNode l = (SequenceNode)node.left();\r
- SequenceNode r = (SequenceNode)node.right();\r
+ if ((node.left() != null) && (node.right() != null)) {\r
+ _reCount((SequenceNode) node.left());\r
+ _reCount((SequenceNode) node.right());\r
\r
- ((SequenceNode)node).count = l.count + r.count;\r
- ((SequenceNode)node).ycount = (l.ycount + r.ycount)/2;\r
+ SequenceNode l = (SequenceNode) node.left();\r
+ SequenceNode r = (SequenceNode) node.right();\r
\r
- } else {\r
- ((SequenceNode)node).count = 1;\r
- ((SequenceNode)node).ycount = ycount++;\r
+ ((SequenceNode) node).count = l.count + r.count;\r
+ ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;\r
+ } else {\r
+ ((SequenceNode) node).count = 1;\r
+ ((SequenceNode) node).ycount = ycount++;\r
+ }\r
}\r
\r
- }\r
public void swapNodes(SequenceNode node) {\r
if (node == null) {\r
return;\r
}\r
- SequenceNode tmp = (SequenceNode)node.left();\r
+\r
+ SequenceNode tmp = (SequenceNode) node.left();\r
\r
node.setLeft(node.right());\r
node.setRight(tmp);\r
}\r
- public void changeDirection(SequenceNode node, SequenceNode dir) {\r
- if (node == null) {\r
- return;\r
- }\r
- if (node.parent() != top) {\r
- changeDirection((SequenceNode)node.parent(), node);\r
-\r
- SequenceNode tmp = (SequenceNode)node.parent();\r
\r
- if (dir == node.left()) {\r
- node.setParent(dir);\r
- node.setLeft(tmp);\r
- } else if (dir == node.right()) {\r
- node.setParent(dir);\r
- node.setRight(tmp);\r
- }\r
+ public void changeDirection(SequenceNode node, SequenceNode dir) {\r
+ if (node == null) {\r
+ return;\r
+ }\r
\r
- } else {\r
- if (dir == node.left()) {\r
- node.setParent(node.left());\r
+ if (node.parent() != top) {\r
+ changeDirection((SequenceNode) node.parent(), node);\r
\r
- if (top.left() == node) {\r
- node.setRight(top.right());\r
- } else {\r
- node.setRight(top.left());\r
- }\r
- } else {\r
- node.setParent(node.right());\r
+ SequenceNode tmp = (SequenceNode) node.parent();\r
\r
- if (top.left() == node) {\r
- node.setLeft(top.right());\r
+ if (dir == node.left()) {\r
+ node.setParent(dir);\r
+ node.setLeft(tmp);\r
+ } else if (dir == node.right()) {\r
+ node.setParent(dir);\r
+ node.setRight(tmp);\r
+ }\r
} else {\r
- node.setLeft(top.left());\r
+ if (dir == node.left()) {\r
+ node.setParent(node.left());\r
+\r
+ if (top.left() == node) {\r
+ node.setRight(top.right());\r
+ } else {\r
+ node.setRight(top.left());\r
+ }\r
+ } else {\r
+ node.setParent(node.right());\r
+\r
+ if (top.left() == node) {\r
+ node.setLeft(top.right());\r
+ } else {\r
+ node.setLeft(top.left());\r
+ }\r
+ }\r
}\r
- }\r
}\r
- }\r
+\r
public void setMaxDist(SequenceNode node) {\r
this.maxdist = maxdist;\r
}\r
+\r
public SequenceNode getMaxDist() {\r
return maxdist;\r
}\r
+\r
public SequenceNode getTopNode() {\r
return top;\r
}\r
-\r
}\r
\r
\r
-\r
class Cluster {\r
+ int[] value;\r
\r
- int[] value;\r
-\r
- public Cluster(int[] value) {\r
- this.value = value;\r
- }\r
-\r
+ public Cluster(int[] value) {\r
+ this.value = value;\r
+ }\r
}\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.analysis;\r
\r
-import jalview.math.*;\r
import jalview.datamodel.*;\r
+\r
+import jalview.math.*;\r
+\r
import jalview.util.*;\r
\r
import java.awt.*;\r
+\r
import java.io.*;\r
\r
-public class PCA implements Runnable {\r
- Matrix m;\r
- Matrix symm;\r
- Matrix m2;\r
\r
- double[] eigenvalue;\r
- Matrix eigenvector;\r
+public class PCA implements Runnable {\r
+ Matrix m;\r
+ Matrix symm;\r
+ Matrix m2;\r
+ double[] eigenvalue;\r
+ Matrix eigenvector;\r
+\r
+ public PCA(Matrix m) {\r
+ this.m = m;\r
+ }\r
\r
- public PCA(Matrix m) {\r
- this.m = m;\r
- }\r
+ public PCA(SequenceI[] s) {\r
+ Runtime rt = Runtime.getRuntime();\r
+\r
+ BinarySequence[] bs = new BinarySequence[s.length];\r
+ int ii = 0;\r
+\r
+ while ((ii < s.length) && (s[ii] != null)) {\r
+ bs[ii] = new BinarySequence(s[ii]);\r
+ bs[ii].encode();\r
+ ii++;\r
+ }\r
+\r
+ BinarySequence[] bs2 = new BinarySequence[s.length];\r
+ ii = 0;\r
+\r
+ while ((ii < s.length) && (s[ii] != null)) {\r
+ bs2[ii] = new BinarySequence(s[ii]);\r
+ bs2[ii].blosumEncode();\r
+ ii++;\r
+ }\r
+\r
+ //System.out.println("Created binary encoding");\r
+ //printMemory(rt);\r
+ int count = 0;\r
+\r
+ while ((count < bs.length) && (bs[count] != null)) {\r
+ count++;\r
+ }\r
+\r
+ double[][] seqmat = new double[count][bs[0].getDBinary().length];\r
+ double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];\r
+ int i = 0;\r
+\r
+ while (i < count) {\r
+ seqmat[i] = bs[i].getDBinary();\r
+ seqmat2[i] = bs2[i].getDBinary();\r
+ i++;\r
+ }\r
+\r
+ //System.out.println("Created array");\r
+ //printMemory(rt);\r
+ // System.out.println(" --- Original matrix ---- ");\r
+ m = new Matrix(seqmat, count, bs[0].getDBinary().length);\r
+ m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length);\r
+\r
+ //System.out.println("Created matrix");\r
+ printMemory(rt);\r
+ }\r
\r
- public PCA(SequenceI[] s) {\r
- Runtime rt = Runtime.getRuntime();\r
+ public static void printMemory(Runtime rt) {\r
+ System.out.println("PCA:Free memory = " + rt.freeMemory());\r
+ }\r
\r
- BinarySequence[] bs = new BinarySequence[s.length];\r
- int ii = 0;\r
- while (ii < s.length && s[ii] != null) {\r
+ public Matrix getM() {\r
+ return m;\r
+ }\r
\r
- bs[ii] = new BinarySequence(s[ii]);\r
- bs[ii].encode();\r
- ii++;\r
+ public double[] getEigenvector(int i) {\r
+ return eigenvector.getColumn(i);\r
}\r
\r
- BinarySequence[] bs2 = new BinarySequence[s.length];\r
- ii = 0;\r
- while (ii < s.length && s[ii] != null) {\r
+ public double getEigenvalue(int i) {\r
+ return eigenvector.d[i];\r
+ }\r
\r
- bs2[ii] = new BinarySequence(s[ii]);\r
- bs2[ii].blosumEncode();\r
- ii++;\r
+ public float[][] getComponents(int l, int n, int mm) {\r
+ return getComponents(l, n, mm, 1);\r
}\r
\r
+ public float[][] getComponents(int l, int n, int mm, float factor) {\r
+ float[][] out = new float[m.rows][3];\r
\r
- //System.out.println("Created binary encoding");\r
- //printMemory(rt);\r
+ for (int i = 0; i < m.rows; i++) {\r
+ out[i][0] = (float) component(i, l) * factor;\r
+ out[i][1] = (float) component(i, n) * factor;\r
+ out[i][2] = (float) component(i, mm) * factor;\r
+ }\r
\r
- int count=0;\r
- while (count < bs.length && bs[count] != null) {\r
- count++;\r
- }\r
- double[][] seqmat = new double[count][bs[0].getDBinary().length];\r
- double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];\r
- int i=0;\r
- while (i < count) {\r
- seqmat[i] = bs[i].getDBinary();\r
- seqmat2[i] = bs2[i].getDBinary();\r
- i++;\r
+ return out;\r
}\r
- //System.out.println("Created array");\r
- //printMemory(rt);\r
- // System.out.println(" --- Original matrix ---- ");\r
- m = new Matrix(seqmat,count,bs[0].getDBinary().length);\r
- m2 = new Matrix(seqmat2,count,bs2[0].getDBinary().length);\r
-\r
- //System.out.println("Created matrix");\r
- printMemory(rt);\r
- }\r
-\r
- public static void printMemory(Runtime rt) {\r
- System.out.println("PCA:Free memory = " + rt.freeMemory());\r
- }\r
-\r
- public Matrix getM() {\r
- return m;\r
- }\r
-\r
- public double[] getEigenvector(int i) {\r
- return eigenvector.getColumn(i);\r
- }\r
-\r
- public double getEigenvalue(int i) {\r
- return eigenvector.d[i];\r
- }\r
- public float[][] getComponents(int l, int n, int mm) {\r
- return getComponents(l,n,mm,1);\r
- }\r
- public float[][] getComponents(int l, int n, int mm, float factor) {\r
- float[][] out = new float[m.rows][3];\r
-\r
- for (int i = 0; i < m.rows;i++) {\r
- out[i][0] = (float)component(i,l)*factor;\r
- out[i][1] = (float)component(i,n)*factor;\r
- out[i][2] = (float)component(i,mm)*factor;\r
- }\r
- return out;\r
- }\r
\r
- public double[] component(int n) {\r
- // n = index of eigenvector\r
- double[] out = new double[m.rows];\r
+ public double[] component(int n) {\r
+ // n = index of eigenvector\r
+ double[] out = new double[m.rows];\r
\r
- for (int i=0; i < m.rows; i++) {\r
- out[i] = component(i,n);\r
- }\r
- return out;\r
- }\r
- public double component(int row, int n) {\r
- double out = 0.0;\r
+ for (int i = 0; i < m.rows; i++) {\r
+ out[i] = component(i, n);\r
+ }\r
\r
- for (int i = 0; i < symm.cols; i++) {\r
- out += symm.value[row][i] * eigenvector.value[i][n];\r
+ return out;\r
}\r
- return out/eigenvector.d[n];\r
- }\r
\r
- public void checkEigenvector(int n,PrintStream ps) {\r
- ps.println(" --- Eigenvector " + n + " --- ");\r
+ public double component(int row, int n) {\r
+ double out = 0.0;\r
\r
- double[] eigenv = eigenvector.getColumn(n);\r
+ for (int i = 0; i < symm.cols; i++) {\r
+ out += (symm.value[row][i] * eigenvector.value[i][n]);\r
+ }\r
\r
- for (int i=0; i < eigenv.length;i++) {\r
- Format.print(ps,"%15.4f",eigenv[i]);\r
+ return out / eigenvector.d[n];\r
}\r
\r
- System.out.println();\r
+ public void checkEigenvector(int n, PrintStream ps) {\r
+ ps.println(" --- Eigenvector " + n + " --- ");\r
+\r
+ double[] eigenv = eigenvector.getColumn(n);\r
\r
- double[] neigenv = symm.vectorPostMultiply(eigenv);\r
- System.out.println(" --- symmat * eigenv / lambda --- ");\r
- if (eigenvector.d[n] > 1e-4) {\r
- for (int i=0; i < neigenv.length;i++) {\r
- Format.print(System.out,"%15.4f",neigenv[i]/eigenvector.d[n]);\r
- }\r
+ for (int i = 0; i < eigenv.length; i++) {\r
+ Format.print(ps, "%15.4f", eigenv[i]);\r
+ }\r
+\r
+ System.out.println();\r
+\r
+ double[] neigenv = symm.vectorPostMultiply(eigenv);\r
+ System.out.println(" --- symmat * eigenv / lambda --- ");\r
+\r
+ if (eigenvector.d[n] > 1e-4) {\r
+ for (int i = 0; i < neigenv.length; i++) {\r
+ Format.print(System.out, "%15.4f", neigenv[i] / eigenvector.d[n]);\r
+ }\r
+ }\r
+\r
+ System.out.println();\r
}\r
- System.out.println();\r
- }\r
-\r
- public void run() {\r
- Matrix mt = m.transpose();\r
- // System.out.println(" --- OrigT * Orig ---- ");\r
- eigenvector = mt.preMultiply(m2);\r
- // eigenvector.print(System.out);\r
- symm = eigenvector.copy();\r
-\r
- //TextArea ta = new TextArea(25,72);\r
- //TextAreaPrintStream taps = new TextAreaPrintStream(System.out,ta);\r
- //Frame f = new Frame("PCA output");\r
- //f.resize(500,500);\r
- //f.setLayout(new BorderLayout());\r
- //f.add("Center",ta);\r
- //f.show();\r
- //symm.print(taps);\r
- long tstart = System.currentTimeMillis();\r
- eigenvector.tred();\r
- long tend = System.currentTimeMillis();\r
- //taps.println("Time take for tred = " + (tend-tstart) + "ms");\r
- //taps.println(" ---Tridiag transform matrix ---");\r
-\r
- //taps.println(" --- D vector ---");\r
- //eigenvector.printD(taps);\r
- //taps.println();\r
- //taps.println(" --- E vector ---");\r
- // eigenvector.printE(taps);\r
- //taps.println();\r
-\r
- // Now produce the diagonalization matrix\r
- tstart = System.currentTimeMillis();\r
- eigenvector.tqli();\r
- tend = System.currentTimeMillis();\r
- //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");\r
-\r
- //System.out.println(" --- New diagonalization matrix ---");\r
-\r
- //System.out.println(" --- Eigenvalues ---");\r
- //eigenvector.printD(taps);\r
-\r
- //System.out.println();\r
-\r
- // for (int i=0; i < eigenvector.cols; i++) {\r
- // checkEigenvector(i,taps);\r
- // taps.println();\r
- // }\r
-\r
- // taps.println();\r
- // taps.println("Transformed sequences = ");\r
- // Matrix trans = m.preMultiply(eigenvector);\r
- // trans.print(System.out);\r
- }\r
\r
+ public void run() {\r
+ Matrix mt = m.transpose();\r
+\r
+ // System.out.println(" --- OrigT * Orig ---- ");\r
+ eigenvector = mt.preMultiply(m2);\r
+\r
+ // eigenvector.print(System.out);\r
+ symm = eigenvector.copy();\r
+\r
+ //TextArea ta = new TextArea(25,72);\r
+ //TextAreaPrintStream taps = new TextAreaPrintStream(System.out,ta);\r
+ //Frame f = new Frame("PCA output");\r
+ //f.resize(500,500);\r
+ //f.setLayout(new BorderLayout());\r
+ //f.add("Center",ta);\r
+ //f.show();\r
+ //symm.print(taps);\r
+ long tstart = System.currentTimeMillis();\r
+ eigenvector.tred();\r
+\r
+ long tend = System.currentTimeMillis();\r
+\r
+ //taps.println("Time take for tred = " + (tend-tstart) + "ms");\r
+ //taps.println(" ---Tridiag transform matrix ---");\r
+ //taps.println(" --- D vector ---");\r
+ //eigenvector.printD(taps);\r
+ //taps.println();\r
+ //taps.println(" --- E vector ---");\r
+ // eigenvector.printE(taps);\r
+ //taps.println();\r
+ // Now produce the diagonalization matrix\r
+ tstart = System.currentTimeMillis();\r
+ eigenvector.tqli();\r
+ tend = System.currentTimeMillis();\r
+\r
+ //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");\r
+ //System.out.println(" --- New diagonalization matrix ---");\r
+ //System.out.println(" --- Eigenvalues ---");\r
+ //eigenvector.printD(taps);\r
+ //System.out.println();\r
+ // for (int i=0; i < eigenvector.cols; i++) {\r
+ // checkEigenvector(i,taps);\r
+ // taps.println();\r
+ // }\r
+ // taps.println();\r
+ // taps.println("Transformed sequences = ");\r
+ // Matrix trans = m.preMultiply(eigenvector);\r
+ // trans.print(System.out);\r
+ }\r
}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.analysis;
-
-import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
-
+*/\r
+package jalview.analysis;\r
+\r
+import jalview.datamodel.SequenceI;\r
+\r
+import java.util.Hashtable;\r
+\r
+\r
/**
* <p>Title: </p>
*
*
* @author not attributable
* @version 1.0
- */
-public class SeqsetUtils
-{
+ */\r
+public class SeqsetUtils {\r
/**
- * Store essential properties of a sequence in a hashtable for later recovery
- * Keys are Name, Start, End, SeqFeatures, PdbId
- * @param seq SequenceI
- * @return Hashtable
- */
- public static Hashtable SeqCharacterHash(SequenceI seq) {
- Hashtable sqinfo = new Hashtable();
- sqinfo.put("Name", seq.getName());
- sqinfo.put("Start", new Integer(seq.getStart()));
- sqinfo.put("End", new Integer(seq.getEnd()));
- sqinfo.put("SeqFeatures", seq.getSequenceFeatures());
- sqinfo.put("PdbId", (seq.getPDBId()!=null) ? seq.getPDBId() : new String("") );
- return sqinfo;
- }
- /**
- * Recover essential properties of a sequence from a hashtable
- * TODO: replace these methods with something more elegant.
- * @param sq SequenceI
- * @param sqinfo Hashtable
- * @return boolean
- */
- public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) {
- boolean namePresent = true;
- String oldname = (String) sqinfo.get("Name");
- Integer start = (Integer) sqinfo.get("Start");
- Integer end = (Integer) sqinfo.get("End");
- java.util.Vector sfeatures = (java.util.Vector) sqinfo.get("SeqFeatures");
- String pdbid = (String) sqinfo.get("PdbId");
- if (oldname==null)
- namePresent = false;
- else
- sq.setName(oldname);
- if (!pdbid.equals(""))
- sq.setPDBId(pdbid);
-
- if ((start!=null) && (end!=null)) {
- sq.setStart(start.intValue());
- sq.setEnd(end.intValue());
- }
- if (sfeatures!=null)
- sq.setSequenceFeatures(sfeatures);
- return namePresent;
- }
-
- /**
- * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
- * @param i int
- * @return String
- */
- public static String unique_name(int i) {
- return new String("Sequence"+i);
- }
-
- public static Hashtable uniquify(SequenceI[] sequences, boolean write_names)
- {
- // Generate a safely named sequence set and a hash to recover the sequence names
- Hashtable map = new Hashtable();
- String[] un_names = new String[sequences.length];
- if (!write_names)
-
- for (int i = 0; i < sequences.length; i++)
- {
- String safename = new String("Sequence" + i);
- map.put(safename, SeqCharacterHash(sequences[i]));
- if (write_names)
- sequences[i].setName(safename);
- }
- return map;
- }
-
- public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
- {
- // recover unsafe sequence names for a sequence set
- boolean allfound = true;
- for (int i = 0; i < sequences.length; i++)
- {
- if (map.containsKey(sequences[i].getName()))
- {
- Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());
- SeqCharacterUnhash(sequences[i], sqinfo);
- }
- else
- {
- allfound = false;
- }
- }
- return allfound;
- }
-
-}
+ * Store essential properties of a sequence in a hashtable for later recovery
+ * Keys are Name, Start, End, SeqFeatures, PdbId
+ * @param seq SequenceI
+ * @return Hashtable
+ */\r
+ public static Hashtable SeqCharacterHash(SequenceI seq) {\r
+ Hashtable sqinfo = new Hashtable();\r
+ sqinfo.put("Name", seq.getName());\r
+ sqinfo.put("Start", new Integer(seq.getStart()));\r
+ sqinfo.put("End", new Integer(seq.getEnd()));\r
+ sqinfo.put("SeqFeatures", seq.getSequenceFeatures());\r
+ sqinfo.put("PdbId",\r
+ (seq.getPDBId() != null) ? seq.getPDBId() : new String(""));\r
+\r
+ return sqinfo;\r
+ }\r
+\r
+ /**
+ * Recover essential properties of a sequence from a hashtable
+ * TODO: replace these methods with something more elegant.
+ * @param sq SequenceI
+ * @param sqinfo Hashtable
+ * @return boolean
+ */\r
+ public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) {\r
+ boolean namePresent = true;\r
+ String oldname = (String) sqinfo.get("Name");\r
+ Integer start = (Integer) sqinfo.get("Start");\r
+ Integer end = (Integer) sqinfo.get("End");\r
+ java.util.Vector sfeatures = (java.util.Vector) sqinfo.get(\r
+ "SeqFeatures");\r
+ String pdbid = (String) sqinfo.get("PdbId");\r
+\r
+ if (oldname == null) {\r
+ namePresent = false;\r
+ } else {\r
+ sq.setName(oldname);\r
+ }\r
+\r
+ if (!pdbid.equals("")) {\r
+ sq.setPDBId(pdbid);\r
+ }\r
+\r
+ if ((start != null) && (end != null)) {\r
+ sq.setStart(start.intValue());\r
+ sq.setEnd(end.intValue());\r
+ }\r
+\r
+ if (sfeatures != null) {\r
+ sq.setSequenceFeatures(sfeatures);\r
+ }\r
+\r
+ return namePresent;\r
+ }\r
+\r
+ /**
+ * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
+ * @param i int
+ * @return String
+ */\r
+ public static String unique_name(int i) {\r
+ return new String("Sequence" + i);\r
+ }\r
+\r
+ public static Hashtable uniquify(SequenceI[] sequences, boolean write_names) {\r
+ // Generate a safely named sequence set and a hash to recover the sequence names\r
+ Hashtable map = new Hashtable();\r
+ String[] un_names = new String[sequences.length];\r
+\r
+ if (!write_names) {\r
+ for (int i = 0; i < sequences.length; i++) {\r
+ String safename = new String("Sequence" + i);\r
+ map.put(safename, SeqCharacterHash(sequences[i]));\r
+\r
+ if (write_names) {\r
+ sequences[i].setName(safename);\r
+ }\r
+ }\r
+ }\r
+\r
+ return map;\r
+ }\r
+\r
+ public static boolean deuniquify(Hashtable map, SequenceI[] sequences) {\r
+ // recover unsafe sequence names for a sequence set\r
+ boolean allfound = true;\r
+\r
+ for (int i = 0; i < sequences.length; i++) {\r
+ if (map.containsKey(sequences[i].getName())) {\r
+ Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());\r
+ SeqCharacterUnhash(sequences[i], sqinfo);\r
+ } else {\r
+ allfound = false;\r
+ }\r
+ }\r
+\r
+ return allfound;\r
+ }\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.analysis;
-
-import java.util.Vector;
-import java.util.Hashtable;
-import jalview.datamodel.SequenceI;
-
+*/\r
+package jalview.analysis;\r
+\r
+import jalview.datamodel.SequenceI;\r
+\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
+\r
+\r
/**
* <p>Title: </p>
* SequenceIdMatcher
*
* @author not attributable
* @version 1.0
- */
-public class SequenceIdMatcher
-{
-
- private class SeqIdName
- {
- String id;
-
- SeqIdName(String s)
- {
- id = new String(s);
- }
-
- public int hashCode()
- {
- return (id.substring(0, 4).hashCode());
- }
-
- public boolean equals(Object s)
- {
- if (s instanceof SeqIdName)
- {
- return this.equals( (SeqIdName) s);
- }
- else
- {
- if (s instanceof String)
- {
- return this.equals( (String) s);
- }
- }
- return false;
- }
-
- public boolean equals(SeqIdName s)
- {
- if (id.startsWith(s.id) || s.id.startsWith(id))
- {
- return true;
- }
- return false;
- }
-
- public boolean equals(String s)
- {
- if (id.startsWith(s) || s.startsWith(id))
- {
- return true;
- }
- return false;
- }
- }
-
- private Hashtable names;
-
- public SequenceIdMatcher(SequenceI[] seqs)
- {
- names = new Hashtable();
- for (int i = 0; i < seqs.length; i++)
- {
- names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
- }
- }
-
- SequenceI findIdMatch(SequenceI seq)
- {
- SeqIdName nam = new SeqIdName(seq.getName());
- if (names.containsKey(nam))
- {
- return (SequenceI) names.get(nam);
- }
- return null;
- }
-
- SequenceI findIdMatch(String seqnam)
- {
- SeqIdName nam = new SeqIdName(seqnam);
- if (names.containsKey(nam))
- {
- return (SequenceI) names.get(nam);
- }
- return null;
- }
-
- /**
- * findIdMatch
- *
- * Return pointers to sequences (or sequence object containers)
- * which have same Id as a given set of different sequence objects
- *
- * @param seqs SequenceI[]
- * @return SequenceI[]
- */
-
- SequenceI[] findIdMatch(SequenceI[] seqs)
- {
- SequenceI[] namedseqs = new SequenceI[seqs.length];
-
- int i = 0;
- SeqIdName nam;
- if (seqs.length > 0)
- {
- do
- {
- nam = new SeqIdName(seqs[i].getName());
- if (names.containsKey(nam))
- {
- namedseqs[i] = (SequenceI) names.get(nam);
- }
- else
- {
- namedseqs[i] = null;
- }
- }
- while (i++ < seqs.length);
- }
- return namedseqs;
- }
-
-}
+ */\r
+public class SequenceIdMatcher {\r
+ private Hashtable names;\r
+\r
+ public SequenceIdMatcher(SequenceI[] seqs) {\r
+ names = new Hashtable();\r
+\r
+ for (int i = 0; i < seqs.length; i++) {\r
+ names.put(new SeqIdName(seqs[i].getName()), seqs[i]);\r
+ }\r
+ }\r
+\r
+ SequenceI findIdMatch(SequenceI seq) {\r
+ SeqIdName nam = new SeqIdName(seq.getName());\r
+\r
+ if (names.containsKey(nam)) {\r
+ return (SequenceI) names.get(nam);\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+ SequenceI findIdMatch(String seqnam) {\r
+ SeqIdName nam = new SeqIdName(seqnam);\r
+\r
+ if (names.containsKey(nam)) {\r
+ return (SequenceI) names.get(nam);\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+ /**
+ * findIdMatch
+ *
+ * Return pointers to sequences (or sequence object containers)
+ * which have same Id as a given set of different sequence objects
+ *
+ * @param seqs SequenceI[]
+ * @return SequenceI[]
+ */\r
+ SequenceI[] findIdMatch(SequenceI[] seqs) {\r
+ SequenceI[] namedseqs = new SequenceI[seqs.length];\r
+\r
+ int i = 0;\r
+ SeqIdName nam;\r
+\r
+ if (seqs.length > 0) {\r
+ do {\r
+ nam = new SeqIdName(seqs[i].getName());\r
+\r
+ if (names.containsKey(nam)) {\r
+ namedseqs[i] = (SequenceI) names.get(nam);\r
+ } else {\r
+ namedseqs[i] = null;\r
+ }\r
+ } while (i++ < seqs.length);\r
+ }\r
+\r
+ return namedseqs;\r
+ }\r
+\r
+ private class SeqIdName {\r
+ String id;\r
+\r
+ SeqIdName(String s) {\r
+ id = new String(s);\r
+ }\r
+\r
+ public int hashCode() {\r
+ return (id.substring(0, 4).hashCode());\r
+ }\r
+\r
+ public boolean equals(Object s) {\r
+ if (s instanceof SeqIdName) {\r
+ return this.equals((SeqIdName) s);\r
+ } else {\r
+ if (s instanceof String) {\r
+ return this.equals((String) s);\r
+ }\r
+ }\r
+\r
+ return false;\r
+ }\r
+\r
+ public boolean equals(SeqIdName s) {\r
+ if (id.startsWith(s.id) || s.id.startsWith(id)) {\r
+ return true;\r
+ }\r
+\r
+ return false;\r
+ }\r
+\r
+ public boolean equals(String s) {\r
+ if (id.startsWith(s) || s.startsWith(id)) {\r
+ return true;\r
+ }\r
+\r
+ return false;\r
+ }\r
+ }\r
+}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.schemes.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class APopupMenu extends java.awt.PopupMenu\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+\r
+public class APopupMenu\r
+ extends java.awt.PopupMenu\r
{\r
Menu groupMenu = new Menu();\r
protected MenuItem clustalColour = new MenuItem();\r
MenuItem noColourmenuItem = new MenuItem();\r
protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
\r
-\r
AlignmentPanel ap;\r
Menu sequenceMenu = new Menu();\r
MenuItem sequenceName = new MenuItem();\r
sequence = seq;\r
\r
try\r
- { jbInit(); }\r
- catch(Exception e)\r
- { e.printStackTrace(); }\r
-\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg!=null)\r
+ if (sg != null)\r
{\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
showBoxes.setState(sg.getDisplayBoxes());\r
}\r
\r
- if( !ap.av.alignment.getGroups().contains(sg))\r
- groupMenu.remove(unGroupMenuItem);\r
-\r
- if(seq==null)\r
- remove(sequenceMenu);\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
+ {\r
+ groupMenu.remove(unGroupMenuItem);\r
+ }\r
\r
+ if (seq == null)\r
+ {\r
+ remove(sequenceMenu);\r
+ }\r
\r
}\r
- private void jbInit() throws Exception\r
+\r
+ private void jbInit()\r
+ throws Exception\r
{\r
groupMenu.setLabel("Group");\r
groupMenu.setLabel("Define");\r
}\r
});\r
\r
-\r
nucleotideMenuItem.setLabel("Nucleotide");\r
nucleotideMenuItem.addActionListener(new ActionListener()\r
{\r
});\r
conservationMenuItem.setLabel("Conservation");\r
\r
-\r
}\r
\r
void refresh()\r
{\r
SequenceGroup sg = getGroup();\r
- SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
- if( superG !=null)\r
- superG.setSuperGroupProperties( sg );\r
+ SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
+ if (superG != null)\r
+ {\r
+ superG.setSuperGroupProperties(sg);\r
+ }\r
\r
ap.seqPanel.seqCanvas.repaint();\r
}\r
refresh();\r
}\r
\r
-\r
protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
getGroup().cs = new HydrophobicColourScheme();\r
refresh();\r
}\r
\r
-\r
-\r
protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
{\r
SequenceGroup sg = getGroup();\r
{\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
ap.av.alignment.getWidth()));\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
+ getGroup().getName());\r
if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
+ {\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
\r
SliderPanel.showPIDSlider();\r
\r
-\r
}\r
else // remove PIDColouring\r
{\r
\r
}\r
\r
-\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- new UserDefinedColours( ap, getGroup());\r
+ new UserDefinedColours(ap, getGroup());\r
}\r
\r
protected void PIDColour_actionPerformed(ActionEvent e)\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ ap.av.alignment.getWidth()));\r
\r
refresh();\r
}\r
\r
-\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
getGroup().cs = null;\r
refresh();\r
}\r
\r
- protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
+ protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
{\r
SequenceGroup sg = getGroup();\r
\r
- if(conservationMenuItem.getState())\r
+ if (conservationMenuItem.getState())\r
{\r
\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ ap.av.alignment.getWidth());\r
\r
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
sg.cs = ccs;\r
\r
}\r
else // remove ConservationColouring\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
+ ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
+ sg.cs = ccs.cs;\r
}\r
\r
- refresh();\r
+ refresh();\r
}\r
\r
-\r
protected void analyze_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for(int i=0; i<sg.sequences.size(); i++)\r
- {\r
- Sequence tmp = (Sequence)sg.sequences.elementAt(i);\r
- sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText( sb.toString() );\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
+ SequenceGroup sg = getGroup();\r
+ StringBuffer sb = new StringBuffer();\r
+\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ Sequence tmp = (Sequence) sg.sequences.elementAt(i);\r
+ sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
+ sb.append("\n");\r
+ }\r
+\r
+ sb.append("Something amazing will happen soon");\r
+ cap.setText(sb.toString());\r
\r
}\r
\r
\r
void unGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
}\r
\r
-\r
public void showColourText_itemStateChanged(ItemEvent itemEvent)\r
{\r
getGroup().setColourText(showColourText.getState());\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
import java.awt.event.*;\r
import java.util.*;\r
\r
-\r
-public class AlignFrame extends GAlignFrame\r
+public class AlignFrame\r
+ extends GAlignFrame\r
{\r
final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
+ final AlignViewport viewport;\r
public static final int NEW_WINDOW_WIDTH = 700;\r
public static final int NEW_WINDOW_HEIGHT = 500;\r
jalview.bin.JalviewLite applet;\r
try\r
{\r
treeFile = treeFile;\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
+ getCodeBase() + treeFile, "URL");\r
fin.parse();\r
\r
if (fin.getTree() != null)\r
{\r
TreePanel tp = null;\r
tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- fin, "FromFile", applet.getCodeBase()+treeFile);\r
+ fin, "FromFile", applet.getCodeBase() + treeFile);\r
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
addTreeMenuItem(tp, treeFile);\r
}\r
}\r
}\r
\r
-\r
}\r
\r
public void inputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
}\r
\r
-\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);\r
- cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Alignment output - " + e.getActionCommand(),\r
+ 600, 500);\r
+ cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().\r
+ getSequences()));\r
}\r
\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
Stack redoList = new Stack();\r
\r
void updateEditMenuBar()\r
- {\r
- if(historyList.size()>0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem)historyList.peek();\r
- undoMenuItem.setLabel("Undo "+hi.getDescription());\r
- }\r
- else\r
- {\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- }\r
+ {\r
+ if (historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ HistoryItem hi = (HistoryItem) historyList.peek();\r
+ undoMenuItem.setLabel("Undo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ }\r
\r
- if(redoList.size()>0)\r
- {\r
- redoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem)redoList.peek();\r
- redoMenuItem.setLabel("Redo "+hi.getDescription());\r
- }\r
- else\r
- {\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- }\r
- }\r
-\r
- public void addHistoryItem(HistoryItem hi)\r
- {\r
- historyList.push(hi);\r
- updateEditMenuBar();\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem)historyList.pop();\r
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));\r
- restoreHistoryItem(hi);\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem)redoList.pop();\r
- restoreHistoryItem(hi);\r
- updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
- }\r
+ if (redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+ HistoryItem hi = (HistoryItem) redoList.peek();\r
+ redoMenuItem.setLabel("Redo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ }\r
+ }\r
+\r
+ public void addHistoryItem(HistoryItem hi)\r
+ {\r
+ historyList.push(hi);\r
+ updateEditMenuBar();\r
+ }\r
+\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) historyList.pop();\r
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
+ HistoryItem.HIDE));\r
+ restoreHistoryItem(hi);\r
+ }\r
\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) redoList.pop();\r
+ restoreHistoryItem(hi);\r
+ updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ alignPanel.repaint();\r
+ }\r
\r
- // used by undo and redo\r
- void restoreHistoryItem(HistoryItem hi)\r
- {\r
- if(hi.getType()== HistoryItem.SORT)\r
+ // used by undo and redo\r
+ void restoreHistoryItem(HistoryItem hi)\r
+ {\r
+ if (hi.getType() == HistoryItem.SORT)\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
{\r
- for(int i=0; i<hi.getSequences().size(); i++)\r
- viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);\r
+ viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
+ elementAt(i), i);\r
}\r
- else\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
{\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
+ if (restore.getLength() == 0)\r
{\r
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
- if(restore.getLength()==0)\r
- {\r
- // log.System.out.println(hi.getHidden().elementAt(i));\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- viewport.alignment.getSequences().insertElementAt(\r
- restore,\r
- hi.getAlignIndex(i));\r
- }\r
- else\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ // log.System.out.println(hi.getHidden().elementAt(i));\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ viewport.alignment.getSequences().insertElementAt(\r
+ restore,\r
+ hi.getAlignIndex(i));\r
}\r
- if(hi.getType()==HistoryItem.PASTE)\r
+ else\r
{\r
- for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)\r
- viewport.alignment.deleteSequence(i);\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
}\r
}\r
+ if (hi.getType() == HistoryItem.PASTE)\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 1;\r
+ i > hi.getSequences().size() - 1; i--)\r
+ {\r
+ viewport.alignment.deleteSequence(i);\r
+ }\r
+ }\r
+ }\r
\r
- updateEditMenuBar();\r
-\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
- }\r
+ updateEditMenuBar();\r
\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ alignPanel.repaint();\r
+ }\r
\r
public void moveSelectedSequences(boolean up)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
if (sg == null)\r
+ {\r
return;\r
+ }\r
\r
if (up)\r
{\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
if (!sg.sequences.contains(seq))\r
+ {\r
continue;\r
+ }\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
if (sg.sequences.contains(temp))\r
+ {\r
continue;\r
+ }\r
\r
viewport.alignment.getSequences().setElementAt(temp, i);\r
viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
if (!sg.sequences.contains(seq))\r
+ {\r
continue;\r
+ }\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
if (sg.sequences.contains(temp))\r
+ {\r
continue;\r
+ }\r
\r
viewport.alignment.getSequences().setElementAt(temp, i);\r
viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
alignPanel.repaint();\r
}\r
\r
-\r
StringBuffer copiedSequences;\r
protected void copy_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getSelectionGroup()==null)\r
- return;\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- copiedSequences = new StringBuffer();\r
- Hashtable orderedSeqs = new Hashtable();\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ copiedSequences = new StringBuffer();\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
- orderedSeqs.put(index+"", seq);\r
- }\r
+ orderedSeqs.put(index + "", seq);\r
+ }\r
\r
- int index=0;\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
- SequenceI seq = null;\r
- while( seq == null )\r
- {\r
- if(orderedSeqs.containsKey(index+""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
- break;\r
- }\r
- else\r
- index++;\r
- }\r
+ int index = 0;\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = null;\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
\r
- copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
- +seq.findPosition( sg.getEndRes() )+ "\t"\r
- +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
- }\r
+ copiedSequences.append(seq.getName() + "\t" +\r
+ seq.findPosition(sg.getStartRes()) + "\t"\r
+ + seq.findPosition(sg.getEndRes()) + "\t"\r
+ +\r
+ sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
+ }\r
\r
}\r
\r
-\r
protected void pasteNew_actionPerformed(ActionEvent e)\r
{\r
paste(true);\r
\r
protected void pasteThis_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));\r
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
+ HistoryItem.PASTE));\r
paste(false);\r
}\r
\r
void paste(boolean newAlignment)\r
{\r
- try{\r
+ try\r
+ {\r
if (copiedSequences == null)\r
+ {\r
return;\r
+ }\r
\r
StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
Vector seqs = new Vector();\r
String name = st.nextToken();\r
int start = Integer.parseInt(st.nextToken());\r
int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
+ Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
\r
- if(!newAlignment)\r
+ if (!newAlignment)\r
+ {\r
viewport.alignment.addSequence(sequence);\r
+ }\r
else\r
+ {\r
seqs.addElement(sequence);\r
+ }\r
}\r
\r
- if(newAlignment)\r
+ if (newAlignment)\r
{\r
SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- for(int i=0; i<seqs.size(); i++)\r
- newSeqs[i] = (SequenceI)seqs.elementAt(i);\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
\r
AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
String newtitle = new String("Copied sequences");\r
- if( getTitle().startsWith("Copied sequences"))\r
- newtitle = getTitle();\r
- else\r
- newtitle = newtitle.concat("- from "+getTitle());\r
- jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
+ if (getTitle().startsWith("Copied sequences"))\r
+ {\r
+ newtitle = getTitle();\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + getTitle());\r
+ }\r
+ jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
}\r
else\r
{\r
alignPanel.repaint();\r
}\r
\r
- }catch(Exception ex){}// could be anything being pasted in here\r
+ }\r
+ catch (Exception ex)\r
+ {} // could be anything being pasted in here\r
\r
}\r
\r
-\r
protected void cut_actionPerformed(ActionEvent e)\r
{\r
copy_actionPerformed(null);\r
\r
protected void delete_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+ HistoryItem.HIDE));\r
if (viewport.getSelectionGroup() == null)\r
+ {\r
return;\r
+ }\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i=0;i < sg.sequences.size(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.getAlignment().findIndex(seq);\r
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
- if(seq.getSequence().length()<1)\r
- viewport.getAlignment().deleteSequence(seq);\r
+ if (seq.getSequence().length() < 1)\r
+ {\r
+ viewport.getAlignment().deleteSequence(seq);\r
+ }\r
else\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
+ {\r
+ viewport.getAlignment().getSequences().setElementAt(seq, index);\r
+ }\r
+ }\r
\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);\r
- if(viewport.getAlignment().getHeight()<1)\r
- try\r
- {\r
- this.setVisible(false);\r
- }catch(Exception ex){}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
+ viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ try\r
+ {\r
+ this.setVisible(false);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
\r
}\r
\r
-\r
-\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.alignment.deleteAllGroups();\r
alignPanel.repaint();\r
}\r
\r
-\r
-\r
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = new SequenceGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i));\r
+ }\r
sg.setEndRes(viewport.alignment.getWidth());\r
viewport.setSelectionGroup(sg);\r
alignPanel.repaint();\r
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));\r
+ }\r
\r
PaintRefresher.Refresh(null);\r
}\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
{\r
- addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,\r
+ addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
HistoryItem.HIDE));\r
int min = colSel.getMin();\r
viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0,min);\r
+ colSel.compensateForEdit(0, min);\r
\r
- if(viewport.getSelectionGroup()!=null)\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ }\r
\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(!sg.adjustForRemoveLeft(min))\r
+ if (!sg.adjustForRemoveLeft(min))\r
+ {\r
viewport.alignment.deleteGroup(sg);\r
+ }\r
}\r
\r
alignPanel.repaint();\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
{\r
- addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,\r
+ addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
HistoryItem.HIDE));\r
int max = colSel.getMax();\r
viewport.getAlignment().trimRight(max);\r
- if(viewport.getSelectionGroup()!=null)\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ }\r
\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(!sg.adjustForRemoveRight(max))\r
+ if (!sg.adjustForRemoveRight(max))\r
+ {\r
viewport.alignment.deleteGroup(sg);\r
+ }\r
}\r
\r
-\r
-\r
alignPanel.repaint();\r
}\r
\r
HistoryItem.HIDE));\r
SequenceI current;\r
int jSize;\r
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
current = viewport.getAlignment().getSequenceAt(i);\r
jSize = current.getLength();\r
- for (int j=0; j < jSize; j++)\r
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
+ for (int j = 0; j < jSize; j++)\r
+ {\r
+ if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
current.deleteCharAt(j);\r
j--;\r
jSize--;\r
}\r
+ }\r
}\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
alignPanel.repaint();\r
}\r
\r
-\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
Finder finder = new Finder(alignPanel);\r
}\r
\r
-\r
public void font_actionPerformed(ActionEvent e)\r
{\r
Frame frame = new Frame();\r
- FontChooser fc = new FontChooser( alignPanel, frame);\r
+ FontChooser fc = new FontChooser(alignPanel, frame);\r
frame.add(fc);\r
- jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
\r
}\r
\r
protected void fullSeqId_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowFullId( fullSeqId.getState() );\r
+ viewport.setShowFullId(fullSeqId.getState());\r
alignPanel.fontChanged();\r
alignPanel.repaint();\r
}\r
\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setColourText( colourTextMenuItem.getState() );\r
- alignPanel.repaint();\r
+ viewport.setColourText(colourTextMenuItem.getState());\r
+ alignPanel.repaint();\r
}\r
\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setWrapAlignment( wrapMenuItem.getState() );\r
- alignPanel.setWrapAlignment( wrapMenuItem.getState() );\r
- scaleAbove.setEnabled( wrapMenuItem.getState() );\r
- scaleLeft.setEnabled( wrapMenuItem.getState());\r
- scaleRight.setEnabled( wrapMenuItem.getState());\r
+ viewport.setWrapAlignment(wrapMenuItem.getState());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
+ scaleAbove.setEnabled(wrapMenuItem.getState());\r
+ scaleLeft.setEnabled(wrapMenuItem.getState());\r
+ scaleRight.setEnabled(wrapMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
alignPanel.repaint();\r
}\r
\r
-\r
-\r
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowBoxes( viewBoxesMenuItem.getState() );\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowText( viewTextMenuItem.getState() );\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
-\r
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setRenderGaps(renderGapsMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
-\r
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
+ if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
{\r
annotationPanelMenuItem.setState(false);\r
return;\r
}\r
- viewport.setShowAnnotation( annotationPanelMenuItem.getState() );\r
- alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
}\r
\r
public void overviewMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if (alignPanel.overviewPanel != null)\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
return;\r
+ }\r
\r
Frame frame = new Frame();\r
OverviewPanel overview = new OverviewPanel(alignPanel);\r
frame.add(overview);\r
// +50 must allow for applet frame window\r
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.preferredSize().width, overview.preferredSize().height+50);\r
+ overview.preferredSize().width,\r
+ overview.preferredSize().height + 50);\r
\r
frame.pack();\r
frame.addWindowListener(new WindowAdapter()\r
- { public void windowClosing(WindowEvent e)\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
{\r
- alignPanel.setOverviewPanel(null);\r
+ alignPanel.setOverviewPanel(null);\r
};\r
});\r
\r
- alignPanel.setOverviewPanel( overview );\r
-\r
+ alignPanel.setOverviewPanel(overview);\r
\r
}\r
\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
- changeColour( null );\r
+ changeColour(null);\r
}\r
\r
-\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
}\r
\r
public void zappoColour_actionPerformed(ActionEvent e)\r
changeColour(new TaylorColourScheme());\r
}\r
\r
-\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour( new HydrophobicColourScheme() );\r
+ changeColour(new HydrophobicColourScheme());\r
}\r
\r
public void helixColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(new HelixColourScheme() );\r
+ changeColour(new HelixColourScheme());\r
}\r
\r
-\r
public void strandColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new StrandColourScheme());\r
}\r
\r
-\r
public void turnColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new TurnColourScheme());\r
}\r
\r
-\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(new BuriedColourScheme() );\r
+ changeColour(new BuriedColourScheme());\r
}\r
\r
public void nucleotideColour_actionPerformed(ActionEvent e)\r
changeColour(new NucleotideColourScheme());\r
}\r
\r
-\r
protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
}\r
\r
-\r
-\r
void changeColour(ColourSchemeI cs)\r
{\r
int threshold = 0;\r
\r
- if ( viewport.getAbovePIDThreshold() )\r
+ if (viewport.getAbovePIDThreshold())\r
{\r
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
\r
if (cs instanceof ResidueColourScheme)\r
+ {\r
( (ResidueColourScheme) cs).setThreshold(threshold);\r
+ }\r
else if (cs instanceof ScoreColourScheme)\r
+ {\r
( (ScoreColourScheme) cs).setThreshold(threshold);\r
+ }\r
\r
viewport.setGlobalColourScheme(cs);\r
}\r
else if (cs instanceof ResidueColourScheme)\r
+ {\r
( (ResidueColourScheme) cs).setThreshold(0);\r
+ }\r
else if (cs instanceof ScoreColourScheme)\r
+ {\r
( (ScoreColourScheme) cs).setThreshold(0);\r
-\r
-\r
+ }\r
\r
if (viewport.getConservationSelected())\r
{\r
ccs = new ConservationColourScheme(c, cs);\r
\r
// MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( viewport.vconsensus );\r
+ ccs.setConsensus(viewport.vconsensus);\r
viewport.setGlobalColourScheme(ccs);\r
\r
SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
}\r
else\r
{\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
- cs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(cs);\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ if (cs != null)\r
+ {\r
+ cs.setConsensus(viewport.vconsensus);\r
+ }\r
+ viewport.setGlobalColourScheme(cs);\r
}\r
\r
-\r
- if(viewport.getColourAppliesToAllGroups())\r
+ if (viewport.getColourAppliesToAllGroups())\r
{\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
}\r
else\r
+ {\r
try\r
{\r
sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
ex.printStackTrace();\r
sg.cs = cs;\r
}\r
+ }\r
\r
- if(viewport.getAbovePIDThreshold())\r
+ if (viewport.getAbovePIDThreshold())\r
{\r
if (sg.cs instanceof ResidueColourScheme)\r
+ {\r
( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
\r
- sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
}\r
\r
- if( viewport.getConservationSelected() )\r
+ if (viewport.getConservationSelected())\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0, viewport.alignment.getWidth()-1);\r
+ sg.sequences, 0,\r
+ viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
// MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
sg.cs = ccs;\r
}\r
else\r
}\r
}\r
\r
- if(alignPanel.getOverviewPanel()!=null)\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
\r
alignPanel.repaint();\r
}\r
\r
protected void modifyPID_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
- "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
+ "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
}\r
\r
protected void modifyConservation_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getConservationSelected())\r
+ if (viewport.getConservationSelected())\r
{\r
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
"Background");\r
}\r
}\r
\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setConservationSelected(conservationMenuItem.getState());\r
\r
viewport.setAbovePIDThreshold(false);\r
abovePIDThreshold.setState(false);\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour( ( (ConservationColourScheme) cs).cs);\r
+ }\r
else\r
- changeColour( cs );\r
+ {\r
+ changeColour(cs);\r
+ }\r
\r
modifyConservation_actionPerformed(null);\r
}\r
\r
ColourSchemeI cs = viewport.getGlobalColourScheme();\r
\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour( ( (ConservationColourScheme) cs).cs);\r
+ }\r
else\r
- changeColour( cs );\r
+ {\r
+ changeColour(cs);\r
+ }\r
\r
modifyPID_actionPerformed(null);\r
}\r
\r
-\r
-\r
public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
+ UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
}\r
\r
public void PIDColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour( new PIDColourScheme() );\r
+ changeColour(new PIDColourScheme());\r
}\r
\r
-\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(new Blosum62ColourScheme() );\r
+ changeColour(new Blosum62ColourScheme());\r
}\r
\r
-\r
-\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));\r
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(),\r
+ viewport.getAlignment().getSequenceAt(0));\r
alignPanel.repaint();\r
}\r
\r
public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));\r
- AlignmentSorter.sortByID( viewport.getAlignment() );\r
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
alignPanel.repaint();\r
}\r
\r
public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));\r
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
AlignmentSorter.sortGroups(viewport.getAlignment());\r
alignPanel.repaint();\r
RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
Frame frame = new Frame();\r
frame.add(sp);\r
- jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
+ 400, 120);\r
\r
}\r
\r
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getSelectionGroup().getSize()>1)\r
+ if (viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(viewport));\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
- if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
- || viewport.getAlignment().getHeight()<4)\r
+ if ( (viewport.getSelectionGroup() != null &&\r
+ viewport.getSelectionGroup().getSize() < 4 &&\r
+ viewport.getSelectionGroup().getSize() > 0)\r
+ || viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
}\r
\r
- try{\r
+ try\r
+ {\r
PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
Frame frame = new Frame();\r
frame.add(pcaPanel);\r
- jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- }\r
-\r
+ jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
+ 400, 400);\r
+ }\r
+ catch (java.lang.OutOfMemoryError ex)\r
+ {\r
+ }\r
\r
}\r
\r
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
}\r
\r
-\r
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
{\r
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
//are the sequences aligned?\r
- if(!viewport.alignment.isAligned())\r
+ if (!viewport.alignment.isAligned())\r
{\r
return;\r
}\r
type, pwType, 0, viewport.alignment.getWidth());\r
}\r
\r
- addTreeMenuItem(tp, title);\r
+ addTreeMenuItem(tp, title);\r
\r
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
}\r
\r
void addTreeMenuItem(final TreePanel treePanel, String title)\r
});\r
}\r
\r
- protected void documentation_actionPerformed(ActionEvent e) {\r
+ protected void documentation_actionPerformed(ActionEvent e)\r
+ {\r
\r
jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
\r
\r
protected void about_actionPerformed(ActionEvent e)\r
{\r
- class AboutPanel extends Canvas\r
+ class AboutPanel\r
+ extends Canvas\r
{\r
public void paint(Graphics g)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getSize().width, getSize().height);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
FontMetrics fm = g.getFontMetrics();\r
int fh = fm.getHeight();\r
- int y=5, x=7;\r
+ int y = 5, x = 7;\r
g.setColor(Color.black);\r
g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("JalView - Release 2.0", 200,y+=fh);\r
+ g.drawString("JalView - Release 2.0", 200, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
- g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);\r
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);\r
- g.drawString("For any issues relating to Jalview, email help@jalview.org", x,y+=fh);\r
- g.drawString("If you use JalView, please cite:",x,y+=fh+8);\r
- g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);\r
- g.drawString("Bioinformatics, 2004 12;426-7.",x,y+=fh);\r
+ g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
+ x, y += fh * 2);\r
+ g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "For any issues relating to Jalview, email help@jalview.org", x,\r
+ y += fh);\r
+ g.drawString("If you use JalView, please cite:", x, y += fh + 8);\r
+ g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
+ x, y += fh);\r
+ g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);\r
}\r
}\r
+\r
Frame frame = new Frame();\r
frame.add(new AboutPanel());\r
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);\r
-\r
-\r
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\r
}\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
+import java.util.*;\r
+\r
import java.awt.*;\r
-import jalview.bin.*;\r
+\r
import jalview.analysis.*;\r
+import jalview.bin.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import java.util.*;\r
\r
public class AlignViewport\r
{\r
int endSeq;\r
\r
boolean showFullId = true;\r
- boolean showText=true;\r
- boolean showColourText=false;\r
- boolean showBoxes=true;\r
- boolean wrapAlignment=false;\r
+ boolean showText = true;\r
+ boolean showColourText = false;\r
+ boolean showBoxes = true;\r
+ boolean wrapAlignment = false;\r
boolean renderGaps = true;\r
boolean showSequenceFeatures = false;\r
boolean showAnnotation = true;\r
\r
SequenceGroup selectionGroup = new SequenceGroup();\r
\r
- int charHeight;\r
- int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
+ int charHeight;\r
+ int charWidth;\r
+ int chunkWidth;\r
+ int chunkHeight;\r
\r
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
+ Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ AlignmentI alignment;\r
\r
ColumnSelection colSel = new ColumnSelection();\r
\r
NJTree currentTree = null;\r
\r
boolean scaleAboveWrapped = true;\r
- boolean scaleLeftWrapped = true;\r
+ boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
\r
public AlignViewport(AlignmentI al, JalviewLite applet)\r
{\r
setAlignment(al);\r
this.startRes = 0;\r
- this.endRes = al.getWidth()-1;\r
+ this.endRes = al.getWidth() - 1;\r
this.startSeq = 0;\r
- this.endSeq = al.getHeight()-1;\r
+ this.endSeq = al.getHeight() - 1;\r
setFont(font);\r
\r
-\r
- if(applet!=null)\r
+ if (applet != null)\r
{\r
String param = applet.getParameter("showFullId");\r
if (param != null)\r
+ {\r
showFullId = Boolean.valueOf(param).booleanValue();\r
+ }\r
\r
param = applet.getParameter("showAnnotation");\r
if (param != null)\r
+ {\r
showAnnotation = Boolean.valueOf(param).booleanValue();\r
+ }\r
\r
param = applet.getParameter("showConservation");\r
if (param != null)\r
+ {\r
showConservation = Boolean.valueOf(param).booleanValue();\r
+ }\r
\r
param = applet.getParameter("showQuality");\r
if (param != null)\r
+ {\r
showQuality = Boolean.valueOf(param).booleanValue();\r
+ }\r
\r
param = applet.getParameter("showConsensus");\r
if (param != null)\r
+ {\r
showConsensus = Boolean.valueOf(param).booleanValue();\r
+ }\r
}\r
// We must set conservation and consensus before setting colour,\r
// as Blosum and Clustal require this to be done\r
updateConservation();\r
updateConsensus();\r
\r
- if(applet!=null && applet.getParameter("defaultColour")!=null)\r
+ if (applet != null && applet.getParameter("defaultColour") != null)\r
{\r
globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
applet.getParameter("defaultColour"));\r
- if(globalColourScheme!=null)\r
- globalColourScheme.setConsensus( vconsensus );\r
- }\r
- }\r
-\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(vconsensus);\r
+ }\r
+ }\r
+ }\r
\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
+ public void showSequenceFeatures(boolean b)\r
+ {\r
+ showSequenceFeatures = b;\r
+ }\r
\r
public Vector vconsensus;\r
AlignmentAnnotation consensus;\r
Conservation cons = new jalview.analysis.Conservation("All",\r
jalview.schemes.ResidueProperties.propHash, 3,\r
alignment.getSequences(), 0,\r
- alignment.getWidth()-1);\r
+ alignment.getWidth() - 1);\r
cons.calculate();\r
cons.verdict(false, ConsPercGaps);\r
cons.findQuality();\r
int alWidth = alignment.getWidth();\r
- Annotation [] annotations = new Annotation[alWidth];\r
- Annotation [] qannotations = new Annotation[alWidth];\r
+ Annotation[] annotations = new Annotation[alWidth];\r
+ Annotation[] qannotations = new Annotation[alWidth];\r
String sequence = cons.getConsSequence().getSequence();\r
- float minR,minG,minB, maxR,maxG,maxB;\r
+ float minR, minG, minB, maxR, maxG, maxB;\r
minR = 0.3f;\r
minG = 0.0f;\r
minB = 0f;\r
- maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality\r
+ maxR = 1.0f - minR;\r
+ maxG = 0.9f - minG;\r
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
float min = 0f;\r
float max = 11f;\r
float qmin = cons.qualityRange[0].floatValue();\r
{\r
float value = 0;\r
try\r
+ {\r
+ value = Integer.parseInt(sequence.charAt(i) + "");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ if (sequence.charAt(i) == '*')\r
{\r
- value = Integer.parseInt(sequence.charAt(i) + "");\r
+ value = 11;\r
}\r
- catch (Exception ex)\r
+ if (sequence.charAt(i) == '+')\r
{\r
- if (sequence.charAt(i) == '*') value = 11;\r
- if (sequence.charAt(i) == '+') value = 10;\r
+ value = 10;\r
}\r
- float vprop = value-min;\r
- vprop/=max;\r
+ }\r
+ float vprop = value - min;\r
+ vprop /= max;\r
\r
annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+ "", ' ', value,\r
+ new Color(minR + maxR * vprop,\r
+ minG + maxG * vprop,\r
+ minB + maxB * vprop));\r
// Quality calc\r
- value = ((Double) cons.quality.elementAt(i)).floatValue();\r
+ value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
vprop = value - qmin;\r
- vprop/=qmax;\r
+ vprop /= qmax;\r
qannotations[i] = new Annotation(" ",\r
- String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+ String.valueOf(value), ' ', value,\r
+ new\r
+ Color(minR + maxR * vprop,\r
+ minG + maxG * vprop,\r
+ minB + maxB * vprop));\r
}\r
\r
- if(conservation==null)\r
+ if (conservation == null)\r
{\r
conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than "+ConsPercGaps+"% gaps",\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps",\r
annotations,\r
0f, // cons.qualityRange[0].floatValue(),\r
11f, // cons.qualityRange[1].floatValue()\r
1);\r
- if(showConservation)\r
- alignment.addAnnotation(conservation);\r
+ if (showConservation)\r
+ {\r
+ alignment.addAnnotation(conservation);\r
+ }\r
quality = new AlignmentAnnotation("Quality",\r
"Alignment Quality based on Blosum62 scores",\r
qannotations,\r
cons.qualityRange[0].floatValue(),\r
cons.qualityRange[1].floatValue(),\r
1);\r
- if(showQuality)\r
+ if (showQuality)\r
+ {\r
alignment.addAnnotation(quality);\r
+ }\r
}\r
- else {\r
+ else\r
+ {\r
conservation.annotations = annotations;\r
quality.annotations = qannotations;\r
quality.graphMax = cons.qualityRange[1].floatValue();\r
}\r
\r
-\r
}\r
\r
public void updateConsensus()\r
{\r
- Annotation [] annotations = new Annotation[alignment.getWidth()];\r
+ Annotation[] annotations = new Annotation[alignment.getWidth()];\r
\r
// this routine prevents vconsensus becoming a new object each time\r
// consenus is calculated. Important for speed of Blosum62\r
// and PID colouring of alignment\r
- if(vconsensus == null)\r
- vconsensus = alignment.getAAFrequency();\r
+ if (vconsensus == null)\r
+ {\r
+ vconsensus = alignment.getAAFrequency();\r
+ }\r
else\r
{\r
- Vector temp = alignment.getAAFrequency();\r
- vconsensus.removeAllElements();\r
- Enumeration e = temp.elements();\r
- while(e.hasMoreElements())\r
- {\r
- vconsensus.addElement(e.nextElement());\r
- }\r
+ Vector temp = alignment.getAAFrequency();\r
+ vconsensus.removeAllElements();\r
+ Enumeration e = temp.elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ vconsensus.addElement(e.nextElement());\r
+ }\r
}\r
Hashtable hash = null;\r
- for (int i = 0; i<alignment.getWidth(); i++)\r
+ for (int i = 0; i < alignment.getWidth(); i++)\r
{\r
- hash = (Hashtable) vconsensus.elementAt(i);\r
- float value = new Float(hash.get("maxCount").toString()).floatValue();\r
- value /= new Float(hash.get("size").toString()).floatValue();\r
-\r
- value *= 100;\r
- String maxRes = hash.get("maxResidue")+" ";\r
- String mouseOver = hash.get("maxResidue")+" ";\r
- if(maxRes.length()>2)\r
- {\r
- mouseOver = "["+maxRes+"] ";\r
- maxRes = "+ ";\r
- }\r
+ hash = (Hashtable) vconsensus.elementAt(i);\r
+ float value = new Float(hash.get("maxCount").toString()).floatValue();\r
+ value /= new Float(hash.get("size").toString()).floatValue();\r
+\r
+ value *= 100;\r
+ String maxRes = hash.get("maxResidue") + " ";\r
+ String mouseOver = hash.get("maxResidue") + " ";\r
+ if (maxRes.length() > 2)\r
+ {\r
+ mouseOver = "[" + maxRes + "] ";\r
+ maxRes = "+ ";\r
+ }\r
\r
- mouseOver += (int)value+"%";\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ mouseOver += (int) value + "%";\r
+ annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
\r
}\r
\r
- if(consensus==null)\r
- {\r
- consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, 1);\r
- if(showConsensus)\r
- alignment.addAnnotation(consensus);\r
- }\r
- else\r
- consensus.annotations = annotations;\r
+ if (consensus == null)\r
+ {\r
+ consensus = new AlignmentAnnotation("Consensus",\r
+ "PID", annotations, 0f, 100f, 1);\r
+ if (showConsensus)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ consensus.annotations = annotations;\r
+ }\r
\r
}\r
\r
-\r
public SequenceGroup getSelectionGroup()\r
{\r
return selectionGroup;\r
selectionGroup = sg;\r
}\r
\r
+ public boolean getConservationSelected()\r
+ {\r
+ return conservationColourSelected;\r
+ }\r
\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
+ public boolean getAbovePIDThreshold()\r
+ {\r
+ return abovePIDThreshold;\r
+ }\r
\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
+ public void setAbovePIDThreshold(boolean b)\r
+ {\r
+ abovePIDThreshold = b;\r
+ }\r
\r
- public int getStartRes() {\r
+ public int getStartRes()\r
+ {\r
return startRes;\r
}\r
\r
- public int getEndRes() {\r
+ public int getEndRes()\r
+ {\r
return endRes;\r
}\r
\r
- public int getStartSeq() {\r
+ public int getStartSeq()\r
+ {\r
return startSeq;\r
}\r
\r
public void setGlobalColourScheme(ColourSchemeI cs)\r
{\r
- globalColourScheme = cs;\r
+ globalColourScheme = cs;\r
}\r
\r
public ColourSchemeI getGlobalColourScheme()\r
return globalColourScheme;\r
}\r
\r
-\r
- public void setStartRes(int res) {\r
+ public void setStartRes(int res)\r
+ {\r
this.startRes = res;\r
}\r
- public void setStartSeq(int seq) {\r
+\r
+ public void setStartSeq(int seq)\r
+ {\r
this.startSeq = seq;\r
}\r
- public void setEndRes(int res) {\r
- if (res > alignment.getWidth()-1) {\r
+\r
+ public void setEndRes(int res)\r
+ {\r
+ if (res > alignment.getWidth() - 1)\r
+ {\r
// log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth()-1;\r
+ res = alignment.getWidth() - 1;\r
}\r
- if (res < 0) {\r
+ if (res < 0)\r
+ {\r
res = 0;\r
}\r
this.endRes = res;\r
}\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
+\r
+ public void setEndSeq(int seq)\r
+ {\r
+ if (seq > alignment.getHeight())\r
+ {\r
seq = alignment.getHeight();\r
}\r
- if (seq < 0) {\r
+ if (seq < 0)\r
+ {\r
seq = 0;\r
}\r
this.endSeq = seq;\r
}\r
- public int getEndSeq() {\r
+\r
+ public int getEndSeq()\r
+ {\r
return endSeq;\r
}\r
\r
- public void setFont(Font f) {\r
+ public void setFont(Font f)\r
+ {\r
font = f;\r
java.awt.Frame temp = new java.awt.Frame();\r
temp.addNotify();\r
setCharWidth(fm.charWidth('M'));\r
}\r
\r
- public Font getFont() {\r
+ public Font getFont()\r
+ {\r
return font;\r
}\r
- public void setCharWidth(int w) {\r
+\r
+ public void setCharWidth(int w)\r
+ {\r
this.charWidth = w;\r
}\r
- public int getCharWidth() {\r
+\r
+ public int getCharWidth()\r
+ {\r
return charWidth;\r
}\r
- public void setCharHeight(int h) {\r
+\r
+ public void setCharHeight(int h)\r
+ {\r
this.charHeight = h;\r
}\r
- public int getCharHeight() {\r
+\r
+ public int getCharHeight()\r
+ {\r
return charHeight;\r
}\r
- public void setChunkWidth(int w) {\r
+\r
+ public void setChunkWidth(int w)\r
+ {\r
this.chunkWidth = w;\r
}\r
- public int getChunkWidth() {\r
+\r
+ public int getChunkWidth()\r
+ {\r
return chunkWidth;\r
}\r
- public void setChunkHeight(int h) {\r
+\r
+ public void setChunkHeight(int h)\r
+ {\r
this.chunkHeight = h;\r
}\r
- public int getChunkHeight() {\r
+\r
+ public int getChunkHeight()\r
+ {\r
return chunkHeight;\r
}\r
- public AlignmentI getAlignment() {\r
+\r
+ public AlignmentI getAlignment()\r
+ {\r
return alignment;\r
}\r
- public void setAlignment(AlignmentI align) {\r
+\r
+ public void setAlignment(AlignmentI align)\r
+ {\r
this.alignment = align;\r
}\r
\r
- public void setWrapAlignment(boolean state) {\r
+ public void setWrapAlignment(boolean state)\r
+ {\r
wrapAlignment = state;\r
}\r
- public void setShowText(boolean state) {\r
+\r
+ public void setShowText(boolean state)\r
+ {\r
showText = state;\r
}\r
\r
- public void setRenderGaps(boolean state){\r
+ public void setRenderGaps(boolean state)\r
+ {\r
renderGaps = state;\r
}\r
\r
-\r
public boolean getColourText()\r
{\r
return showColourText;\r
showColourText = state;\r
}\r
\r
- public void setShowBoxes(boolean state) {\r
+ public void setShowBoxes(boolean state)\r
+ {\r
showBoxes = state;\r
}\r
\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return wrapAlignment;\r
}\r
- public boolean getShowText() {\r
+\r
+ public boolean getShowText()\r
+ {\r
return showText;\r
}\r
- public boolean getShowBoxes() {\r
+\r
+ public boolean getShowBoxes()\r
+ {\r
return showBoxes;\r
}\r
\r
- public char getGapCharacter() {\r
+ public char getGapCharacter()\r
+ {\r
return getAlignment().getGapCharacter();\r
}\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
+\r
+ public void setGapCharacter(char gap)\r
+ {\r
+ if (getAlignment() != null)\r
+ {\r
getAlignment().setGapCharacter(gap);\r
}\r
}\r
- public void setThreshold(int thresh) {\r
+\r
+ public void setThreshold(int thresh)\r
+ {\r
threshold = thresh;\r
}\r
- public int getThreshold() {\r
+\r
+ public int getThreshold()\r
+ {\r
return threshold;\r
}\r
- public void setIncrement(int inc) {\r
+\r
+ public void setIncrement(int inc)\r
+ {\r
increment = inc;\r
}\r
- public int getIncrement() {\r
+\r
+ public int getIncrement()\r
+ {\r
return increment;\r
}\r
- public int getIndex(int y) {\r
- int y1 = 0;\r
+\r
+ public int getIndex(int y)\r
+ {\r
+ int y1 = 0;\r
int starty = getStartSeq();\r
- int endy = getEndSeq();\r
+ int endy = getEndSeq();\r
\r
- for (int i = starty; i <= endy; i++) {\r
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {\r
+ for (int i = starty; i <= endy; i++)\r
+ {\r
+ if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null)\r
+ {\r
int y2 = y1 + getCharHeight();\r
\r
- if (y>=y1 && y <=y2) {\r
+ if (y >= y1 && y <= y2)\r
+ {\r
return i;\r
}\r
- y1 = y2;\r
- } else {\r
+ y1 = y2;\r
+ }\r
+ else\r
+ {\r
return -1;\r
}\r
}\r
return -1;\r
}\r
\r
- public ColumnSelection getColumnSelection() {\r
+ public ColumnSelection getColumnSelection()\r
+ {\r
return colSel;\r
}\r
\r
- public void resetSeqLimits(int height) {\r
- setEndSeq(height/getCharHeight());\r
+ public void resetSeqLimits(int height)\r
+ {\r
+ setEndSeq(height / getCharHeight());\r
}\r
- public void setCurrentTree(NJTree tree) {\r
- currentTree = tree;\r
+\r
+ public void setCurrentTree(NJTree tree)\r
+ {\r
+ currentTree = tree;\r
}\r
- public NJTree getCurrentTree() {\r
+\r
+ public NJTree getCurrentTree()\r
+ {\r
return currentTree;\r
}\r
\r
-\r
public void setColourAppliesToAllGroups(boolean b)\r
- { colourAppliesToAllGroups = b; }\r
+ {\r
+ colourAppliesToAllGroups = b;\r
+ }\r
\r
public boolean getColourAppliesToAllGroups()\r
- {return colourAppliesToAllGroups; }\r
+ {\r
+ return colourAppliesToAllGroups;\r
+ }\r
\r
public boolean getShowFullId()\r
{\r
}\r
\r
public boolean getScaleAboveWrapped()\r
- { return scaleAboveWrapped;}\r
+ {\r
+ return scaleAboveWrapped;\r
+ }\r
\r
public boolean getScaleLeftWrapped()\r
- { return scaleLeftWrapped; }\r
+ {\r
+ return scaleLeftWrapped;\r
+ }\r
\r
public boolean getScaleRightWrapped()\r
- { return scaleRightWrapped; }\r
+ {\r
+ return scaleRightWrapped;\r
+ }\r
\r
public void setScaleAboveWrapped(boolean b)\r
- { scaleAboveWrapped = b; }\r
+ {\r
+ scaleAboveWrapped = b;\r
+ }\r
\r
public void setScaleLeftWrapped(boolean b)\r
- { scaleLeftWrapped = b; }\r
+ {\r
+ scaleLeftWrapped = b;\r
+ }\r
\r
public void setScaleRightWrapped(boolean b)\r
- { scaleRightWrapped = b; }\r
-\r
+ {\r
+ scaleRightWrapped = b;\r
+ }\r
\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GAlignmentPanel;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.jbappletgui.*;\r
+import jalview.schemes.*;\r
+\r
+public class AlignmentPanel\r
+ extends GAlignmentPanel implements AdjustmentListener\r
{\r
\r
- AlignViewport av;\r
+ AlignViewport av;\r
OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
+ SeqPanel seqPanel;\r
+ IdPanel idPanel;\r
IdwidthAdjuster idwidthAdjuster;\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
alignFrame = af;\r
- this.av = av;\r
- seqPanel = new SeqPanel (av, this);\r
- idPanel = new IdPanel (av, this);\r
- scalePanel = new ScalePanel(av, this);\r
+ this.av = av;\r
+ seqPanel = new SeqPanel(av, this);\r
+ idPanel = new IdPanel(av, this);\r
+ scalePanel = new ScalePanel(av, this);\r
idwidthAdjuster = new IdwidthAdjuster(this);\r
annotationPanel = new AnnotationPanel(this);\r
- alabels = new AnnotationLabels(this);\r
-\r
+ alabels = new AnnotationLabels(this);\r
\r
idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
- seqPanel.seqCanvas.addKeyListener( new MyKeyAdapter() );\r
- idPanel.idCanvas.addKeyListener( new MyKeyAdapter() );\r
+ seqPanel.seqCanvas.addKeyListener(new MyKeyAdapter());\r
+ idPanel.idCanvas.addKeyListener(new MyKeyAdapter());\r
\r
- addComponentListener(new ComponentAdapter()\r
- {\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- repaint();\r
- }\r
- });\r
+ addComponentListener(new ComponentAdapter()\r
+ {\r
+ public void componentResized(ComponentEvent evt)\r
+ {\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ repaint();\r
+ }\r
+ });\r
\r
- Dimension d = calculateIdWidth();\r
- idPanel.idCanvas.setSize(d);\r
+ Dimension d = calculateIdWidth();\r
+ idPanel.idCanvas.setSize(d);\r
\r
- hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);\r
- annotationScroller.setSize(annotationPanel.getSize());\r
+ hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);\r
+ annotationScroller.setSize(annotationPanel.getSize());\r
\r
- idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
- annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);\r
- alabels.setSize(d.width,annotationPanel.getSize().height);\r
+ idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
+ annotationSpaceFillerHolder.setSize(d.width,\r
+ annotationPanel.getSize().height);\r
+ alabels.setSize(d.width, annotationPanel.getSize().height);\r
\r
}\r
\r
- class MyKeyAdapter extends KeyAdapter\r
+ class MyKeyAdapter\r
+ extends KeyAdapter\r
{\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- // System.out.println(evt.getKeyCode()); log.\r
- switch(evt.getKeyCode())\r
- {\r
- case 27: // escape key\r
- av.setSelectionGroup(null);\r
- alignFrame.alignPanel.repaint();\r
- break;\r
- case KeyEvent.VK_X:\r
- if(evt.isControlDown())\r
- alignFrame.cut_actionPerformed(null);\r
- break;\r
- case KeyEvent.VK_C:\r
- if(evt.isControlDown())\r
- alignFrame.copy_actionPerformed(null);\r
- break;\r
- case KeyEvent.VK_V:\r
- if(evt.isControlDown())\r
- alignFrame.paste(true);\r
- break;\r
- case KeyEvent.VK_A:\r
- if(evt.isControlDown())\r
- alignFrame.selectAllSequenceMenuItem_actionPerformed(null);\r
- break;\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ // System.out.println(evt.getKeyCode()); log.\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ av.setSelectionGroup(null);\r
+ alignFrame.alignPanel.repaint();\r
+ break;\r
+ case KeyEvent.VK_X:\r
+ if (evt.isControlDown())\r
+ {\r
+ alignFrame.cut_actionPerformed(null);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (evt.isControlDown())\r
+ {\r
+ alignFrame.copy_actionPerformed(null);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ if (evt.isControlDown())\r
+ {\r
+ alignFrame.paste(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_A:\r
+ if (evt.isControlDown())\r
+ {\r
+ alignFrame.selectAllSequenceMenuItem_actionPerformed(null);\r
+ }\r
+ break;\r
case KeyEvent.VK_DOWN:\r
alignFrame.moveSelectedSequences(false);\r
break;\r
alignFrame.moveSelectedSequences(true);\r
break;\r
case KeyEvent.VK_F:\r
- if(evt.isControlDown())\r
- alignFrame.findMenuItem_actionPerformed(null);\r
+ if (evt.isControlDown())\r
+ {\r
+ alignFrame.findMenuItem_actionPerformed(null);\r
+ }\r
break;\r
- }\r
- }\r
+ }\r
+ }\r
}\r
\r
public void fontChanged()\r
// to prevent drawing old image\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- scalePanel.setSize(new Dimension(10, av.charHeight+fm.getDescent()));\r
- idwidthAdjuster.setSize(new Dimension(10, av.charHeight+fm.getDescent()));\r
+ scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));\r
+ idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));\r
\r
annotationPanel.adjustPanelHeight();\r
annotationPanel.repaint();\r
\r
public void setIdWidth(int w, int h)\r
{\r
- idPanel.idCanvas.setSize(w,h);\r
- idPanelHolder.setSize(w,idPanelHolder.getSize().height);\r
- alabels.setSize(w,alabels.getSize().height);\r
+ idPanel.idCanvas.setSize(w, h);\r
+ idPanelHolder.setSize(w, idPanelHolder.getSize().height);\r
+ alabels.setSize(w, alabels.getSize().height);\r
validate();\r
}\r
+\r
Dimension calculateIdWidth()\r
{\r
Frame frame = new Frame();\r
frame.addNotify();\r
Graphics g = frame.getGraphics();\r
- if(g==null)\r
+ if (g == null)\r
{\r
Frame f = new Frame();\r
f.addNotify();\r
FontMetrics fm = g.getFontMetrics(av.font);\r
AlignmentI al = av.getAlignment();\r
\r
- int i = 0;\r
- int idWidth = 0;\r
- String id;\r
- while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
- {\r
- SequenceI s = al.getSequenceAt(i);\r
- if(av.getShowFullId())\r
- id = s.getDisplayId();\r
- else\r
- id = s.getName();\r
-\r
- if (fm.stringWidth(id) > idWidth)\r
- idWidth = fm.stringWidth(id);\r
- i++;\r
- }\r
-\r
- // Also check annotation label widths\r
- i=0;\r
- if(al.getAlignmentAnnotation()!=null)\r
- {\r
- fm = g.getFontMetrics(frame.getFont());\r
- while (i < al.getAlignmentAnnotation().length)\r
- {\r
- String label = al.getAlignmentAnnotation()[i].label;\r
- if (fm.stringWidth(label) > idWidth)\r
- idWidth = fm.stringWidth(label);\r
- i++;\r
- }\r
- }\r
-\r
- return new Dimension(idWidth, idPanel.idCanvas.getSize().height);\r
- }\r
+ int i = 0;\r
+ int idWidth = 0;\r
+ String id;\r
+ while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
+ {\r
+ SequenceI s = al.getSequenceAt(i);\r
+ if (av.getShowFullId())\r
+ {\r
+ id = s.getDisplayId();\r
+ }\r
+ else\r
+ {\r
+ id = s.getName();\r
+ }\r
\r
+ if (fm.stringWidth(id) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(id);\r
+ }\r
+ i++;\r
+ }\r
\r
- public void highlightSearchResults(int [] results)\r
- {\r
- seqPanel.seqCanvas.highlightSearchResults( results );\r
+ // Also check annotation label widths\r
+ i = 0;\r
+ if (al.getAlignmentAnnotation() != null)\r
+ {\r
+ fm = g.getFontMetrics(frame.getFont());\r
+ while (i < al.getAlignmentAnnotation().length)\r
+ {\r
+ String label = al.getAlignmentAnnotation()[i].label;\r
+ if (fm.stringWidth(label) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(label);\r
+ }\r
+ i++;\r
+ }\r
+ }\r
+\r
+ return new Dimension(idWidth, idPanel.idCanvas.getSize().height);\r
+ }\r
+\r
+ public void highlightSearchResults(int[] results)\r
+ {\r
+ seqPanel.seqCanvas.highlightSearchResults(results);\r
\r
- // do we need to scroll the panel?\r
- if(results!=null)\r
+ // do we need to scroll the panel?\r
+ if (results != null)\r
{\r
SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
- int start = seq.findIndex( results[1] )-1;\r
- int end = seq.findIndex( results[2] )-1;\r
- if( av.getStartRes() > start\r
+ int start = seq.findIndex(results[1]) - 1;\r
+ int end = seq.findIndex(results[2]) - 1;\r
+ if (av.getStartRes() > start\r
|| av.getEndRes() < end\r
|| (av.getStartSeq() > results[0]\r
- || av.getEndSeq() < results[0]))\r
+ || av.getEndSeq() < results[0]))\r
+ {\r
setScrollValues(start, results[0]);\r
+ }\r
}\r
\r
- }\r
-\r
-\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
+ }\r
\r
- public void setOverviewPanel(OverviewPanel op)\r
- {\r
- overviewPanel = op;\r
- }\r
+ public OverviewPanel getOverviewPanel()\r
+ {\r
+ return overviewPanel;\r
+ }\r
\r
+ public void setOverviewPanel(OverviewPanel op)\r
+ {\r
+ overviewPanel = op;\r
+ }\r
\r
public void setAnnotationVisible(boolean b)\r
{\r
repaint();\r
}\r
\r
-\r
public void setWrapAlignment(boolean wrap)\r
{\r
scalePanelHolder.setVisible(!wrap);\r
\r
}\r
\r
-\r
public void setColourScheme()\r
{\r
ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
- if(av.getConservationSelected())\r
+ if (av.getConservationSelected())\r
{\r
\r
- Alignment al = (Alignment)av.getAlignment();\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() );\r
+ Alignment al = (Alignment) av.getAlignment();\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth());\r
\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
\r
- av.setGlobalColourScheme( ccs );\r
+ av.setGlobalColourScheme(ccs);\r
\r
}\r
\r
repaint();\r
}\r
\r
-\r
int hextent = 0;\r
int vextent = 0;\r
\r
// return value is true if the scroll is valid\r
public boolean scrollUp(boolean up)\r
{\r
- if(up)\r
+ if (up)\r
{\r
- if(vscroll.getValue()<1)\r
+ if (vscroll.getValue() < 1)\r
+ {\r
return false;\r
- fastPaint = false;\r
+ }\r
+ fastPaint = false;\r
vscroll.setValue(vscroll.getValue() - 1);\r
}\r
else\r
{\r
- if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())\r
- return false;\r
- fastPaint = false;\r
+ if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())\r
+ {\r
+ return false;\r
+ }\r
+ fastPaint = false;\r
vscroll.setValue(vscroll.getValue() + 1);\r
}\r
fastPaint = true;\r
if (right)\r
{\r
if (hscroll.getValue() < 1)\r
+ {\r
return false;\r
+ }\r
fastPaint = false;\r
hscroll.setValue(hscroll.getValue() - 1);\r
}\r
else\r
{\r
if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())\r
+ {\r
return false;\r
+ }\r
fastPaint = false;\r
hscroll.setValue(hscroll.getValue() + 1);\r
}\r
return true;\r
}\r
\r
-\r
public void setScrollValues(int x, int y)\r
{\r
\r
av.setStartRes(x);\r
av.setStartSeq(y);\r
- av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);\r
+ av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);\r
\r
- hextent = seqPanel.seqCanvas.getSize().width/av.charWidth;\r
- vextent = seqPanel.seqCanvas.getSize().height/av.charHeight;\r
+ hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;\r
+ vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;\r
\r
- if(hextent > av.alignment.getWidth())\r
+ if (hextent > av.alignment.getWidth())\r
+ {\r
hextent = av.alignment.getWidth();\r
- if(vextent > av.alignment.getHeight())\r
+ }\r
+ if (vextent > av.alignment.getHeight())\r
+ {\r
vextent = av.alignment.getHeight();\r
+ }\r
\r
- if(hextent+x > av.getAlignment().getWidth())\r
- x = av.getAlignment().getWidth()- hextent;\r
+ if (hextent + x > av.getAlignment().getWidth())\r
+ {\r
+ x = av.getAlignment().getWidth() - hextent;\r
+ }\r
\r
- if(vextent+y > av.getAlignment().getHeight())\r
+ if (vextent + y > av.getAlignment().getHeight())\r
+ {\r
y = av.getAlignment().getHeight() - vextent;\r
+ }\r
\r
- if(y<0)\r
+ if (y < 0)\r
+ {\r
y = 0;\r
+ }\r
\r
- if(x<0)\r
- x=0;\r
-\r
+ if (x < 0)\r
+ {\r
+ x = 0;\r
+ }\r
\r
int endSeq = y + vextent;\r
- if(endSeq>av.alignment.getHeight())\r
+ if (endSeq > av.alignment.getHeight())\r
+ {\r
endSeq = av.alignment.getHeight();\r
+ }\r
\r
-\r
- av.setEndSeq( endSeq );\r
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
+ av.setEndSeq(endSeq);\r
+ hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
+ vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
\r
}\r
\r
-\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
int oldX = av.getStartRes();\r
{\r
int x = hscroll.getValue();\r
av.setStartRes(x);\r
- av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);\r
+ av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -\r
+ 1);\r
}\r
\r
if (evt.getSource() == vscroll)\r
int offy = vscroll.getValue();\r
if (av.getWrapAlignment())\r
{\r
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);\r
- av.setStartRes( vscroll.getValue() * rowSize );\r
- av.setEndRes( (vscroll.getValue()+1) * rowSize );\r
+ int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+ seqCanvas.getSize().width);\r
+ av.setStartRes(vscroll.getValue() * rowSize);\r
+ av.setEndRes( (vscroll.getValue() + 1) * rowSize);\r
}\r
else\r
{\r
av.setStartSeq(offy);\r
- av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height / av.getCharHeight());\r
+ av.setEndSeq(offy +\r
+ seqPanel.seqCanvas.getSize().height / av.getCharHeight());\r
}\r
}\r
\r
- if(overviewPanel!=null)\r
+ if (overviewPanel != null)\r
+ {\r
overviewPanel.setBoxPosition();\r
+ }\r
\r
- if(av.getWrapAlignment() || !fastPaint)\r
+ if (av.getWrapAlignment() || !fastPaint)\r
+ {\r
repaint();\r
+ }\r
else\r
{\r
idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);\r
\r
scalePanel.repaint();\r
if (av.getShowAnnotation())\r
+ {\r
annotationPanel.fastPaint(av.getStartRes() - oldX);\r
+ }\r
}\r
\r
}\r
\r
public void update(Graphics g)\r
{\r
- paint (g);\r
+ paint(g);\r
}\r
\r
-\r
public void paint(Graphics g)\r
{\r
Dimension d = idPanel.idCanvas.getSize();\r
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
- annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);\r
- alabels.setSize(d.width,annotationPanel.getSize().height);\r
+ annotationSpaceFillerHolder.setSize(d.width,\r
+ annotationPanel.getSize().height);\r
+ alabels.setSize(d.width, annotationPanel.getSize().height);\r
\r
alabels.repaint();\r
idPanel.idCanvas.repaint();\r
scalePanel.repaint();\r
annotationPanel.repaint();\r
\r
-\r
if (av.getWrapAlignment())\r
{\r
- int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);\r
+ int max = av.alignment.getWidth() /\r
+ seqPanel.seqCanvas.\r
+ getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);\r
vscroll.setMaximum(max);\r
vscroll.setUnitIncrement(1);\r
vscroll.setVisibleAmount(1);\r
setScrollValues(av.getStartRes(), av.getStartSeq());\r
}\r
\r
-\r
-\r
}\r
}\r
-\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
+\r
import jalview.datamodel.*;\r
\r
-public class AnnotationLabels extends Panel implements ActionListener\r
+public class AnnotationLabels\r
+ extends Panel implements ActionListener\r
{\r
boolean active = false;\r
- AlignmentPanel ap ;\r
+ AlignmentPanel ap;\r
boolean resizing = false;\r
int oldY, mouseX;\r
static String ADDNEW = "Add new row";\r
static String HIDE = "Hide this row";\r
static String DELETE = "Delete this row";\r
- static String SHOWALL="Show all hidden rows";\r
- static String OUTPUT_TEXT="Show Values In Textbox";\r
+ static String SHOWALL = "Show all hidden rows";\r
+ static String OUTPUT_TEXT = "Show Values In Textbox";\r
int selectedRow = 0;\r
int scrollOffset = 0;\r
\r
this.ap = ap;\r
setLayout(null);\r
addMouseListener(new MouseAdapter()\r
- {public void mousePressed(MouseEvent evt)\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
{\r
doMousePressed(evt);\r
}\r
{\r
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
\r
- if(evt.getActionCommand().equals(HIDE))\r
- {\r
- aa[selectedRow].visible = false;\r
- }\r
- else if(evt.getActionCommand().equals(SHOWALL))\r
- {\r
- for(int i=0; i<aa.length; i++)\r
- aa[i].visible = true;\r
- }\r
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- ap.alignFrame.getTitle() + " - " +\r
- aa[selectedRow].label, 500, 100);\r
- cap.setText(aa[selectedRow].toString());\r
- }\r
-\r
- ap.annotationPanel.adjustPanelHeight();\r
- setSize(getSize().width,ap.annotationPanel.getSize().height);\r
- ap.validate();\r
- ap.repaint();\r
+ if (evt.getActionCommand().equals(HIDE))\r
+ {\r
+ aa[selectedRow].visible = false;\r
+ }\r
+ else if (evt.getActionCommand().equals(SHOWALL))\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ aa[i].visible = true;\r
+ }\r
+ }\r
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ ap.alignFrame.getTitle() + " - " +\r
+ aa[selectedRow].label, 500, 100);\r
+ cap.setText(aa[selectedRow].toString());\r
+ }\r
+\r
+ ap.annotationPanel.adjustPanelHeight();\r
+ setSize(getSize().width, ap.annotationPanel.getSize().height);\r
+ ap.validate();\r
+ ap.repaint();\r
}\r
\r
public void doMousePressed(MouseEvent evt)\r
for (int i = 0; i < aa.length; i++)\r
{\r
if (!aa[i].visible)\r
+ {\r
continue;\r
+ }\r
\r
height += aa[i].height;\r
if (y < height)\r
{\r
FontMetrics fm = g.getFontMetrics(g.getFont());\r
g.setColor(Color.white);\r
- g.fillRect(0,0, getSize().width, getSize().height);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
\r
g.translate(0, scrollOffset);\r
g.setColor(Color.black);\r
\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
- int y = g.getFont().getSize();\r
- int x = 0;\r
-\r
- if(aa!=null)\r
- for(int i=0; i<aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
-\r
- x = getSize().width - fm.stringWidth(aa[i].label)-3;\r
-\r
- if(aa[i].isGraph)\r
- y+=(aa[i].height/3);\r
-\r
- g.drawString(aa[i].label, x, y);\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
+ int y = g.getFont().getSize();\r
+ int x = 0;\r
\r
- if(aa[i].isGraph)\r
- y+=(2*aa[i].height/3);\r
- else\r
- y+=aa[i].height;\r
- }\r
+ if (aa != null)\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ x = getSize().width - fm.stringWidth(aa[i].label) - 3;\r
+\r
+ if (aa[i].isGraph)\r
+ {\r
+ y += (aa[i].height / 3);\r
+ }\r
+\r
+ g.drawString(aa[i].label, x, y);\r
+\r
+ if (aa[i].isGraph)\r
+ {\r
+ y += (2 * aa[i].height / 3);\r
+ }\r
+ else\r
+ {\r
+ y += aa[i].height;\r
+ }\r
+ }\r
+ }\r
}\r
\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
-public class AnnotationPanel extends Panel implements AdjustmentListener\r
+import jalview.datamodel.*;\r
+\r
+public class AnnotationPanel\r
+ extends Panel implements AdjustmentListener\r
{\r
AlignViewport av;\r
AlignmentPanel ap;\r
- int activeRow =-1;\r
+ int activeRow = -1;\r
\r
Vector activeRes;\r
- static String HELIX ="Helix";\r
- static String SHEET ="Sheet";\r
- static String LABEL ="Label";\r
- static String REMOVE="Remove Annotation";\r
- static String COLOUR="Colour";\r
+ static String HELIX = "Helix";\r
+ static String SHEET = "Sheet";\r
+ static String LABEL = "Label";\r
+ static String REMOVE = "Remove Annotation";\r
+ static String COLOUR = "Colour";\r
static Color HELIX_COLOUR = Color.red.darker();\r
static Color SHEET_COLOUR = Color.green.darker().darker();\r
\r
-\r
Image image;\r
Graphics gg;\r
FontMetrics fm;\r
- int imgWidth=0;\r
+ int imgWidth = 0;\r
\r
boolean fastPaint = false;\r
\r
public static int GRAPH_HEIGHT = 40;\r
\r
-\r
-\r
public AnnotationPanel(AlignmentPanel ap)\r
{\r
this.ap = ap;\r
adjustPanelHeight();\r
\r
addMouseMotionListener(new MouseMotionAdapter()\r
- {public void mouseMoved(MouseEvent evt)\r
- { doMouseMoved(evt); }\r
+ {\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ doMouseMoved(evt);\r
+ }\r
});\r
\r
- // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
+ // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
}\r
\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
- ap.alabels.setScrollOffset( -evt.getValue() );\r
+ ap.alabels.setScrollOffset( -evt.getValue());\r
}\r
\r
public void adjustPanelHeight()\r
// setHeight of panels\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
int height = 0;\r
- if(aa!=null)\r
- for (int i = 0; i < aa.length; i++)\r
+ if (aa != null)\r
{\r
- if(!aa[i].visible)\r
- continue;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
\r
- aa[i].height = 0;\r
+ aa[i].height = 0;\r
\r
- if(aa[i].hasText)\r
- aa[i].height += av.charHeight;\r
- if (aa[i].hasIcons)\r
- aa[i].height += 16;\r
+ if (aa[i].hasText)\r
+ {\r
+ aa[i].height += av.charHeight;\r
+ }\r
+ if (aa[i].hasIcons)\r
+ {\r
+ aa[i].height += 16;\r
+ }\r
\r
- if (aa[i].isGraph)\r
- aa[i].height += GRAPH_HEIGHT;\r
+ if (aa[i].isGraph)\r
+ {\r
+ aa[i].height += GRAPH_HEIGHT;\r
+ }\r
\r
- if(aa[i].height==0)\r
- aa[i].height = 20;\r
- height += aa[i].height;\r
+ if (aa[i].height == 0)\r
+ {\r
+ aa[i].height = 20;\r
+ }\r
+ height += aa[i].height;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ height = 20;\r
}\r
- else height=20;\r
\r
- this.setSize(getSize().width, height);\r
- ap.annotationScroller.setSize(getSize().width, height);\r
+ this.setSize(getSize().width, height);\r
+ ap.annotationScroller.setSize(getSize().width, height);\r
\r
// ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);\r
\r
- repaint();\r
+ repaint();\r
\r
}\r
\r
public void addEditableColumn(int i)\r
{\r
- if(activeRow==-1)\r
+ if (activeRow == -1)\r
{\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- for(int j=0; j<aa.length; j++)\r
- if(aa[j].editable)\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ for (int j = 0; j < aa.length; j++)\r
+ {\r
+ if (aa[j].editable)\r
{\r
activeRow = j;\r
break;\r
}\r
+ }\r
}\r
\r
- if(activeRes==null)\r
+ if (activeRes == null)\r
{\r
activeRes = new Vector();\r
activeRes.addElement(String.valueOf(i));\r
activeRes.addElement(String.valueOf(i));\r
}\r
\r
- public void doMouseMoved(MouseEvent evt)\r
- {\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
- return;\r
-\r
- int row = -1;\r
- int height=0;\r
- for(int i=0; i<aa.length; i++)\r
- {\r
-\r
- if( aa[i].visible )\r
- height += aa[i].height;\r
+ public void doMouseMoved(MouseEvent evt)\r
+ {\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (aa == null)\r
+ {\r
+ return;\r
+ }\r
\r
- if(evt.getY()<height)\r
- {\r
- row = i;\r
- break;\r
- }\r
- }\r
+ int row = -1;\r
+ int height = 0;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)\r
- {\r
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +\r
- " " +\r
- aa[row].annotations[res].description);\r
- ap.alignFrame.statusBar.setText(text.toString());\r
- }\r
- }\r
+ if (aa[i].visible)\r
+ {\r
+ height += aa[i].height;\r
+ }\r
\r
+ if (evt.getY() < height)\r
+ {\r
+ row = i;\r
+ break;\r
+ }\r
+ }\r
\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)\r
+ {\r
+ StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +\r
+ " " +\r
+ aa[row].annotations[res].description);\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
+ }\r
\r
public void update(Graphics g)\r
{\r
\r
public void paint(Graphics g)\r
{\r
- imgWidth = (av.endRes-av.startRes+1) *av.charWidth;\r
+ imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
\r
- if(image==null || imgWidth != image.getWidth(this))\r
- {\r
- image = createImage(imgWidth, ap.annotationPanel.getSize().height);\r
- gg = image.getGraphics();\r
- gg.setFont(av.getFont());\r
- fm = gg.getFontMetrics();\r
- fastPaint = false;\r
+ if (image == null || imgWidth != image.getWidth(this))\r
+ {\r
+ image = createImage(imgWidth, ap.annotationPanel.getSize().height);\r
+ gg = image.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ fm = gg.getFontMetrics();\r
+ fastPaint = false;\r
}\r
\r
- if(fastPaint)\r
+ if (fastPaint)\r
{\r
g.drawImage(image, 0, 0, this);\r
fastPaint = false;\r
return;\r
}\r
\r
- drawComponent( gg, av.startRes, av.endRes+1);\r
- g.drawImage( image, 0, 0, this);\r
+ drawComponent(gg, av.startRes, av.endRes + 1);\r
+ g.drawImage(image, 0, 0, this);\r
\r
}\r
\r
public void fastPaint(int horizontal)\r
-{\r
- if( horizontal == 0\r
- || av.alignment.getAlignmentAnnotation()==null\r
- || av.alignment.getAlignmentAnnotation().length<1\r
- )\r
{\r
- repaint();\r
- return;\r
- }\r
-\r
- gg.copyArea( 0,0, imgWidth, getSize().height, -horizontal*av.charWidth, 0 );\r
- int sr=av.startRes, er=av.endRes+1, transX=0;\r
-\r
- if(horizontal>0) // scrollbar pulled right, image to the left\r
- {\r
- transX = (er-sr-horizontal)*av.charWidth;\r
- sr = er - horizontal ;\r
- }\r
- else if(horizontal<0)\r
- {\r
- er = sr-horizontal;\r
- }\r
+ if (horizontal == 0\r
+ || av.alignment.getAlignmentAnnotation() == null\r
+ || av.alignment.getAlignmentAnnotation().length < 1\r
+ )\r
+ {\r
+ repaint();\r
+ return;\r
+ }\r
\r
+ gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);\r
+ int sr = av.startRes, er = av.endRes + 1, transX = 0;\r
\r
- gg.translate(transX, 0);\r
+ if (horizontal > 0) // scrollbar pulled right, image to the left\r
+ {\r
+ transX = (er - sr - horizontal) * av.charWidth;\r
+ sr = er - horizontal;\r
+ }\r
+ else if (horizontal < 0)\r
+ {\r
+ er = sr - horizontal;\r
+ }\r
\r
- drawComponent(gg, sr, er);\r
+ gg.translate(transX, 0);\r
\r
- gg.translate( -transX, 0 );\r
+ drawComponent(gg, sr, er);\r
\r
- fastPaint = true;\r
- repaint();\r
-}\r
+ gg.translate( -transX, 0);\r
\r
+ fastPaint = true;\r
+ repaint();\r
+ }\r
\r
public void drawComponent(Graphics g, int startRes, int endRes)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,(endRes-startRes) *av.charWidth, getSize().height);\r
- if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);\r
+ if (av.alignment.getAlignmentAnnotation() == null ||\r
+ av.alignment.getAlignmentAnnotation().length < 1)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getSize().width, getSize().height);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations",20,15);\r
+ g.drawString("Alignment has no annotations", 20, 15);\r
return;\r
}\r
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- int j, x=0, y=0;\r
- char [] lastSS = new char[aa.length];\r
- int [] lastSSX= new int[aa.length] ;\r
- int iconOffset = av.charHeight/2;\r
+ int j, x = 0, y = 0;\r
+ char[] lastSS = new char[aa.length];\r
+ int[] lastSSX = new int[aa.length];\r
+ int iconOffset = av.charHeight / 2;\r
boolean validRes = false;\r
//\u03B2 \u03B1\r
\r
- for(int i=0; i<aa.length; i++)\r
+ for (int i = 0; i < aa.length; i++)\r
{\r
AlignmentAnnotation row = aa[i];\r
- if(!row.visible)\r
+ if (!row.visible)\r
+ {\r
continue;\r
+ }\r
\r
- if(row.isGraph)\r
+ if (row.isGraph)\r
{\r
// this is so that we draw the characters below the graph\r
y += row.height;\r
- if(row.hasText)\r
+ if (row.hasText)\r
+ {\r
y -= av.charHeight;\r
+ }\r
+ }\r
+ if (row.hasText)\r
+ {\r
+ iconOffset = av.charHeight / 2;\r
}\r
- if(row.hasText)\r
- iconOffset = av.charHeight/2;\r
else\r
+ {\r
iconOffset = 0;\r
+ }\r
\r
- for(j=startRes; j<endRes; j++)\r
+ for (j = startRes; j < endRes; j++)\r
{\r
- if(row.annotations.length<=j || row.annotations[j]==null)\r
- validRes = false;\r
- else\r
- validRes = true;\r
-\r
- x = (j-startRes)*av.charWidth;\r
-\r
-\r
- if(activeRow==i)\r
- {\r
+ if (row.annotations.length <= j || row.annotations[j] == null)\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
\r
- g.setColor(Color.red);\r
+ x = (j - startRes) * av.charWidth;\r
\r
- if(activeRes!=null)\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.elementAt(n).toString()) ;\r
- if (v == j)\r
- g.fillRect( (j-startRes) * av.charWidth, y, av.charWidth, row.height);\r
- }\r
- }\r
+ if (activeRow == i)\r
+ {\r
\r
+ g.setColor(Color.red);\r
\r
+ if (activeRes != null)\r
+ {\r
+ for (int n = 0; n < activeRes.size(); n++)\r
+ {\r
+ int v = Integer.parseInt(activeRes.elementAt(n).toString());\r
+ if (v == j)\r
+ {\r
+ g.fillRect( (j - startRes) * av.charWidth, y, av.charWidth,\r
+ row.height);\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- if(validRes && row.annotations[j].displayCharacter.length()>0)\r
- {\r
- int charOffset = (av.charWidth - fm.charWidth(row.annotations[j].displayCharacter.charAt(0)))/2;\r
- g.setColor( row.annotations[j].colour);\r
- if(j==0)\r
+ if (validRes && row.annotations[j].displayCharacter.length() > 0)\r
+ {\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[j].displayCharacter.\r
+ charAt(0))) / 2;\r
+ g.setColor(row.annotations[j].colour);\r
+ if (j == 0)\r
{\r
if (row.annotations[0].secondaryStructure == 'H'\r
|| row.annotations[0].secondaryStructure == 'E')\r
+ {\r
g.drawString(row.annotations[j].displayCharacter, x,\r
y + iconOffset + 2);\r
+ }\r
}\r
- else if( (row.annotations[j].secondaryStructure=='H'\r
- || row.annotations[j].secondaryStructure=='E') &&\r
- (row.annotations[j-1]==null ||\r
- row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))\r
+ else if ( (row.annotations[j].secondaryStructure == 'H'\r
+ || row.annotations[j].secondaryStructure == 'E') &&\r
+ (row.annotations[j - 1] == null ||\r
+ row.annotations[j].secondaryStructure !=\r
+ row.annotations[j - 1].secondaryStructure))\r
+ {\r
\r
- g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
+ g.drawString(row.annotations[j].displayCharacter, x,\r
+ y + iconOffset + 2);\r
+ }\r
\r
- if(!row.hasIcons)\r
+ if (!row.hasIcons)\r
+ {\r
g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
y + iconOffset + 2);\r
- }\r
-\r
- if(row.hasIcons)\r
- if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
- g.fillPolygon(new int[] {x - 4, x- 4, x }\r
- , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
- break;\r
- case 'C':\r
- break;\r
- default :\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
- }\r
-\r
- if(validRes)\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
- else\r
- lastSS[i] = ' ';\r
- lastSSX[i] = x;\r
- }\r
-\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0,0,180));\r
- int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);\r
-\r
- if(row.windowLength>1)\r
- {\r
- int total =0;\r
- for(int i2=j- (row.windowLength/2); i2<j+(row.windowLength/2); i2++)\r
- {\r
- if(i2<0 || i2>=av.alignment.getWidth())\r
- continue;\r
-\r
- total += row.annotations[i2].value;\r
- }\r
-\r
- total/=row.windowLength;\r
- height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
-\r
- }\r
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y-height, av.charWidth, height );\r
- }\r
+ }\r
+ }\r
+\r
+ if (row.hasIcons)\r
+ {\r
+ if (!validRes || row.annotations[j].secondaryStructure != lastSS[i])\r
+ {\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i],\r
+ 7, 8, 8);\r
+ break;\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4,\r
+ 7);\r
+ g.fillPolygon(new int[]\r
+ {x - 4, x - 4, x}\r
+ , new int[]\r
+ {y + iconOffset, y + 14 + iconOffset,\r
+ y + 8 + iconOffset}, 3);\r
+ break;\r
+ case 'C':\r
+ break;\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
+ break;\r
+ }\r
+\r
+ if (validRes)\r
+ {\r
+ lastSS[i] = row.annotations[j].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS[i] = ' ';\r
+ }\r
+ lastSSX[i] = x;\r
+ }\r
+ }\r
+\r
+ if (validRes && row.isGraph)\r
+ {\r
+ g.setColor(new Color(0, 0, 180));\r
+ int height = (int) ( (row.annotations[j].value / row.graphMax) *\r
+ GRAPH_HEIGHT);\r
+\r
+ if (row.windowLength > 1)\r
+ {\r
+ int total = 0;\r
+ for (int i2 = j - (row.windowLength / 2);\r
+ i2 < j + (row.windowLength / 2); i2++)\r
+ {\r
+ if (i2 < 0 || i2 >= av.alignment.getWidth())\r
+ {\r
+ continue;\r
+ }\r
+\r
+ total += row.annotations[i2].value;\r
+ }\r
\r
+ total /= row.windowLength;\r
+ height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);\r
+\r
+ }\r
+ g.setColor(row.annotations[j].colour);\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ }\r
\r
}\r
\r
- x+=av.charWidth;\r
+ x += av.charWidth;\r
\r
- if(row.hasIcons)\r
- switch (lastSS[i])\r
+ if (row.hasIcons)\r
{\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4+ iconOffset, x - lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4+ iconOffset, x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x}\r
- , new int[]\r
- {y + iconOffset, y + 14+ iconOffset, y + 7+ iconOffset}\r
- , 3);\r
- break;\r
- case 'C':\r
- break;\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i], 7,\r
+ 8, 8);\r
+ break;\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ {x - 4, x - 4, x}\r
+ , new int[]\r
+ {y + iconOffset, y + 14 + iconOffset,\r
+ y + 7 + iconOffset}\r
+ , 3);\r
+ break;\r
+ case 'C':\r
+ break;\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
+ break;\r
\r
+ }\r
}\r
\r
- if(row.isGraph && row.hasText)\r
- y+=av.charHeight;\r
- if(!row.isGraph)\r
- y+=aa[i].height;\r
+ if (row.isGraph && row.hasText)\r
+ {\r
+ y += av.charHeight;\r
+ }\r
+ if (!row.isGraph)\r
+ {\r
+ y += aa[i].height;\r
+ }\r
}\r
}\r
\r
// used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\r
+ public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,width, y);\r
- g.setColor(new Color(0,0,180));\r
+ g.fillRect(0, 0, width, y);\r
+ g.setColor(new Color(0, 0, 180));\r
int x = 0;\r
- for(int j=0; j<aa.annotations.length; j++)\r
+ for (int j = 0; j < aa.annotations.length; j++)\r
{\r
g.setColor(new Color(0, 0, 180));\r
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );\r
+ int height = (int) ( (aa.annotations[j].value / aa.graphMax) *\r
+ GRAPH_HEIGHT);\r
g.fillRect(x, y - height, av.charWidth, height);\r
- x+=av.charWidth;\r
+ x += av.charWidth;\r
}\r
}\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
/**\r
* NOTE: Columns are zero based.\r
*/\r
-public class ColumnSelection{\r
+public class ColumnSelection\r
+{\r
Vector selected = new Vector();\r
\r
- public void addElement(int col) {\r
+ public void addElement(int col)\r
+ {\r
selected.addElement(new Integer(col));\r
}\r
\r
- public void clear() {\r
+ public void clear()\r
+ {\r
selected.removeAllElements();\r
}\r
\r
- public void removeElement(int col) {\r
+ public void removeElement(int col)\r
+ {\r
Integer colInt = new Integer(col);\r
- if (selected.contains(colInt)) {\r
+ if (selected.contains(colInt))\r
+ {\r
selected.removeElement(colInt);\r
- } else {\r
- System.err.println("WARNING: Tried to remove Integer NOT in ColumnSelection");\r
+ }\r
+ else\r
+ {\r
+ System.err.println(\r
+ "WARNING: Tried to remove Integer NOT in ColumnSelection");\r
}\r
}\r
\r
- public boolean contains(int col) {\r
+ public boolean contains(int col)\r
+ {\r
return selected.contains(new Integer(col));\r
}\r
\r
- public int columnAt(int i) {\r
- return ((Integer)selected.elementAt(i)).intValue();\r
+ public int columnAt(int i)\r
+ {\r
+ return ( (Integer) selected.elementAt(i)).intValue();\r
}\r
\r
- public int size() {\r
+ public int size()\r
+ {\r
return selected.size();\r
}\r
\r
- public int getMax() {\r
+ public int getMax()\r
+ {\r
int max = -1;\r
\r
- for (int i=0;i<selected.size();i++) {\r
- if (columnAt(i) > max) {\r
+ for (int i = 0; i < selected.size(); i++)\r
+ {\r
+ if (columnAt(i) > max)\r
+ {\r
max = columnAt(i);\r
}\r
}\r
return max;\r
}\r
\r
- public int getMin() {\r
+ public int getMin()\r
+ {\r
int min = 1000000000;\r
\r
- for (int i=0;i<selected.size();i++) {\r
- if (columnAt(i) < min) {\r
+ for (int i = 0; i < selected.size(); i++)\r
+ {\r
+ if (columnAt(i) < min)\r
+ {\r
min = columnAt(i);\r
}\r
}\r
return min;\r
}\r
\r
- public Vector asVector() {\r
+ public Vector asVector()\r
+ {\r
return selected;\r
}\r
\r
- public void compensateForEdit(int start, int change) {\r
- for (int i=0; i < size();i++) {\r
+ public void compensateForEdit(int start, int change)\r
+ {\r
+ for (int i = 0; i < size(); i++)\r
+ {\r
int temp = columnAt(i);\r
\r
if (temp >= start)\r
- selected.setElementAt(new Integer(temp-change),i);\r
+ {\r
+ selected.setElementAt(new Integer(temp - change), i);\r
+ }\r
}\r
}\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GCutAndPasteTransfer;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class CutAndPasteTransfer extends GCutAndPasteTransfer\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbappletgui.*;\r
+\r
+public class CutAndPasteTransfer\r
+ extends GCutAndPasteTransfer\r
{\r
public CutAndPasteTransfer(boolean forImport)\r
{\r
super();\r
\r
- if(!forImport)\r
+ if (!forImport)\r
{\r
buttonPanel.setVisible(false);\r
}\r
}\r
\r
-\r
public String getText()\r
{\r
return textarea.getText();\r
textarea.setText(text);\r
}\r
\r
-\r
protected void ok_actionPerformed(ActionEvent e)\r
{\r
String text = getText();\r
\r
Frame frame = (Frame)this.getParent();\r
frame.setVisible(false);\r
- }\r
-\r
- protected void cancel_actionPerformed(ActionEvent e) {\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
- }\r
-\r
-\r
+ }\r
\r
+ protected void cancel_actionPerformed(ActionEvent e)\r
+ {\r
+ Frame frame = (Frame)this.getParent();\r
+ frame.setVisible(false);\r
+ }\r
\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
import java.util.*;\r
\r
+import java.awt.*;\r
+\r
+import jalview.datamodel.*;\r
+\r
public class FeatureRenderer\r
{\r
AlignViewport av;\r
\r
SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
+ SequenceGroup[] allGroups = null;\r
Color resBoxColour;\r
Graphics graphics;\r
\r
this.av = av;\r
}\r
\r
-\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)\r
+ public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int x1, int y1, int width,\r
+ int height)\r
{\r
Vector features = seq.getSequenceFeatures();\r
Enumeration e = features.elements();\r
- while( e.hasMoreElements() )\r
+ while (e.hasMoreElements())\r
{\r
- SequenceFeature sf = (SequenceFeature)e.nextElement();\r
- if(sf.getStart()>seq.getEnd())\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ if (sf.getStart() > seq.getEnd())\r
+ {\r
continue;\r
+ }\r
\r
- int fstart = seq.findIndex(sf.getStart())-1;\r
- int fend = seq.findIndex(sf.getEnd())-1;\r
+ int fstart = seq.findIndex(sf.getStart()) - 1;\r
+ int fend = seq.findIndex(sf.getEnd()) - 1;\r
\r
- if( (fstart<=end && fend>=start) )\r
+ if ( (fstart <= end && fend >= start))\r
{\r
- if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
- fstart = 0;// but the feature end is still valid!!\r
+ if (fstart < 0) // fix for if the feature we have starts before the sequence start,\r
+ {\r
+ fstart = 0; // but the feature end is still valid!!\r
+ }\r
\r
- if(fstart==fend)\r
+ if (fstart == fend)\r
{\r
g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
+ g.fillRoundRect( (fstart - start) * width, y1, width, height, 4, 4);\r
g.setColor(Color.white);\r
\r
char s = seq.getSequence().charAt(fstart);\r
FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s))/2;\r
- int pady = height/5;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + width * (fstart - start),\r
+ y1 + height - pady);\r
\r
}\r
else\r
for (int i = fstart; i <= fend; i++)\r
{\r
char s = seq.getSequence().charAt(i);\r
- if( jalview.util.Comparison.isGap(s) )\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
continue;\r
+ }\r
\r
g.setColor(Color.blue);\r
- g.fillRect( (i-start) * width, y1, width, height);\r
+ g.fillRect( (i - start) * width, y1, width, height);\r
\r
g.setColor(Color.white);\r
\r
int charOffset = (width - fm.charWidth(s)) / 2;\r
int pady = height / 5;\r
g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i-start),\r
+ charOffset + x1 + width * (i - start),\r
y1 + height - pady);\r
}\r
}\r
}\r
\r
}\r
- }\r
+ }\r
\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GFinder;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
import java.util.*;\r
+\r
import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.jbappletgui.*;\r
\r
-public class Finder extends GFinder\r
+public class Finder\r
+ extends GFinder\r
{\r
AlignViewport av;\r
AlignmentPanel ap;\r
this.ap = ap;\r
frame = new Frame();\r
frame.add(this);\r
- jalview.bin.JalviewLite.addFrame(frame, "Find", 340,120);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);\r
frame.repaint();\r
frame.addWindowListener(new WindowAdapter()\r
- {public void windowClosing(WindowEvent evt)\r
- { ap.highlightSearchResults( null ); }\r
- });\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ ap.highlightSearchResults(null);\r
+ }\r
+ });\r
}\r
\r
public void textfield_actionPerformed(ActionEvent e)\r
\r
public void findAll_actionPerformed(ActionEvent e)\r
{\r
- resIndex=0;\r
- seqIndex=0;\r
+ resIndex = 0;\r
+ seqIndex = 0;\r
doSearch(true);\r
}\r
\r
public void cancel_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
// if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( null );\r
- ap.idPanel.highlightSearchResults( null );\r
- // frame.setClosed(true);\r
- }catch(Exception ex){ }\r
+ ap.highlightSearchResults(null);\r
+ ap.idPanel.highlightSearchResults(null);\r
+ // frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
}\r
\r
-\r
public void createNewGroup_actionPerformed(ActionEvent e)\r
{\r
- Color [] newColors = new Color[24];\r
- for(int i=0; i<24; i++)\r
- newColors[i] = new Color(60,160,115);\r
-\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
- String searchString = textfield.getText();\r
+ Color[] newColors = new Color[24];\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ newColors[i] = new Color(60, 160, 115);\r
+ }\r
\r
- searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(\r
+ newColors);\r
+ String searchString = textfield.getText();\r
\r
+ searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
\r
- for(int i=0; i<searchResults.size(); i+=3)\r
+ for (int i = 0; i < searchResults.size(); i += 3)\r
{\r
// its possible edits may have occurred since search was performed\r
// account for this here\r
\r
- SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );\r
- int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;\r
- int endRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;\r
+ SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(searchResults.\r
+ elementAt(i).toString()));\r
+ int startRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i +\r
+ 1).toString())) - 1;\r
+ int endRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + 2).\r
+ toString())) - 1;\r
\r
- SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes );\r
+ SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
+ startRes, endRes);\r
sg.addSequence(seq);\r
av.alignment.addGroup(sg);\r
- searchGroup.addGroup( sg );\r
+ searchGroup.addGroup(sg);\r
\r
}\r
\r
ap.av.alignment.addSuperGroup(searchGroup);\r
- ap.highlightSearchResults( null );\r
+ ap.highlightSearchResults(null);\r
}\r
\r
-\r
void doSearch(boolean findAll)\r
{\r
createNewGroup.setEnabled(false);\r
\r
String searchString = textfield.getText().toUpperCase();\r
\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
+ com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
\r
searchResults = new Vector();\r
- int [] allResults = null;\r
+ int[] allResults = null;\r
\r
Sequence seq;\r
- String item=null;\r
+ String item = null;\r
boolean found = false;\r
\r
////// is the searchString a residue number?\r
- try{\r
+ try\r
+ {\r
int res = Integer.parseInt(searchString);\r
found = true;\r
\r
- if(av.getSelectionGroup().getSize()>0)\r
- seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));\r
+ if (av.getSelectionGroup().getSize() > 0)\r
+ {\r
+ seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
+ }\r
else\r
- seq = (Sequence)av.getAlignment().getSequenceAt(0);\r
+ {\r
+ seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
+ }\r
\r
- searchResults.addElement( Integer.toString( av.getAlignment().findIndex(seq) ) );\r
- searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );\r
- searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );\r
+ searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));\r
+ searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));\r
+ searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));\r
\r
- }catch(NumberFormatException ex){}\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {}\r
///////////////////////////////////////////////\r
\r
\r
int end = av.alignment.getHeight();\r
\r
SequenceGroup selection = av.getSelectionGroup();\r
- if(selection!=null)\r
- if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))\r
- selection = null;\r
-\r
- while( !found && seqIndex<end)\r
+ if (selection != null)\r
{\r
- seq = (Sequence)av.alignment.getSequenceAt(seqIndex);\r
+ if (selection.getSize() < 1 ||\r
+ (selection.getEndRes() - selection.getStartRes() < 2))\r
+ {\r
+ selection = null;\r
+ }\r
+ }\r
\r
+ while (!found && seqIndex < end)\r
+ {\r
+ seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
\r
- if(selection!=null && !selection.sequences.contains(seq))\r
+ if (selection != null && !selection.sequences.contains(seq))\r
{\r
seqIndex++;\r
- resIndex=0;\r
+ resIndex = 0;\r
continue;\r
}\r
\r
item = seq.getSequence().toUpperCase();\r
\r
- if(selection!=null && selection.getEndRes()<av.alignment.getWidth())\r
- item = item.substring(0, selection.getEndRes()+1);\r
+ if (selection != null && selection.getEndRes() < av.alignment.getWidth())\r
+ {\r
+ item = item.substring(0, selection.getEndRes() + 1);\r
+ }\r
\r
///Shall we ignore gaps????\r
StringBuffer noGaps = new StringBuffer();\r
- int insertCount=0;\r
+ int insertCount = 0;\r
Vector spaces = new Vector();\r
\r
- for (int j=0; j < item.length(); j++)\r
+ for (int j = 0; j < item.length(); j++)\r
{\r
\r
- if(!jalview.util.Comparison.isGap(item.charAt(j)))\r
- {\r
- noGaps.append(item.charAt(j));\r
- spaces.addElement(new Integer(insertCount));\r
- }\r
+ if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
+ {\r
+ noGaps.append(item.charAt(j));\r
+ spaces.addElement(new Integer(insertCount));\r
+ }\r
else\r
- insertCount++;\r
+ {\r
+ insertCount++;\r
+ }\r
}\r
\r
-\r
-\r
- for(int r = resIndex; r<noGaps.length(); r++)\r
+ for (int r = resIndex; r < noGaps.length(); r++)\r
{\r
\r
- if( regex.searchFrom( noGaps.toString(), r ) )\r
- {\r
- resIndex = regex.matchedFrom();\r
- if(selection!=null && ( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) )<selection.getStartRes())\r
- continue;\r
-\r
- searchResults.addElement( Integer.toString( seqIndex) );\r
- int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );\r
- int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );\r
- searchResults.addElement( sres+"" );\r
- searchResults.addElement( eres+"" );\r
-\r
-\r
- if(!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
- break;\r
- }\r
-\r
- r=resIndex;\r
- }\r
+ if (regex.searchFrom(noGaps.toString(), r))\r
+ {\r
+ resIndex = regex.matchedFrom();\r
+ if (selection != null &&\r
+ (resIndex + Integer.parseInt(spaces.elementAt(resIndex).toString())) <\r
+ selection.getStartRes())\r
+ {\r
+ continue;\r
+ }\r
+\r
+ searchResults.addElement(Integer.toString(seqIndex));\r
+ int sres = seq.findPosition(resIndex +\r
+ Integer.parseInt(spaces.\r
+ elementAt(resIndex).toString()));\r
+ int eres = seq.findPosition(regex.matchedTo() - 1 +\r
+ Integer.parseInt(\r
+ spaces.elementAt(regex.matchedTo() - 1).\r
+ toString()));\r
+ searchResults.addElement(sres + "");\r
+ searchResults.addElement(eres + "");\r
+\r
+ if (!findAll)\r
+ {\r
+ // thats enough, break and display the result\r
+ found = true;\r
+ resIndex++;\r
+ break;\r
+ }\r
+\r
+ r = resIndex;\r
+ }\r
}\r
- if(!found)\r
+ if (!found)\r
{\r
seqIndex++;\r
resIndex = 0;\r
}\r
}\r
\r
-\r
Vector idMatch = new Vector();\r
- for(int id = 0; id<av.alignment.getHeight(); id++)\r
+ for (int id = 0; id < av.alignment.getHeight(); id++)\r
{\r
- if( regex.search( av.alignment.getSequenceAt(id).getName() ) )\r
- idMatch.addElement( av.alignment.getSequenceAt(id) );\r
+ if (regex.search(av.alignment.getSequenceAt(id).getName()))\r
+ {\r
+ idMatch.addElement(av.alignment.getSequenceAt(id));\r
+ }\r
}\r
\r
- if(searchResults.size()==0 && idMatch.size()>0)\r
- ap.idPanel.highlightSearchResults( idMatch );\r
-\r
+ if (searchResults.size() == 0 && idMatch.size() > 0)\r
+ {\r
+ ap.idPanel.highlightSearchResults(idMatch);\r
+ }\r
\r
- if(searchResults.size()>0)\r
+ if (searchResults.size() > 0)\r
{\r
allResults = new int[searchResults.size()];\r
- for(int i=0; i<searchResults.size(); i++)\r
+ for (int i = 0; i < searchResults.size(); i++)\r
+ {\r
allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());\r
+ }\r
\r
createNewGroup.setEnabled(true);\r
}\r
else\r
{\r
- resIndex=0;\r
- seqIndex=0;\r
+ resIndex = 0;\r
+ seqIndex = 0;\r
}\r
\r
// if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( allResults );\r
+ ap.highlightSearchResults(allResults);\r
\r
if (findAll)\r
{\r
- String message = (searchResults.size()/3) + " matches found.";\r
+ String message = (searchResults.size() / 3) + " matches found.";\r
System.out.println(message);\r
}\r
\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GFontChooser;\r
-import jalview.appletgui.*;\r
import java.awt.*;\r
-import java.awt.event.*;\r
\r
+import jalview.jbappletgui.*;\r
\r
-public class FontChooser extends GFontChooser\r
+public class FontChooser\r
+ extends GFontChooser\r
{\r
AlignmentPanel ap;\r
Font oldFont;\r
\r
this.ap = ap;\r
String fonts[] = Toolkit.getDefaultToolkit().getFontList();\r
- for(int i=0; i<fonts.length; i++)\r
+ for (int i = 0; i < fonts.length; i++)\r
+ {\r
fontName.addItem(fonts[i]);\r
+ }\r
\r
- for(int i=1; i<31; i++)\r
- fontSize.addItem(i+"");\r
+ for (int i = 1; i < 31; i++)\r
+ {\r
+ fontSize.addItem(i + "");\r
+ }\r
\r
- fontStyle.addItem("plain");\r
- fontStyle.addItem("bold");\r
- fontStyle.addItem("italic");\r
+ fontStyle.addItem("plain");\r
+ fontStyle.addItem("bold");\r
+ fontStyle.addItem("italic");\r
\r
- oldFont = ap.av.getFont();\r
- fontName.select(oldFont.getName());\r
- fontSize.select(oldFont.getSize()+"");\r
- fontStyle.select(oldFont.getStyle());\r
+ oldFont = ap.av.getFont();\r
+ fontName.select(oldFont.getName());\r
+ fontSize.select(oldFont.getSize() + "");\r
+ fontStyle.select(oldFont.getStyle());\r
\r
- init = false;\r
+ init = false;\r
}\r
\r
protected void ok_actionPerformed()\r
{\r
- frame.setVisible(false);\r
- if(ap.getOverviewPanel()!=null)\r
- ap.getOverviewPanel().updateOverviewImage();\r
+ frame.setVisible(false);\r
+ if (ap.getOverviewPanel() != null)\r
+ {\r
+ ap.getOverviewPanel().updateOverviewImage();\r
+ }\r
}\r
\r
protected void cancel_actionPerformed()\r
ap.av.setFont(oldFont);\r
ap.repaint();\r
fontName.select(oldFont.getName());\r
- fontSize.select(oldFont.getSize()+"");\r
+ fontSize.select(oldFont.getSize() + "");\r
fontStyle.select(oldFont.getStyle());\r
\r
frame.setVisible(false);\r
{\r
Font newFont = new Font(fontName.getSelectedItem().toString(),\r
fontStyle.getSelectedIndex(),\r
- Integer.parseInt(fontSize.getSelectedItem().toString())\r
- );\r
+ Integer.parseInt(fontSize.getSelectedItem().\r
+ toString())\r
+ );\r
ap.av.setFont(newFont);\r
ap.fontChanged();\r
}\r
\r
-\r
protected void fontName_actionPerformed()\r
{\r
- if(init) return;\r
+ if (init)\r
+ {\r
+ return;\r
+ }\r
changeFont();\r
}\r
\r
protected void fontSize_actionPerformed()\r
{\r
- if(init) return;\r
+ if (init)\r
+ {\r
+ return;\r
+ }\r
changeFont();\r
}\r
\r
protected void fontStyle_actionPerformed()\r
{\r
- if(init) return;\r
+ if (init)\r
+ {\r
+ return;\r
+ }\r
changeFont();\r
}\r
\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
-import jalview.datamodel.*;\r
+\r
import jalview.analysis.*;\r
-public class IdCanvas extends Panel\r
+import jalview.datamodel.*;\r
+\r
+public class IdCanvas\r
+ extends Panel\r
{\r
protected AlignViewport av;\r
\r
- protected boolean showScores = true;\r
+ protected boolean showScores = true;\r
\r
- protected int maxIdLength = -1;\r
- protected String maxIdStr = null;\r
+ protected int maxIdLength = -1;\r
+ protected String maxIdStr = null;\r
Image image;\r
Graphics gg;\r
- int imgHeight=0;\r
+ int imgHeight = 0;\r
boolean fastPaint = false;\r
\r
java.util.Vector searchResults;\r
public IdCanvas(AlignViewport av)\r
{\r
setLayout(null);\r
- this.av = av;\r
+ this.av = av;\r
PaintRefresher.Register(this);\r
}\r
\r
- public void drawIdString(Graphics gg,SequenceI s,int i, int starty, int ypos) {\r
- int charHeight = av.getCharHeight();\r
+ public void drawIdString(Graphics gg, SequenceI s, int i, int starty,\r
+ int ypos)\r
+ {\r
+ int charHeight = av.getCharHeight();\r
\r
- if(searchResults!=null && searchResults.contains(s))\r
- {\r
- gg.setColor(Color.black);\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);\r
- gg.setColor(Color.white);\r
- }\r
- else if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {\r
- gg.setColor(Color.lightGray);\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);\r
- gg.setColor(Color.white);\r
- } else {\r
- gg.setColor(s.getColor());\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);\r
- gg.setColor(Color.black);\r
- }\r
+ if (searchResults != null && searchResults.contains(s))\r
+ {\r
+ gg.setColor(Color.black);\r
+ gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
+ getSize().width, charHeight);\r
+ gg.setColor(Color.white);\r
+ }\r
+ else if (av.getSelectionGroup() != null &&\r
+ av.getSelectionGroup().sequences.contains(s))\r
+ {\r
+ gg.setColor(Color.lightGray);\r
+ gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
+ getSize().width, charHeight);\r
+ gg.setColor(Color.white);\r
+ }\r
+ else\r
+ {\r
+ gg.setColor(s.getColor());\r
+ gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
+ getSize().width, charHeight);\r
+ gg.setColor(Color.black);\r
+ }\r
\r
- String string = s.getName();\r
- if(av.getShowFullId())\r
- string = s.getDisplayId();\r
+ String string = s.getName();\r
+ if (av.getShowFullId())\r
+ {\r
+ string = s.getDisplayId();\r
+ }\r
\r
- gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight- (charHeight/5));\r
+ gg.drawString(string, 0,\r
+ AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +\r
+ charHeight - (charHeight / 5));\r
\r
}\r
\r
public void fastPaint(int vertical)\r
{\r
- if(gg==null)\r
- { repaint(); return;}\r
+ if (gg == null)\r
+ {\r
+ repaint();\r
+ return;\r
+ }\r
\r
- gg.copyArea( 0,0, getSize().width, imgHeight, 0, -vertical*av.charHeight );\r
+ gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);\r
\r
- int ss=av.startSeq, es=av.endSeq, transY = 0;\r
+ int ss = av.startSeq, es = av.endSeq, transY = 0;\r
if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\r
- if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time\r
- ss = av.startSeq;\r
- else\r
- transY = imgHeight - vertical * av.charHeight;\r
- }\r
- else if (vertical < 0)\r
- {\r
- es = ss - vertical;\r
- if(es > av.endSeq)\r
- es = av.endSeq;\r
- }\r
-\r
-\r
-\r
- gg.translate(0, transY);\r
+ {\r
+ ss = es - vertical;\r
+ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time\r
+ {\r
+ ss = av.startSeq;\r
+ }\r
+ else\r
+ {\r
+ transY = imgHeight - vertical * av.charHeight;\r
+ }\r
+ }\r
+ else if (vertical < 0)\r
+ {\r
+ es = ss - vertical;\r
+ if (es > av.endSeq)\r
+ {\r
+ es = av.endSeq;\r
+ }\r
+ }\r
\r
- drawIds(ss, es);\r
+ gg.translate(0, transY);\r
\r
- gg.translate( 0, -transY );\r
+ drawIds(ss, es);\r
\r
+ gg.translate(0, -transY);\r
\r
- fastPaint = true;\r
- repaint();\r
+ fastPaint = true;\r
+ repaint();\r
}\r
\r
public void update(Graphics g)\r
{\r
paint(g);\r
}\r
+\r
public void paint(Graphics g)\r
{\r
- if(getSize().height<0 || getSize().width<0)\r
+ if (getSize().height < 0 || getSize().width < 0)\r
+ {\r
return;\r
+ }\r
if (fastPaint)\r
{\r
fastPaint = false;\r
imgHeight = getSize().height;\r
imgHeight -= imgHeight % av.charHeight;\r
\r
- if (imgHeight<1)\r
+ if (imgHeight < 1)\r
+ {\r
return;\r
+ }\r
\r
- if(image==null || imgHeight!=image.getHeight(this))\r
+ if (image == null || imgHeight != image.getHeight(this))\r
{\r
image = createImage(getSize().width, imgHeight);\r
gg = image.getGraphics();\r
gg.setFont(av.getFont());\r
}\r
\r
- //Fill in the background\r
- gg.setColor(Color.white);\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+ //Fill in the background\r
+ gg.setColor(Color.white);\r
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
av.getFont().getSize());\r
- gg.setFont(italic);\r
+ gg.setFont(italic);\r
\r
gg.fillRect(0, 0, getSize().width, getSize().height);\r
- drawIds( av.getStartSeq(), av.endSeq);\r
+ drawIds(av.getStartSeq(), av.endSeq);\r
g.drawImage(image, 0, 0, this);\r
}\r
\r
void drawIds(int starty, int endy)\r
{\r
- Color currentColor = Color.white;\r
+ Color currentColor = Color.white;\r
Color currentTextColor = Color.black;\r
\r
if (av.getWrapAlignment())\r
{\r
\r
- int rowSize = av.getEndRes() - av.getStartRes();\r
- // Draw the rest of the panels\r
-\r
- for(int ypos=2*av.charHeight, row=av.startRes;\r
- ypos <= getSize().height && row<av.alignment.getWidth();\r
- ypos += av.chunkHeight, row+=rowSize )\r
- {\r
- for (int i = starty; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- drawIdString(gg, s, i, 0, ypos);\r
- }\r
- }\r
+ int rowSize = av.getEndRes() - av.getStartRes();\r
+ // Draw the rest of the panels\r
\r
+ for (int ypos = 2 * av.charHeight, row = av.startRes;\r
+ ypos <= getSize().height && row < av.alignment.getWidth();\r
+ ypos += av.chunkHeight, row += rowSize)\r
+ {\r
+ for (int i = starty; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ drawIdString(gg, s, i, 0, ypos);\r
+ }\r
+ }\r
\r
- } else\r
+ }\r
+ else\r
{\r
\r
//Now draw the id strings\r
{\r
// Selected sequence colours\r
\r
- if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ if (searchResults != null &&\r
+ searchResults.contains(av.alignment.getSequenceAt(i)))\r
{\r
gg.setColor(Color.black);\r
currentColor = Color.black;\r
currentTextColor = Color.white;\r
- }\r
- else if (av.getSelectionGroup()!= null\r
- && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))\r
+ }\r
+ else if (av.getSelectionGroup() != null\r
+ &&\r
+ av.getSelectionGroup().sequences.contains(av.alignment.\r
+ getSequenceAt(i)))\r
{\r
currentColor = Color.lightGray;\r
currentTextColor = Color.black;\r
\r
gg.setColor(currentTextColor);\r
String string = av.alignment.getSequenceAt(i).getName();\r
- if(av.getShowFullId())\r
+ if (av.getShowFullId())\r
+ {\r
string = av.alignment.getSequenceAt(i).getDisplayId();\r
+ }\r
gg.drawString(string, 0,\r
AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +\r
av.charHeight - (av.charHeight / 5));\r
\r
// add a border\r
gg.setColor(Color.white);\r
- gg.fillRect(getSize().width-4,0,4,getSize().height);\r
+ gg.fillRect(getSize().width - 4, 0, 4, getSize().height);\r
}\r
\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
\r
import jalview.datamodel.*;\r
\r
-public class IdPanel extends Panel implements MouseListener, MouseMotionListener {\r
+public class IdPanel\r
+ extends Panel implements MouseListener, MouseMotionListener\r
+{\r
\r
- protected IdCanvas idCanvas;\r
- protected AlignViewport av;\r
+ protected IdCanvas idCanvas;\r
+ protected AlignViewport av;\r
protected AlignmentPanel alignPanel;\r
ScrollThread scrollThread = null;\r
\r
- int offy;\r
- int width;\r
+ int offy;\r
+ int width;\r
int lastid = -1;\r
boolean mouseDragging = false;\r
\r
public IdPanel(AlignViewport av, AlignmentPanel parent)\r
{\r
- this.av = av;\r
+ this.av = av;\r
alignPanel = parent;\r
idCanvas = new IdCanvas(av);\r
setLayout(new BorderLayout());\r
idCanvas.addMouseMotionListener(this);\r
}\r
\r
- public void mouseMoved(MouseEvent e) {}\r
+ public void mouseMoved(MouseEvent e)\r
+ {}\r
\r
-\r
- public void mouseDragged(MouseEvent e) {\r
+ public void mouseDragged(MouseEvent e)\r
+ {\r
mouseDragging = true;\r
\r
int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y -= 2 * av.charHeight;\r
+ }\r
int seq = av.getIndex(y);\r
\r
- if(seq<0)\r
+ if (seq < 0)\r
+ {\r
return;\r
+ }\r
\r
if (seq < lastid)\r
+ {\r
selectSeqs(lastid - 1, seq);\r
+ }\r
else if (seq > lastid)\r
+ {\r
selectSeqs(lastid + 1, seq);\r
+ }\r
\r
lastid = seq;\r
alignPanel.repaint();\r
{\r
if (e.getClickCount() == 2)\r
{\r
- int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
-\r
- int seq = av.getIndex(y);\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
-\r
- try{\r
- jalview.bin.JalviewLite.showURL(\r
- "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +\r
- "]+-vn+2");\r
- }catch(Exception ex){ex.printStackTrace();}\r
+ int y = e.getY();\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y -= 2 * av.charHeight;\r
+ }\r
+\r
+ int seq = av.getIndex(y);\r
+ String id = av.getAlignment().getSequenceAt(seq).getName();\r
+\r
+ try\r
+ {\r
+ jalview.bin.JalviewLite.showURL(\r
+ "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +\r
+ "]+-vn+2");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
\r
}\r
+\r
public void mouseEntered(MouseEvent e)\r
{\r
- if(scrollThread!=null)\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
}\r
\r
- public void mouseExited (MouseEvent e)\r
+ public void mouseExited(MouseEvent e)\r
{\r
- if(av.getWrapAlignment())\r
+ if (av.getWrapAlignment())\r
+ {\r
return;\r
+ }\r
\r
- if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)\r
+ if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)\r
{\r
scrollThread = new ScrollThread(true);\r
}\r
\r
- if(mouseDragging && e.getY()>=getSize().height && av.alignment.getHeight()>av.getEndSeq())\r
+ if (mouseDragging && e.getY() >= getSize().height &&\r
+ av.alignment.getHeight() > av.getEndSeq())\r
{\r
scrollThread = new ScrollThread(false);\r
}\r
}\r
\r
-\r
- public void mousePressed(MouseEvent e) {\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
if (e.getClickCount() == 2)\r
+ {\r
return;\r
+ }\r
\r
int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y -= 2 * av.charHeight;\r
+ }\r
\r
int seq = av.getIndex(y);\r
if (seq == -1)\r
+ {\r
return;\r
+ }\r
\r
- if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)\r
+ if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
+ InputEvent.BUTTON3_MASK)\r
{\r
APopupMenu popup = new APopupMenu(alignPanel, null);\r
this.add(popup);\r
return;\r
}\r
\r
-\r
- if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)\r
+ if (!e.isControlDown() && !e.isShiftDown() &&\r
+ av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null)\r
{\r
\r
SequenceGroup selection = new SequenceGroup();\r
SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));\r
selection.setStartRes(0);\r
- selection.setEndRes(av.alignment.getWidth()-1);\r
- for (int i =0; i< sg.getSize(); i++)\r
+ selection.setEndRes(av.alignment.getWidth() - 1);\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
selection.addSequence(sg.getSequenceAt(i));\r
+ }\r
\r
av.setSelectionGroup(selection);\r
return;\r
}\r
\r
- if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))\r
+ if (av.getSelectionGroup() == null ||\r
+ (!e.isControlDown() && av.getSelectionGroup() != null))\r
+ {\r
av.setSelectionGroup(new SequenceGroup());\r
+ }\r
\r
av.getSelectionGroup().setStartRes(0);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);\r
+ av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);\r
\r
- if(e.isShiftDown() && lastid!=-1)\r
+ if (e.isShiftDown() && lastid != -1)\r
+ {\r
selectSeqs(lastid, seq);\r
+ }\r
else\r
+ {\r
selectSeq(seq);\r
+ }\r
\r
alignPanel.repaint();\r
}\r
av.getSelectionGroup().addOrRemove(pickedSeq);\r
}\r
\r
- void selectSeqs(int start, int end) {\r
+ void selectSeqs(int start, int end)\r
+ {\r
\r
lastid = start;\r
if (end < start)\r
- {\r
- int tmp = start;\r
- start = end;\r
- end = tmp;\r
- lastid = end;\r
- }\r
-\r
- for (int i = start; i <= end; i++)\r
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));\r
+ {\r
+ int tmp = start;\r
+ start = end;\r
+ end = tmp;\r
+ lastid = end;\r
+ }\r
\r
- }\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));\r
+ }\r
\r
+ }\r
\r
public void mouseReleased(MouseEvent e)\r
{\r
- if(scrollThread!=null)\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
\r
mouseDragging = false;\r
PaintRefresher.Refresh(this);\r
}\r
\r
- public void highlightSearchResults( java.util.Vector found )\r
+ public void highlightSearchResults(java.util.Vector found)\r
{\r
- idCanvas.setHighlighted( found );\r
+ idCanvas.setHighlighted(found);\r
\r
- if(found == null)\r
+ if (found == null)\r
+ {\r
return;\r
+ }\r
\r
- int index = av.alignment.findIndex( (SequenceI)found.elementAt(0));\r
+ int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));\r
\r
// do we need to scroll the panel?\r
- if(av.getStartSeq()>index || av.getEndSeq()<index)\r
- alignPanel.setScrollValues( av.getStartRes(), index);\r
+ if (av.getStartSeq() > index || av.getEndSeq() < index)\r
+ {\r
+ alignPanel.setScrollValues(av.getStartRes(), index);\r
+ }\r
}\r
\r
// this class allows scrolling off the bottom of the visible alignment\r
running = true;\r
while (running)\r
{\r
- if(alignPanel.scrollUp(up))\r
+ if (alignPanel.scrollUp(up))\r
{\r
// scroll was ok, so add new sequence to selection\r
int seq = av.getStartSeq();\r
- if(!up)\r
+ if (!up)\r
+ {\r
seq = av.getEndSeq();\r
+ }\r
\r
if (seq < lastid)\r
+ {\r
selectSeqs(lastid - 1, seq);\r
+ }\r
else if (seq > lastid)\r
+ {\r
selectSeqs(lastid + 1, seq);\r
+ }\r
\r
lastid = seq;\r
}\r
else\r
+ {\r
running = false;\r
+ }\r
\r
alignPanel.repaint();\r
try\r
{}\r
}\r
}\r
-}\r
+ }\r
\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
\r
-\r
-public class IdwidthAdjuster extends Panel implements MouseListener, MouseMotionListener\r
+public class IdwidthAdjuster\r
+ extends Panel implements MouseListener, MouseMotionListener\r
{\r
boolean active = false;\r
- int oldX=0;\r
+ int oldX = 0;\r
Image image;\r
- AlignmentPanel ap ;\r
+ AlignmentPanel ap;\r
\r
public IdwidthAdjuster(AlignmentPanel ap)\r
{\r
setLayout(null);\r
this.ap = ap;\r
java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
- if (url != null)\r
- image = java.awt.Toolkit.getDefaultToolkit().getImage(url);\r
+ if (url != null)\r
+ {\r
+ image = java.awt.Toolkit.getDefaultToolkit().getImage(url);\r
+ }\r
\r
addMouseListener(this);\r
addMouseMotionListener(this);\r
}\r
\r
public void mousePressed(MouseEvent evt)\r
- { oldX = evt.getX(); }\r
+ {\r
+ oldX = evt.getX();\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ active = false;\r
+ repaint();\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ active = true;\r
+ repaint();\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ active = false;\r
+ repaint();\r
+ }\r
\r
- public void mouseReleased(MouseEvent evt){ active = false; repaint(); }\r
- public void mouseEntered(MouseEvent evt) { active = true; repaint();}\r
- public void mouseExited(MouseEvent evt) { active = false; repaint();}\r
public void mouseDragged(MouseEvent evt)\r
{\r
active = true;\r
Dimension d = ap.idPanel.idCanvas.getSize();\r
int dif = evt.getX() - oldX;\r
\r
- if(d.width+dif>20 || dif>0)\r
+ if (d.width + dif > 20 || dif > 0)\r
{\r
- ap.setIdWidth(d.width + dif,d.height);\r
+ ap.setIdWidth(d.width + dif, d.height);\r
this.setSize(d.width + dif, getSize().height);\r
}\r
\r
oldX = evt.getX();\r
}\r
\r
- public void mouseMoved(MouseEvent evt) {}\r
- public void mouseClicked(MouseEvent evt) {}\r
+ public void mouseMoved(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {}\r
\r
public void paint(Graphics g)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0, getSize().width, getSize().height);\r
- if(active)\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ if (active)\r
{\r
- if(image!=null)\r
- g.drawImage(image, getSize().width-20, 2, this);\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, getSize().width - 20, 2, this);\r
+ }\r
}\r
}\r
\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
\r
-public class OverviewPanel extends Panel implements Runnable\r
+public class OverviewPanel\r
+ extends Panel implements Runnable\r
{\r
Image miniMe;\r
AlignViewport av;\r
float scaleh = 1f;\r
\r
public int width, sequencesHeight;\r
- int graphHeight=30;\r
- int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;\r
+ int graphHeight = 30;\r
+ int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;\r
\r
boolean resizing = false;\r
\r
nullFrame.addNotify();\r
\r
// scale the initial size of overviewpanel to shape of alignment\r
- float initialScale = (float)av.alignment.getWidth()/(float)av.alignment.getHeight();\r
- if(av.alignment.getWidth() > av.alignment.getHeight())\r
+ float initialScale = (float) av.alignment.getWidth() /\r
+ (float) av.alignment.getHeight();\r
+ if (av.alignment.getWidth() > av.alignment.getHeight())\r
{\r
// wider\r
width = 400;\r
- sequencesHeight = (int)(400f/initialScale);\r
+ sequencesHeight = (int) (400f / initialScale);\r
}\r
else\r
{\r
// taller\r
- width = (int)(400f*initialScale);\r
+ width = (int) (400f * initialScale);\r
sequencesHeight = 300;\r
- if(width<120)\r
+ if (width < 120)\r
+ {\r
width = 120;\r
+ }\r
}\r
\r
- setSize (new Dimension(width, sequencesHeight+graphHeight));\r
+ setSize(new Dimension(width, sequencesHeight + graphHeight));\r
addComponentListener(new ComponentAdapter()\r
- {\r
+ {\r
\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- if( getSize().width!=width || getSize().height!=sequencesHeight+graphHeight)\r
- {\r
- updateOverviewImage();\r
- }\r
- }\r
- });\r
+ public void componentResized(ComponentEvent evt)\r
+ {\r
+ if (getSize().width != width ||\r
+ getSize().height != sequencesHeight + graphHeight)\r
+ {\r
+ updateOverviewImage();\r
+ }\r
+ }\r
+ });\r
\r
addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- { doMouseDragged(evt);}\r
- });\r
+ {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ doMouseDragged(evt);\r
+ }\r
+ });\r
\r
addMouseListener(new MouseAdapter()\r
{\r
public void mousePressed(MouseEvent evt)\r
- { doMousePressed(evt);}\r
+ {\r
+ doMousePressed(evt);\r
+ }\r
+\r
public void mouseReleased(MouseEvent evt)\r
- { doMouseReleased(evt);}\r
+ {\r
+ doMouseReleased(evt);\r
+ }\r
});\r
\r
updateOverviewImage();\r
boxX = evt.getX();\r
boxY = evt.getY();\r
checkValid();\r
- if(!resizing)\r
- ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),\r
- (int)(boxY/scaleh/av.getCharHeight()) );\r
+ if (!resizing)\r
+ {\r
+ ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
+ (int) (boxY / scaleh / av.getCharHeight()));\r
+ }\r
}\r
\r
public void doMouseDragged(MouseEvent evt)\r
boxX = evt.getX();\r
boxY = evt.getY();\r
checkValid();\r
- if(!resizing)\r
- ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),\r
- (int)(boxY/scaleh/av.getCharHeight()) );\r
+ if (!resizing)\r
+ {\r
+ ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
+ (int) (boxY / scaleh / av.getCharHeight()));\r
+ }\r
repaint();\r
ap.repaint();\r
}\r
void checkValid()\r
{\r
if (boxY < 0)\r
+ {\r
boxY = 0;\r
+ }\r
\r
if (boxY > sequencesHeight - boxHeight)\r
- boxY = sequencesHeight - boxHeight+1;\r
+ {\r
+ boxY = sequencesHeight - boxHeight + 1;\r
+ }\r
\r
if (boxX < 0)\r
+ {\r
boxX = 0;\r
+ }\r
\r
if (boxX > width - boxWidth)\r
+ {\r
boxX = width - boxWidth;\r
+ }\r
}\r
\r
public void updateOverviewImage()\r
{\r
- if(resizing)\r
+ if (resizing)\r
{\r
return;\r
}\r
int alwidth = av.alignment.getWidth();\r
int alheight = av.alignment.getHeight();\r
\r
- if(getSize().width>0 && getSize().height>0)\r
+ if (getSize().width > 0 && getSize().height > 0)\r
{\r
width = getSize().width;\r
sequencesHeight = getSize().height - graphHeight;\r
}\r
\r
- setSize (new Dimension(width, sequencesHeight+graphHeight));\r
+ setSize(new Dimension(width, sequencesHeight + graphHeight));\r
\r
- int fullsizeWidth = alwidth * av.getCharWidth();\r
+ int fullsizeWidth = alwidth * av.getCharWidth();\r
int fullsizeHeight = alheight * av.getCharHeight();\r
\r
scalew = (float) width / (float) fullsizeWidth;\r
Graphics g = consensus.getGraphics();\r
ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);\r
mg.drawImage(consensus, 0, sequencesHeight, width,\r
- sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
-\r
+ sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
\r
boolean oldRenderGaps = av.renderGaps;\r
- try{\r
- // We'll have to draw the full size alignment in chunks, as an image of the\r
- // whole alignment requires too much memory\r
+ try\r
+ {\r
+ // We'll have to draw the full size alignment in chunks, as an image of the\r
+ // whole alignment requires too much memory\r
\r
// Max size depends on the font size, the following is a\r
// guess at a size which works\r
- int maxSize = 2000 / av.getFont().getSize();\r
+ int maxSize = 2000 / av.getFont().getSize();\r
Image block;\r
- int blockx=0, blocky=0, blockw=0, blockh=0, eRes=0, eSeq=0;\r
+ int blockx = 0, blocky = 0, blockw = 0, blockh = 0, eRes = 0, eSeq = 0;\r
\r
av.setRenderGaps(false);\r
- for(int sRes=0, chunkx=0; sRes<alwidth; sRes+=maxSize, chunkx++)\r
+ for (int sRes = 0, chunkx = 0; sRes < alwidth; sRes += maxSize, chunkx++)\r
{\r
- eSeq = 0;\r
- eRes+=maxSize;\r
- if(eRes>alwidth)\r
- eRes = alwidth;\r
-\r
- for(int sSeq=0, chunky=0; sSeq<alheight; sSeq+=maxSize, chunky++)\r
+ eSeq = 0;\r
+ eRes += maxSize;\r
+ if (eRes > alwidth)\r
+ {\r
+ eRes = alwidth;\r
+ }\r
+\r
+ for (int sSeq = 0, chunky = 0; sSeq < alheight; sSeq += maxSize, chunky++)\r
+ {\r
+ eSeq += maxSize;\r
+ if (eSeq > alheight)\r
{\r
- eSeq+=maxSize;\r
- if(eSeq>alheight)\r
- eSeq = alheight;\r
+ eSeq = alheight;\r
+ }\r
\r
- blocky = 0;\r
- blockx = (int)((float)sRes/(float)alwidth * width);\r
+ blocky = 0;\r
+ blockx = (int) ( (float) sRes / (float) alwidth * width);\r
\r
- block = nullFrame.createImage((eRes-sRes)*av.charWidth, (eSeq-sSeq)*av.charHeight);\r
- g = block.getGraphics();\r
+ block = nullFrame.createImage( (eRes - sRes) * av.charWidth,\r
+ (eSeq - sSeq) * av.charHeight);\r
+ g = block.getGraphics();\r
\r
- ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);\r
+ ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq,\r
+ 0);\r
\r
- blockh = (int)( (float)(eSeq-sSeq)/(float)alheight * sequencesHeight )+1 ;\r
- blockw = (int)( (float)(eRes-sRes)/(float)alwidth * width )+1;\r
+ blockh = (int) ( (float) (eSeq - sSeq) / (float) alheight *\r
+ sequencesHeight) + 1;\r
+ blockw = (int) ( (float) (eRes - sRes) / (float) alwidth * width) + 1;\r
\r
- blocky += (int) ((float)sSeq/(float)alheight* sequencesHeight);\r
+ blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);\r
\r
- mg.drawImage(block, blockx,\r
- blocky ,\r
- blockx + blockw,\r
- blocky + blockh,\r
+ mg.drawImage(block, blockx,\r
+ blocky,\r
+ blockx + blockw,\r
+ blocky + blockh,\r
\r
- 0, 0, block.getWidth(null),block.getHeight(null), this);\r
+ 0, 0, block.getWidth(null), block.getHeight(null), this);\r
\r
block = null;\r
- }\r
+ }\r
\r
}\r
\r
- }catch(OutOfMemoryError error)\r
- { System.err.println("Out of memory when trying to calculate the overview window image!"); }\r
-\r
+ }\r
+ catch (OutOfMemoryError error)\r
+ {\r
+ System.err.println(\r
+ "Out of memory when trying to calculate the overview window image!");\r
+ }\r
\r
av.setRenderGaps(oldRenderGaps);\r
resizing = false;\r
\r
public void setBoxPosition()\r
{\r
- boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
- boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
- boxWidth = (int) ((av.getEndRes()-av.getStartRes()+1)* av.getCharWidth() * scalew) ;\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;\r
- repaint();\r
+ boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
+ boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
+ boxWidth = (int) ( (av.getEndRes() - av.getStartRes() + 1) *\r
+ av.getCharWidth() * scalew);\r
+ boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;\r
+ repaint();\r
}\r
\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
+ public void update(Graphics g)\r
+ {\r
+ paint(g);\r
+ }\r
\r
public void paint(Graphics g)\r
{\r
- if(resizing)\r
+ if (resizing)\r
{\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getSize().width, getSize().height);\r
g.setColor(Color.black);\r
\r
g.setFont(new Font("Verdana", Font.BOLD, 15));\r
- g.drawString("Recalculating", 5, sequencesHeight/2);\r
- g.drawString("Overview.....", 5, sequencesHeight/2 +20);\r
+ g.drawString("Recalculating", 5, sequencesHeight / 2);\r
+ g.drawString("Overview.....", 5, sequencesHeight / 2 + 20);\r
}\r
else\r
{\r
- if(miniMe!=null)\r
- g.drawImage(miniMe, 0,0,this);\r
+ if (miniMe != null)\r
+ {\r
+ g.drawImage(miniMe, 0, 0, this);\r
+ }\r
\r
g.setColor(Color.red);\r
g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2);\r
+ g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
}\r
}\r
\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.PCA;\r
-import jalview.jbappletgui.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.jbappletgui.*;\r
\r
-public class PCAPanel extends GPCAPanel implements Runnable\r
+public class PCAPanel\r
+ extends GPCAPanel implements Runnable\r
{\r
PCA pca;\r
int top;\r
// do stuff\r
}\r
\r
- public PCAPanel(AlignViewport av, SequenceI[] s) {\r
+ public PCAPanel(AlignViewport av, SequenceI[] s)\r
+ {\r
\r
this.av = av;\r
- if(av.getSelectionGroup().getSize()>3)\r
+ if (av.getSelectionGroup().getSize() > 3)\r
{\r
s = new Sequence[av.getSelectionGroup().getSize()];\r
- for(int i=0; i<s.length; i++)\r
+ for (int i = 0; i < s.length; i++)\r
+ {\r
s[i] = av.getSelectionGroup().getSequenceAt(i);\r
+ }\r
}\r
\r
-\r
- if(s==null)\r
+ if (s == null)\r
{\r
s = new Sequence[av.getAlignment().getHeight()];\r
for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
s[i] = av.getAlignment().getSequenceAt(i);\r
- }\r
+ }\r
+ }\r
\r
//////////////////////This part was done in PCATHread originally. Is it too slow???\r
pca = new PCA(s);\r
pca.run();\r
\r
// Now find the component coordinates\r
- int ii=0;\r
+ int ii = 0;\r
while (ii < s.length && s[ii] != null)\r
{\r
ii++;\r
\r
double[][] comps = new double[ii][ii];\r
\r
- for (int i=0; i < ii; i++ )\r
+ for (int i = 0; i < ii; i++)\r
{\r
if (pca.getEigenvalue(i) > 1e-4)\r
{\r
- comps[i] = pca.component(i);\r
+ comps[i] = pca.component(i);\r
}\r
}\r
\r
yCombobox.select(1);\r
zCombobox.select(2);\r
\r
- top = pca.getM().rows-1;\r
+ top = pca.getM().rows - 1;\r
\r
Vector points = new Vector();\r
- float[][] scores = pca.getComponents(top-1,top-2,top-3,100);\r
+ float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);\r
\r
- for (int i =0; i < pca.getM().rows; i++ )\r
+ for (int i = 0; i < pca.getM().rows; i++)\r
{\r
- SequencePoint sp = new SequencePoint(s[i],scores[i]);\r
+ SequencePoint sp = new SequencePoint(s[i], scores[i]);\r
points.addElement(sp);\r
}\r
\r
- rc = new RotatableCanvas(av,points,pca.getM().rows);\r
+ rc = new RotatableCanvas(av, points, pca.getM().rows);\r
\r
//rc.printPoints();\r
\r
add(rc, BorderLayout.CENTER);\r
}\r
\r
-\r
void doDimensionChange()\r
{\r
- if(top==0)\r
+ if (top == 0)\r
+ {\r
return;\r
+ }\r
\r
int dim1 = top - xCombobox.getSelectedIndex();\r
int dim2 = top - yCombobox.getSelectedIndex();\r
int dim3 = top - zCombobox.getSelectedIndex();\r
\r
- float[][] scores = pca.getComponents(dim1,dim2,dim3,100);\r
- for (int i=0; i < pca.getM().rows; i++) {\r
- ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];\r
+ float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);\r
+ for (int i = 0; i < pca.getM().rows; i++)\r
+ {\r
+ ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];\r
}\r
\r
rc.img = null;\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
-import java.awt.*;\r
+\r
import java.util.*;\r
\r
+import java.awt.*;\r
+\r
public class PaintRefresher\r
{\r
static Vector components = new Vector();\r
\r
public static void Register(Component c)\r
{\r
- if(!components.contains(c))\r
+ if (!components.contains(c))\r
+ {\r
components.addElement(c);\r
+ }\r
else\r
+ {\r
components.removeElement(c);\r
+ }\r
}\r
\r
public static void Refresh(Component c)\r
{\r
Component temp;\r
Enumeration e = components.elements();\r
- while( e.hasMoreElements() )\r
+ while (e.hasMoreElements())\r
{\r
- temp = (Component)e.nextElement();\r
+ temp = (Component) e.nextElement();\r
\r
- if(!temp.isValid())\r
- components.removeElement( temp );\r
- else if( temp == c )\r
- continue;\r
+ if (!temp.isValid())\r
+ {\r
+ components.removeElement(temp);\r
+ }\r
+ else if (temp == c)\r
+ {\r
+ continue;\r
+ }\r
\r
temp.repaint();\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.jbappletgui.GPairwiseAlignPanel;\r
-import jalview.analysis.*;\r
-import java.awt.event.*;\r
import java.util.*;\r
\r
+import java.awt.event.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.jbappletgui.*;\r
\r
-public class PairwiseAlignPanel extends GPairwiseAlignPanel\r
+public class PairwiseAlignPanel\r
+ extends GPairwiseAlignPanel\r
{\r
- Vector sequences = new Vector();\r
- AlignViewport av;\r
+ Vector sequences = new Vector();\r
+ AlignViewport av;\r
\r
- public PairwiseAlignPanel(AlignViewport av)\r
+ public PairwiseAlignPanel(AlignViewport av)\r
+ {\r
+ super();\r
+ this.av = av;\r
+ float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().\r
+ getHeight()];\r
+ double totscore = 0;\r
+ int count = av.getSelectionGroup().getSize();\r
+\r
+ int acount = 0;\r
+ for (int i = 1; i < count; i++)\r
{\r
- super();\r
- this.av = av;\r
- float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];\r
- double totscore = 0;\r
- int count = av.getSelectionGroup().getSize();\r
-\r
- int acount = 0;\r
- for (int i = 1; i < count; i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- acount++;\r
- AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
- av.getSelectionGroup().getSequenceAt(j),"pep");\r
-\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
- scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length;\r
- totscore = totscore + scores[i][j];\r
+ for (int j = 0; j < i; j++)\r
+ {\r
+ acount++;\r
+ AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
+ av.getSelectionGroup().getSequenceAt(j),\r
+ "pep");\r
+\r
+ as.calcScoreMatrix();\r
+ as.traceAlignment();\r
+ as.printAlignment();\r
+ scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
+ totscore = totscore + scores[i][j];\r
+\r
+ textarea.append(as.getOutput());\r
+ sequences.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));\r
+ sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));\r
\r
- textarea.append(as.getOutput());\r
- sequences.addElement( new Sequence( as.getS1().getName(), as.getAStr1()) );\r
- sequences.addElement( new Sequence( as.getS2().getName(), as.getAStr2()) );\r
-\r
-\r
- }\r
- }\r
+ }\r
+ }\r
\r
- if (count > 2)\r
+ if (count > 2)\r
+ {\r
+ for (int i = 0; i < count; i++)\r
+ {\r
+ for (int j = 0; j < i; j++)\r
{\r
- for (int i = 0; i < count;i++)\r
- for (int j = 0; j < i; j++)\r
- jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);\r
+ jalview.util.Format.print(System.out, "%7.3f",\r
+ scores[i][j] / totscore);\r
}\r
}\r
-\r
+ }\r
+ }\r
\r
protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
{\r
\r
- Sequence [] seq = new Sequence[sequences.size()];\r
-\r
- for (int i=0;i<sequences.size();i++)\r
- seq[i] = (Sequence) sequences.elementAt(i);\r
+ Sequence[] seq = new Sequence[sequences.size()];\r
\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ seq[i] = (Sequence) sequences.elementAt(i);\r
+ }\r
\r
- AlignFrame af = new AlignFrame(new Alignment(seq));\r
- jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
+ AlignFrame af = new AlignFrame(new Alignment(seq));\r
+ jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
\r
}\r
\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.*;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
import java.util.*;\r
\r
-public class RedundancyPanel extends GSliderPanel\r
+import java.awt.event.*;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.jbappletgui.*;\r
+\r
+public class RedundancyPanel\r
+ extends GSliderPanel\r
{\r
AlignmentPanel ap;\r
\r
SequenceI[] oldAlignment;\r
\r
-\r
public RedundancyPanel(AlignmentPanel ap)\r
{\r
this.ap = ap;\r
{\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
+ valueField.setText(slider.getValue() + "");\r
}\r
});\r
\r
slider.setMinimum(0);\r
slider.setMaximum(100);\r
- slider.setValue(100 );\r
+ slider.setValue(100);\r
\r
}\r
\r
public void applyButton_actionPerformed(ActionEvent e)\r
{\r
- float threshold = slider.getValue();\r
- Vector del;\r
+ float threshold = slider.getValue();\r
+ Vector del;\r
+\r
+ oldAlignment = new SequenceI[ap.av.alignment.getHeight()];\r
+ for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
+ {\r
+ oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),\r
+ ap.av.alignment.getSequenceAt(i).\r
+ getSequence());\r
+ }\r
+\r
+ undoButton.setEnabled(true);\r
+\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg != null && sg.getSize() > 1)\r
+ {\r
\r
- oldAlignment = new SequenceI[ap.av.alignment.getHeight()];\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
+ del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
{\r
- oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),\r
- ap.av.alignment.getSequenceAt(i).\r
- getSequence());\r
+ sg.deleteSequence( (SequenceI) del.elementAt(i));\r
}\r
+ }\r
\r
- undoButton.setEnabled(true);\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg != null && sg.getSize() > 1)\r
- {\r
-\r
- del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
- for (int i = 0; i < del.size(); i++)\r
- if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
- sg.deleteSequence( (SequenceI) del.elementAt(i));\r
-\r
- }\r
- else\r
- {\r
- Vector s = new Vector();\r
- int i=0;\r
- while(i < ap.av.alignment.getHeight())\r
- {\r
- s.addElement( ap.av.alignment.getSequenceAt(i) );\r
- i++;\r
- }\r
- del = ap.av.alignment.removeRedundancy(threshold,s);\r
- for (int j=0; j < del.size(); j++)\r
- {\r
- if (sg.sequences.contains((SequenceI)del.elementAt(j)))\r
- sg.deleteSequence((SequenceI)del.elementAt(j));\r
-\r
- }\r
- }\r
-\r
- ap.repaint();\r
+ }\r
+ else\r
+ {\r
+ Vector s = new Vector();\r
+ int i = 0;\r
+ while (i < ap.av.alignment.getHeight())\r
+ {\r
+ s.addElement(ap.av.alignment.getSequenceAt(i));\r
+ i++;\r
+ }\r
+ del = ap.av.alignment.removeRedundancy(threshold, s);\r
+ for (int j = 0; j < del.size(); j++)\r
+ {\r
+ if (sg.sequences.contains( (SequenceI) del.elementAt(j)))\r
+ {\r
+ sg.deleteSequence( (SequenceI) del.elementAt(j));\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ ap.repaint();\r
\r
}\r
\r
public void undoButton_actionPerformed(ActionEvent e)\r
{\r
- undoButton.setEnabled(false);\r
- ap.av.setAlignment( new Alignment(oldAlignment) );\r
- oldAlignment = null;\r
- ap.repaint();\r
+ undoButton.setEnabled(false);\r
+ ap.av.setAlignment(new Alignment(oldAlignment));\r
+ oldAlignment = null;\r
+ ap.repaint();\r
}\r
\r
-\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
int i = Integer.parseInt(valueField.getText());\r
slider.setValue(i);\r
}\r
- catch(Exception ex)\r
+ catch (Exception ex)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
+ valueField.setText(slider.getValue() + "");\r
}\r
}\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.math.*;\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
+import java.util.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.math.*;\r
+import jalview.util.*;\r
\r
-public class RotatableCanvas extends Panel implements MouseListener,\r
- MouseMotionListener,\r
- KeyListener\r
- //RubberbandListener,\r
- //SequenceSelectionListener\r
+public class RotatableCanvas\r
+ extends Panel implements MouseListener,\r
+ MouseMotionListener,\r
+ KeyListener\r
+//RubberbandListener,\r
+//SequenceSelectionListener\r
{\r
- RotatableMatrix idmat = new RotatableMatrix(3,3);\r
- RotatableMatrix objmat = new RotatableMatrix(3,3);\r
- RotatableMatrix rotmat = new RotatableMatrix(3,3);\r
+ RotatableMatrix idmat = new RotatableMatrix(3, 3);\r
+ RotatableMatrix objmat = new RotatableMatrix(3, 3);\r
+ RotatableMatrix rotmat = new RotatableMatrix(3, 3);\r
\r
//RubberbandRectangle rubberband;\r
\r
\r
\r
public RotatableCanvas(AlignViewport av,\r
- Vector points, int npoint) {\r
+ Vector points, int npoint)\r
+ {\r
this.points = points;\r
this.npoint = npoint;\r
this.av = av;\r
prefsize = getPreferredSize();\r
orig = new float[npoint][3];\r
\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- for (int j=0; j < 3; j++) {\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
orig[i][j] = sp.coord[j];\r
}\r
}\r
//Initialize the matrices to identity\r
\r
- for (int i = 0; i < 3; i++) {\r
- for (int j = 0; j < 3 ; j++) {\r
- if (i != j) {\r
- idmat.addElement(i,j,0);\r
- objmat.addElement(i,j,0);\r
- rotmat.addElement(i,j,0);\r
- } else {\r
- idmat.addElement(i,j,0);\r
- objmat.addElement(i,j,0);\r
- rotmat.addElement(i,j,0);\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
+ if (i != j)\r
+ {\r
+ idmat.addElement(i, j, 0);\r
+ objmat.addElement(i, j, 0);\r
+ rotmat.addElement(i, j, 0);\r
+ }\r
+ else\r
+ {\r
+ idmat.addElement(i, j, 0);\r
+ objmat.addElement(i, j, 0);\r
+ rotmat.addElement(i, j, 0);\r
}\r
}\r
}\r
\r
addMouseListener(this);\r
addKeyListener(this);\r
- // if (getParent() != null) {\r
- // getParent().addKeyListener(this);\r
+ // if (getParent() != null) {\r
+ // getParent().addKeyListener(this);\r
//}\r
addMouseMotionListener(this);\r
\r
// Add rubberband\r
- // rubberband = new RubberbandRectangle(this);\r
- // rubberband.setActive(true);\r
- // rubberband.addListener(this);\r
+ // rubberband = new RubberbandRectangle(this);\r
+ // rubberband.setActive(true);\r
+ // rubberband.addListener(this);\r
}\r
\r
- /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {\r
- redrawneeded = true;\r
- repaint();\r
- return true;\r
- }\r
+ /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {\r
+ redrawneeded = true;\r
+ repaint();\r
+ return true;\r
+ }\r
\r
- public void removeNotify() {\r
- controller.removeListener(this);\r
- super.removeNotify();\r
- }*/\r
+ public void removeNotify() {\r
+ controller.removeListener(this);\r
+ super.removeNotify();\r
+ }*/\r
\r
- public void initAxes() {\r
- for (int i = 0; i < 3; i++) {\r
- for (int j=0; j < 3; j++) {\r
- if (i != j) {\r
+ public void initAxes()\r
+ {\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
+ if (i != j)\r
+ {\r
axes[i][j] = 0;\r
- } else {\r
+ }\r
+ else\r
+ {\r
axes[i][j] = 1;\r
}\r
}\r
}\r
}\r
\r
- public void findWidth() {\r
+ public void findWidth()\r
+ {\r
max = new float[3];\r
min = new float[3];\r
\r
- max[0] = (float)-1e30;\r
- max[1] = (float)-1e30;\r
- max[2] = (float)-1e30;\r
+ max[0] = (float) - 1e30;\r
+ max[1] = (float) - 1e30;\r
+ max[2] = (float) - 1e30;\r
\r
- min[0] = (float)1e30;\r
- min[1] = (float)1e30;\r
- min[2] = (float)1e30;\r
+ min[0] = (float) 1e30;\r
+ min[1] = (float) 1e30;\r
+ min[2] = (float) 1e30;\r
\r
- for (int i = 0; i < 3; i++) {\r
- for (int j = 0; j < npoint; j++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(j);\r
- if (sp.coord[i] >= max[i]) {\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ for (int j = 0; j < npoint; j++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(j);\r
+ if (sp.coord[i] >= max[i])\r
+ {\r
max[i] = sp.coord[i];\r
}\r
- if (sp.coord[i] <= min[i]) {\r
+ if (sp.coord[i] <= min[i])\r
+ {\r
min[i] = sp.coord[i];\r
}\r
}\r
maxwidth = width[0];\r
\r
if (width[1] > width[0])\r
+ {\r
maxwidth = width[1];\r
+ }\r
if (width[2] > width[1])\r
+ {\r
maxwidth = width[2];\r
+ }\r
\r
//System.out.println("Maxwidth = " + maxwidth);\r
}\r
\r
- public float findScale() {\r
+ public float findScale()\r
+ {\r
int dim, width, height;\r
- if (getSize().width != 0) {\r
+ if (getSize().width != 0)\r
+ {\r
width = getSize().width;\r
height = getSize().height;\r
- } else {\r
+ }\r
+ else\r
+ {\r
width = prefsize.width;\r
height = prefsize.height;\r
}\r
\r
- if (width < height) {\r
+ if (width < height)\r
+ {\r
dim = width;\r
- } else {\r
+ }\r
+ else\r
+ {\r
dim = height;\r
}\r
\r
- return (float)(dim*scalefactor/(2*maxwidth));\r
+ return (float) (dim * scalefactor / (2 * maxwidth));\r
}\r
\r
- public void findCentre() {\r
+ public void findCentre()\r
+ {\r
//Find centre coordinate\r
findWidth();\r
\r
- centre[0] = (max[0] + min[0])/2;\r
- centre[1] = (max[1] + min[1])/2;\r
- centre[2] = (max[2] + min[2])/2;\r
+ centre[0] = (max[0] + min[0]) / 2;\r
+ centre[1] = (max[1] + min[1]) / 2;\r
+ centre[2] = (max[2] + min[2]) / 2;\r
\r
// System.out.println("Centre x " + centre[0]);\r
//System.out.println("Centre y " + centre[1]);\r
//System.out.println("Centre z " + centre[2]);\r
}\r
\r
- public Dimension getPreferredSize() {\r
- if (prefsize != null) {\r
+ public Dimension getPreferredSize()\r
+ {\r
+ if (prefsize != null)\r
+ {\r
return prefsize;\r
- } else {\r
- return new Dimension(400,400);\r
+ }\r
+ else\r
+ {\r
+ return new Dimension(400, 400);\r
}\r
}\r
\r
- public Dimension getMinimumSize() {\r
+ public Dimension getMinimumSize()\r
+ {\r
return getPreferredSize();\r
}\r
\r
- public void paint(Graphics g) {\r
+ public void paint(Graphics g)\r
+ {\r
//Only create the image at the beginning -\r
- if ((img == null) || (prefsize.width != getSize().width) || (prefsize.height != getSize().height)) {\r
+ if ( (img == null) || (prefsize.width != getSize().width) ||\r
+ (prefsize.height != getSize().height))\r
+ {\r
prefsize.width = getSize().width;\r
prefsize.height = getSize().height;\r
\r
scale = findScale();\r
\r
// System.out.println("New scale = " + scale);\r
- img = createImage(getSize().width,getSize().height);\r
+ img = createImage(getSize().width, getSize().height);\r
ig = img.getGraphics();\r
\r
}\r
\r
+ drawBackground(ig, Color.black);\r
+ drawScene(ig);\r
+ if (drawAxes == true)\r
+ {\r
+ drawAxes(ig);\r
+ }\r
\r
- drawBackground(ig,Color.black);\r
- drawScene(ig);\r
- if (drawAxes == true)\r
- {\r
- drawAxes(ig);\r
- }\r
-\r
-\r
- g.drawImage(img,0,0,this);\r
+ g.drawImage(img, 0, 0, this);\r
}\r
\r
- public void drawAxes(Graphics g) {\r
+ public void drawAxes(Graphics g)\r
+ {\r
\r
g.setColor(Color.yellow);\r
- for (int i=0; i < 3 ; i++) {\r
- g.drawLine(getSize().width/2,getSize().height/2,\r
- (int)(axes[i][0]*scale*max[0] + getSize().width/2),\r
- (int)(axes[i][1]*scale*max[1] + getSize().height/2));\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ g.drawLine(getSize().width / 2, getSize().height / 2,\r
+ (int) (axes[i][0] * scale * max[0] + getSize().width / 2),\r
+ (int) (axes[i][1] * scale * max[1] + getSize().height / 2));\r
}\r
}\r
\r
- public void drawBackground(Graphics g, Color col) {\r
+ public void drawBackground(Graphics g, Color col)\r
+ {\r
g.setColor(col);\r
- g.fillRect(0,0,prefsize.width,prefsize.height);\r
+ g.fillRect(0, 0, prefsize.width, prefsize.height);\r
}\r
\r
-\r
- public void drawScene(Graphics g) {\r
+ public void drawScene(Graphics g)\r
+ {\r
boolean darker = false;\r
\r
- int halfwidth = getSize().width/2;\r
- int halfheight = getSize().height/2;\r
+ int halfwidth = getSize().width / 2;\r
+ int halfheight = getSize().height / 2;\r
\r
- for (int i = 0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- int x = (int)((float)(sp.coord[0] - centre[0])*scale) + halfwidth;\r
- int y = (int)((float)(sp.coord[1] - centre[1])*scale) + halfheight;\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ int x = (int) ( (float) (sp.coord[0] - centre[0]) * scale) + halfwidth;\r
+ int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;\r
float z = sp.coord[1] - centre[2];\r
\r
-\r
-\r
-\r
if (sp.sequence.getColor() == Color.black)\r
- g.setColor(Color.white);\r
+ {\r
+ g.setColor(Color.white);\r
+ }\r
else\r
- g.setColor(sp.sequence.getColor());\r
-\r
+ {\r
+ g.setColor(sp.sequence.getColor());\r
+ }\r
\r
if (av.getSelectionGroup() != null)\r
{\r
- if (av.getSelectionGroup().sequences.contains(((SequencePoint)points.elementAt(i)).sequence))\r
+ if (av.getSelectionGroup().sequences.contains( ( (SequencePoint) points.\r
+ elementAt(i)).sequence))\r
+ {\r
g.setColor(Color.gray);\r
+ }\r
}\r
if (z < 0)\r
+ {\r
g.setColor(g.getColor().darker());\r
+ }\r
\r
-\r
- g.fillRect(x-3,y-3,6,6);\r
+ g.fillRect(x - 3, y - 3, 6, 6);\r
g.setColor(Color.red);\r
}\r
// //Now the rectangle\r
// }\r
}\r
\r
- public Dimension minimumsize() {\r
+ public Dimension minimumsize()\r
+ {\r
return prefsize;\r
}\r
\r
- public Dimension preferredsize() {\r
+ public Dimension preferredsize()\r
+ {\r
return prefsize;\r
}\r
\r
- public void keyTyped(KeyEvent evt) { }\r
- public void keyReleased(KeyEvent evt) { }\r
+ public void keyTyped(KeyEvent evt)\r
+ {}\r
\r
- public void keyPressed(KeyEvent evt) {\r
+ public void keyReleased(KeyEvent evt)\r
+ {}\r
+\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
requestFocus();\r
- if (evt.getKeyCode() == KeyEvent.VK_UP) {\r
- scalefactor = (float)(scalefactor * 1.1);\r
+ if (evt.getKeyCode() == KeyEvent.VK_UP)\r
+ {\r
+ scalefactor = (float) (scalefactor * 1.1);\r
scale = findScale();\r
- } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {\r
- scalefactor = (float)(scalefactor * 0.9);\r
+ }\r
+ else if (evt.getKeyCode() == KeyEvent.VK_DOWN)\r
+ {\r
+ scalefactor = (float) (scalefactor * 0.9);\r
scale = findScale();\r
- } else if (evt.getKeyChar() == 's') {\r
+ }\r
+ else if (evt.getKeyChar() == 's')\r
+ {\r
System.err.println("DEBUG: Rectangle selection"); // log.debug\r
- if (rectx2 != -1 && recty2 != -1) {\r
- rectSelect(rectx1,recty1,rectx2,recty2);\r
+ if (rectx2 != -1 && recty2 != -1)\r
+ {\r
+ rectSelect(rectx1, recty1, rectx2, recty2);\r
\r
}\r
}\r
repaint();\r
}\r
\r
- public void printPoints() {\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- Format.print(System.out,"%5d ", i);\r
- for (int j=0; j < 3;j++) {\r
- Format.print(System.out,"%13.3f ",sp.coord[j]);\r
+ public void printPoints()\r
+ {\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ Format.print(System.out, "%5d ", i);\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
+ Format.print(System.out, "%13.3f ", sp.coord[j]);\r
}\r
System.out.println();\r
}\r
}\r
\r
- public void mouseClicked(MouseEvent evt) { }\r
- public void mouseEntered(MouseEvent evt) { }\r
- public void mouseExited(MouseEvent evt) { }\r
- public void mouseReleased(MouseEvent evt) { }\r
+ public void mouseClicked(MouseEvent evt)\r
+ {}\r
\r
- public void mousePressed(MouseEvent evt) {\r
+ public void mouseEntered(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {}\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
int x = evt.getX();\r
int y = evt.getY();\r
\r
rectx2 = -1;\r
recty2 = -1;\r
\r
- SequenceI found = findPoint(x,y);\r
+ SequenceI found = findPoint(x, y);\r
\r
if (found != null)\r
{\r
}\r
else\r
{\r
- av.setSelectionGroup(new SequenceGroup());\r
- av.getSelectionGroup().addOrRemove(found);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth());\r
+ av.setSelectionGroup(new SequenceGroup());\r
+ av.getSelectionGroup().addOrRemove(found);\r
+ av.getSelectionGroup().setEndRes(av.alignment.getWidth());\r
\r
}\r
}\r
repaint();\r
}\r
\r
- // private void fireSequenceSelectionEvent(Selection sel) {\r
- // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));\r
+ // private void fireSequenceSelectionEvent(Selection sel) {\r
+ // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));\r
//}\r
\r
public void mouseMoved(MouseEvent evt)\r
{\r
- // SequenceI found = findPoint(evt.getX(), evt.getY());\r
+ // SequenceI found = findPoint(evt.getX(), evt.getY());\r
}\r
\r
- public void mouseDragged(MouseEvent evt) {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
mx = evt.getX();\r
my = evt.getY();\r
//Check if this is a rectangle drawing drag\r
- if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0) {\r
+ if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)\r
+ {\r
// rectx2 = evt.getX();\r
// recty2 = evt.getY();\r
- } else {\r
+ }\r
+ else\r
+ {\r
rotmat.setIdentity();\r
\r
- rotmat.rotate((float)(my-omy),'x');\r
- rotmat.rotate((float)(mx-omx),'y');\r
+ rotmat.rotate( (float) (my - omy), 'x');\r
+ rotmat.rotate( (float) (mx - omx), 'y');\r
\r
- for (int i = 0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
sp.coord[0] -= centre[0];\r
sp.coord[1] -= centre[1];\r
sp.coord[2] -= centre[2];\r
\r
//Now apply the rotation matrix\r
- sp.coord= rotmat.vectorMultiply(sp.coord);\r
+ sp.coord = rotmat.vectorMultiply(sp.coord);\r
\r
//Now translate back again\r
sp.coord[0] += centre[0];\r
sp.coord[2] += centre[2];\r
}\r
\r
- for (int i=0; i < 3; i++) {\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
axes[i] = rotmat.vectorMultiply(axes[i]);\r
}\r
omx = mx;\r
\r
}\r
\r
- public void rectSelect(int x1, int y1, int x2, int y2) {\r
+ public void rectSelect(int x1, int y1, int x2, int y2)\r
+ {\r
boolean changedSel = false;\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- int tmp1 = (int)((sp.coord[0] - centre[0])*scale + (float)getSize().width/2.0);\r
- int tmp2 = (int)((sp.coord[1] - centre[1])*scale + (float)getSize().height/2.0);\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ int tmp1 = (int) ( (sp.coord[0] - centre[0]) * scale +\r
+ (float) getSize().width / 2.0);\r
+ int tmp2 = (int) ( (sp.coord[1] - centre[1]) * scale +\r
+ (float) getSize().height / 2.0);\r
\r
- if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) {\r
- if (av != null) {\r
+ if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)\r
+ {\r
+ if (av != null)\r
+ {\r
if (!av.getSelectionGroup().sequences.contains(sp.sequence))\r
{\r
changedSel = true;\r
}\r
}\r
}\r
- // if (changedSel) {\r
- // fireSequenceSelectionEvent(av.getSelection());\r
- // }\r
+ // if (changedSel) {\r
+ // fireSequenceSelectionEvent(av.getSelection());\r
+ // }\r
}\r
- public SequenceI findPoint(int x, int y) {\r
\r
- int halfwidth = getSize().width/2;\r
- int halfheight = getSize().height/2;\r
+ public SequenceI findPoint(int x, int y)\r
+ {\r
+\r
+ int halfwidth = getSize().width / 2;\r
+ int halfheight = getSize().height / 2;\r
\r
int found = -1;\r
\r
- for (int i=0; i < npoint; i++) {\r
-\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- int px = (int)((float)(sp.coord[0] - centre[0])*scale) + halfwidth;\r
- int py = (int)((float)(sp.coord[1] - centre[1])*scale) + halfheight;\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) + halfwidth;\r
+ int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;\r
\r
- if (Math.abs(px-x)<3 && Math.abs(py - y) < 3 ) {\r
+ if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)\r
+ {\r
found = i;\r
}\r
}\r
- if (found != -1) {\r
- return ((SequencePoint)points.elementAt(found)).sequence;\r
- } else {\r
+ if (found != -1)\r
+ {\r
+ return ( (SequencePoint) points.elementAt(found)).sequence;\r
+ }\r
+ else\r
+ {\r
return null;\r
}\r
}\r
-/* public boolean handleRubberbandEvent(RubberbandEvent evt) {\r
- System.out.println("Rubberband handler called in RotatableCanvas with " +\r
- evt.getBounds());\r
+ /* public boolean handleRubberbandEvent(RubberbandEvent evt) {\r
+ System.out.println("Rubberband handler called in RotatableCanvas with " +\r
+ evt.getBounds());\r
\r
- Rubberband rb = (Rubberband)evt.getSource();\r
+ Rubberband rb = (Rubberband)evt.getSource();\r
\r
- // Clear the current selection (instance variable)\r
- //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {\r
- // clearSelection();\r
- //}\r
+ // Clear the current selection (instance variable)\r
+ //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {\r
+ // clearSelection();\r
+ //}\r
\r
- if (rb.getComponent() == this) {\r
- Rectangle bounds = evt.getBounds();\r
- rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);\r
- }\r
+ if (rb.getComponent() == this) {\r
+ Rectangle bounds = evt.getBounds();\r
+ rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);\r
+ }\r
\r
- redrawneeded = true;\r
- paint(this.getGraphics());\r
+ redrawneeded = true;\r
+ paint(this.getGraphics());\r
\r
- return true;\r
- }*/\r
+ return true;\r
+ }*/\r
\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class ScalePanel extends Panel\r
+import jalview.datamodel.*;\r
+\r
+public class ScalePanel\r
+ extends Panel\r
{\r
\r
protected int offy = 4;\r
- public int width;\r
+ public int width;\r
\r
protected AlignViewport av;\r
AlignmentPanel ap;\r
public ScalePanel(AlignViewport av, AlignmentPanel ap)\r
{\r
setLayout(null);\r
- this.av = av;\r
+ this.av = av;\r
this.ap = ap;\r
\r
addMouseListener(new MouseAdapter()\r
{\r
doMousePressed(evt);\r
}\r
+\r
public void mouseReleased(MouseEvent evt)\r
{\r
doMouseReleased(evt);\r
\r
}\r
\r
-\r
- public void doMousePressed(MouseEvent evt) {\r
+ public void doMousePressed(MouseEvent evt)\r
+ {\r
int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
+ int res = x / av.getCharWidth() + av.getStartRes();\r
SequenceGroup sg = null;\r
\r
if (av.getColumnSelection().contains(res))\r
+ {\r
av.getColumnSelection().removeElement(res);\r
+ }\r
else\r
{\r
av.getColumnSelection().addElement(res);\r
\r
sg = new SequenceGroup();\r
for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
+ {\r
sg.addSequence(av.alignment.getSequenceAt(i));\r
+ }\r
\r
sg.setStartRes(res);\r
sg.setEndRes(res);\r
\r
public void doMouseReleased(MouseEvent evt)\r
{\r
- if(!stretchingGroup)\r
+ if (!stretchingGroup)\r
+ {\r
return;\r
+ }\r
\r
int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
+ int res = x / av.getCharWidth() + av.getStartRes();\r
\r
- if (! av.getColumnSelection().contains(res))\r
- av.getColumnSelection().addElement(res);\r
+ if (!av.getColumnSelection().contains(res))\r
+ {\r
+ av.getColumnSelection().addElement(res);\r
+ }\r
\r
- SequenceGroup sg = av.getSelectionGroup();\r
+ SequenceGroup sg = av.getSelectionGroup();\r
\r
- if(res>sg.getStartRes())\r
- sg.setEndRes(res);\r
- else if(res<sg.getStartRes())\r
- sg.setStartRes(res);\r
+ if (res > sg.getStartRes())\r
+ {\r
+ sg.setEndRes(res);\r
+ }\r
+ else if (res < sg.getStartRes())\r
+ {\r
+ sg.setStartRes(res);\r
+ }\r
\r
- stretchingGroup = false;\r
- ap.repaint();\r
+ stretchingGroup = false;\r
+ ap.repaint();\r
}\r
\r
public void doMouseDragged(MouseEvent evt)\r
{\r
int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
+ int res = x / av.getCharWidth() + av.getStartRes();\r
\r
SequenceGroup sg = av.getSelectionGroup();\r
- if(sg!=null)\r
+ if (sg != null)\r
{\r
stretchingGroup = true;\r
if (res > sg.getStartRes())\r
+ {\r
sg.setEndRes(res);\r
+ }\r
else if (res < sg.getStartRes())\r
+ {\r
sg.setStartRes(res);\r
+ }\r
\r
- ap.annotationPanel.addEditableColumn(res);\r
+ ap.annotationPanel.addEditableColumn(res);\r
ap.repaint();\r
}\r
}\r
\r
public void paint(Graphics g)\r
{\r
- drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width, getSize().height);\r
+ drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,\r
+ getSize().height);\r
}\r
\r
// scalewidth will normally be screenwidth,\r
- public void drawScale(Graphics gg, int startx, int endx, int width, int height)\r
+ public void drawScale(Graphics gg, int startx, int endx, int width,\r
+ int height)\r
{\r
gg.setFont(av.getFont());\r
\r
//Fill in the background\r
gg.setColor(Color.white);\r
- gg.fillRect(0,0,width, height);\r
+ gg.fillRect(0, 0, width, height);\r
gg.setColor(Color.black);\r
\r
-\r
//Fill the selected columns\r
ColumnSelection cs = av.getColumnSelection();\r
- gg.setColor(new Color(220,0,0));\r
- for (int i=0; i<cs.size(); i++)\r
+ gg.setColor(new Color(220, 0, 0));\r
+ for (int i = 0; i < cs.size(); i++)\r
{\r
- int sel = cs.columnAt(i);\r
- if ( sel >= startx && sel <= endx)\r
- gg.fillRect((sel-startx)*av.charWidth,0,av.charWidth, getSize().height);\r
+ int sel = cs.columnAt(i);\r
+ if (sel >= startx && sel <= endx)\r
+ {\r
+ gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,\r
+ getSize().height);\r
+ }\r
}\r
\r
-\r
// Draw the scale numbers\r
gg.setColor(Color.black);\r
- int scalestartx = (startx/10) * 10;\r
+ int scalestartx = (startx / 10) * 10;\r
\r
FontMetrics fm = gg.getFontMetrics(av.getFont());\r
- int y = av.charHeight -fm.getDescent();\r
+ int y = av.charHeight - fm.getDescent();\r
\r
- if(scalestartx%10==0)\r
- scalestartx+=5;\r
+ if (scalestartx % 10 == 0)\r
+ {\r
+ scalestartx += 5;\r
+ }\r
\r
- for (int i=scalestartx;i < endx; i+= 5)\r
+ for (int i = scalestartx; i < endx; i += 5)\r
{\r
- if(i%10==0)\r
+ if (i % 10 == 0)\r
{\r
gg.drawString(String.valueOf(i), (i - startx - 1) * av.charWidth, y);\r
gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y+2,\r
+ y + 2,\r
(int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y+fm.getDescent()*2);\r
+ y + fm.getDescent() * 2);\r
}\r
else\r
+ {\r
gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y+fm.getDescent(),\r
+ y + fm.getDescent(),\r
(int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y+fm.getDescent()*2);\r
-\r
+ y + fm.getDescent() * 2);\r
+ }\r
\r
}\r
}\r
\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
\r
-public class SeqCanvas extends Panel\r
+public class SeqCanvas\r
+ extends Panel\r
{\r
- FeatureRenderer fr;\r
- SequenceRenderer sr;\r
- Image img;\r
- Graphics gg;\r
- int imgWidth;\r
- int imgHeight;\r
-\r
- AlignViewport av;\r
+ FeatureRenderer fr;\r
+ SequenceRenderer sr;\r
+ Image img;\r
+ Graphics gg;\r
+ int imgWidth;\r
+ int imgHeight;\r
\r
- boolean showScores = false;\r
- boolean displaySearch = false;\r
- int [] searchResults = null;\r
+ AlignViewport av;\r
\r
- int chunkHeight;\r
- int chunkWidth;\r
+ boolean showScores = false;\r
+ boolean displaySearch = false;\r
+ int[] searchResults = null;\r
\r
- boolean fastPaint = false;\r
+ int chunkHeight;\r
+ int chunkWidth;\r
\r
+ boolean fastPaint = false;\r
\r
- public SeqCanvas(AlignViewport av)\r
- {\r
- this.av = av;\r
- fr = new FeatureRenderer(av);\r
- sr = new SequenceRenderer(av);\r
- PaintRefresher.Register(this);\r
+ public SeqCanvas(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ fr = new FeatureRenderer(av);\r
+ sr = new SequenceRenderer(av);\r
+ PaintRefresher.Register(this);\r
\r
- }\r
+ }\r
\r
- void drawNorthScale(Graphics g, int startx, int endx,int ypos) {\r
+ void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
int scalestartx = startx - startx % 10 + 10;\r
\r
g.setColor(Color.black);\r
void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
{\r
FontMetrics fm = getFontMetrics(av.getFont());\r
- ypos+= av.charHeight;\r
- // EAST SCALE\r
+ ypos += av.charHeight;\r
+ // EAST SCALE\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
SequenceI seq = av.alignment.getSequenceAt(i);\r
value = av.alignment.getSequenceAt(i).findPosition(index);\r
break;\r
}\r
- if(value!=-1)\r
+ if (value != -1)\r
{\r
- int x = LABEL_WEST - fm.stringWidth(value+"");\r
- g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5);\r
+ int x = LABEL_WEST - fm.stringWidth(value + "");\r
+ g.drawString(value + "", x,\r
+ ypos + i * av.charHeight - av.charHeight / 5);\r
}\r
}\r
}\r
\r
void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
-{\r
- ypos+= av.charHeight;\r
- // EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
- int index = endx;\r
- int value = -1;\r
- while (index > startx)\r
+ ypos += av.charHeight;\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
+ while (index > startx)\r
{\r
- index--;\r
- continue;\r
- }\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index--;\r
+ continue;\r
+ }\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
- break;\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ break;\r
+ }\r
+ if (value != -1)\r
+ {\r
+ g.drawString(value + "", 0,\r
+ ypos + i * av.charHeight - av.charHeight / 5);\r
+ }\r
}\r
- if(value!=-1)\r
- g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5);\r
- }\r
-\r
-}\r
-\r
\r
+ }\r
\r
-public void fastPaint(int horizontal, int vertical)\r
-{\r
- if (horizontal == 0 && vertical == 0 || gg==null)\r
+ public void fastPaint(int horizontal, int vertical)\r
+ {\r
+ if (horizontal == 0 && vertical == 0 || gg == null)\r
+ {\r
return;\r
+ }\r
\r
gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
-vertical * av.charHeight);\r
sr = er - horizontal;\r
}\r
else if (horizontal < 0)\r
+ {\r
er = sr - horizontal;\r
+ }\r
\r
else if (vertical > 0) // scroll down\r
{\r
ss = es - vertical;\r
- if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time\r
+ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time\r
+ {\r
ss = av.startSeq;\r
+ }\r
else\r
+ {\r
transY = imgHeight - vertical * av.charHeight;\r
+ }\r
}\r
else if (vertical < 0)\r
{\r
es = ss - vertical;\r
- if(es > av.endSeq)\r
+ if (es > av.endSeq)\r
+ {\r
es = av.endSeq;\r
+ }\r
}\r
\r
-\r
gg.translate(transX, transY);\r
\r
gg.setColor(Color.white);\r
- gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);\r
+ gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, (es - ss) * av.charHeight);\r
drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
gg.translate( -transX, -transY);\r
\r
fastPaint = true;\r
repaint();\r
\r
-}\r
+ }\r
\r
-/**\r
- * Definitions of startx and endx (hopefully):\r
- * SMJS This is what I'm working towards!\r
- * startx is the first residue (starting at 0) to display.\r
- * endx is the last residue to display (starting at 0).\r
- * starty is the first sequence to display (starting at 0).\r
- * endy is the last sequence to display (starting at 0).\r
- * NOTE 1: The av limits are set in setFont in this class and\r
- * in the adjustment listener in SeqPanel when the scrollbars move.\r
- */\r
+ /**\r
+ * Definitions of startx and endx (hopefully):\r
+ * SMJS This is what I'm working towards!\r
+ * startx is the first residue (starting at 0) to display.\r
+ * endx is the last residue to display (starting at 0).\r
+ * starty is the first sequence to display (starting at 0).\r
+ * endy is the last sequence to display (starting at 0).\r
+ * NOTE 1: The av limits are set in setFont in this class and\r
+ * in the adjustment listener in SeqPanel when the scrollbars move.\r
+ */\r
public void update(Graphics g)\r
{\r
paint(g);\r
}\r
\r
// this draws the whole of the alignment\r
- imgWidth = this.getSize().width;\r
- imgHeight = this.getSize().height;\r
+ imgWidth = this.getSize().width;\r
+ imgHeight = this.getSize().height;\r
\r
- imgWidth -= imgWidth%av.charWidth;\r
- imgHeight-= imgHeight%av.charHeight;\r
+ imgWidth -= imgWidth % av.charWidth;\r
+ imgHeight -= imgHeight % av.charHeight;\r
\r
- if(imgWidth<1 || imgHeight<1)\r
- return;\r
+ if (imgWidth < 1 || imgHeight < 1)\r
+ {\r
+ return;\r
+ }\r
\r
- if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this))\r
- {\r
- img = createImage(imgWidth, imgHeight);\r
- gg = img.getGraphics();\r
- gg.setFont(av.getFont());\r
- }\r
+ if (img == null || imgWidth != img.getWidth(this) ||\r
+ imgHeight != img.getHeight(this))\r
+ {\r
+ img = createImage(imgWidth, imgHeight);\r
+ gg = img.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ }\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0,0,imgWidth,imgHeight);\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
- chunkWidth = getWrappedCanvasWidth( getSize().width );\r
- chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
+ chunkWidth = getWrappedCanvasWidth(getSize().width);\r
+ chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
\r
av.setChunkHeight(chunkHeight);\r
av.setChunkWidth(chunkWidth);\r
\r
-\r
if (av.getWrapAlignment())\r
+ {\r
drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);\r
+ }\r
else\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);\r
+ {\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes,\r
+ av.startSeq, 0);\r
+ }\r
\r
g.drawImage(img, 0, 0, this);\r
\r
LABEL_EAST = 0;\r
LABEL_WEST = 0;\r
\r
- if(av.scaleRightWrapped)\r
- LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");\r
+ }\r
\r
- if(av.scaleLeftWrapped)\r
- LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");\r
+ }\r
\r
- return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
}\r
\r
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)\r
+ public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
+ int startRes)\r
{\r
- AlignmentI al = av.getAlignment();\r
+ AlignmentI al = av.getAlignment();\r
\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- int LABEL_EAST = 0;\r
- if(av.scaleRightWrapped)\r
- LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );\r
- int LABEL_WEST = 0;\r
- if(av.scaleLeftWrapped)\r
- LABEL_WEST = fm.stringWidth(al.getWidth()+"0");\r
+ int LABEL_EAST = 0;\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(al.getWidth() + "000");\r
+ }\r
+ int LABEL_WEST = 0;\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(al.getWidth() + "0");\r
+ }\r
\r
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
\r
- int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
+ av.endRes = av.startRes + cWidth;\r
\r
- av.endRes = av.startRes + cWidth;\r
+ int endx = startRes + cWidth - 1;\r
+ int ypos = 2 * av.charHeight;\r
\r
- int endx = startRes+cWidth-1;\r
- int ypos = 2*av.charHeight;\r
+ while (ypos <= canvasHeight && startRes < av.alignment.getWidth())\r
+ {\r
+ g.setColor(Color.black);\r
\r
- while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )\r
+ if (av.scaleLeftWrapped)\r
{\r
- g.setColor(Color.black);\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
\r
- if(av.scaleLeftWrapped)\r
- drawWestScale(g, startRes, endx, ypos);\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);\r
+ }\r
\r
- if(av.scaleRightWrapped)\r
- {\r
- g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);\r
- drawEastScale(g, startRes, endx, ypos);\r
- g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);\r
- }\r
+ g.translate(LABEL_WEST, 0);\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ drawNorthScale(g, startRes, endx, ypos);\r
+ }\r
\r
- g.translate(LABEL_WEST,0);\r
- if(av.scaleAboveWrapped)\r
- drawNorthScale(g, startRes, endx, ypos);\r
-\r
-\r
- // When printing we have an extra clipped region,\r
- // the Printable page which we need to account for here\r
- Shape clip = g.getClip();\r
- if(clip==null)\r
- g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);\r
- else\r
- g.setClip(0,\r
- (int)clip.getBounds().y,\r
- cWidth*av.charWidth,\r
- (int)clip.getBounds().height\r
- );\r
-\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
- g.setClip(clip);\r
- g.translate(-LABEL_WEST,0);\r
-\r
- ypos += cHeight;\r
- startRes += cWidth;\r
- endx = startRes + cWidth - 1;\r
-\r
- if (endx > al.getWidth())\r
- endx = al.getWidth();\r
+ // When printing we have an extra clipped region,\r
+ // the Printable page which we need to account for here\r
+ Shape clip = g.getClip();\r
+ if (clip == null)\r
+ {\r
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
+ }\r
+ else\r
+ {\r
+ g.setClip(0,\r
+ (int) clip.getBounds().y,\r
+ cWidth * av.charWidth,\r
+ (int) clip.getBounds().height\r
+ );\r
}\r
\r
- }\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+ g.setClip(clip);\r
+ g.translate( -LABEL_WEST, 0);\r
\r
+ ypos += cHeight;\r
+ startRes += cWidth;\r
+ endx = startRes + cWidth - 1;\r
\r
- synchronized public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
+ if (endx > al.getWidth())\r
+ {\r
+ endx = al.getWidth();\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2,\r
+ int startx, int starty, int offset)\r
+ {\r
\r
g.setFont(av.getFont());\r
sr.renderGaps(av.renderGaps);\r
\r
/// First draw the sequences\r
/////////////////////////////\r
- for (int i = y1 ; i < y2 ;i++)\r
+ for (int i = y1; i < y2; i++)\r
{\r
- nextSeq = av.alignment.getSequenceAt(i);\r
-\r
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,\r
- (x1 - startx) * av.charWidth,\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth,av.charHeight);\r
-\r
- if(av.showSequenceFeatures)\r
- {\r
- fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,\r
- (x1 - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth, av.charHeight);\r
- }\r
+ nextSeq = av.alignment.getSequenceAt(i);\r
+\r
+ sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
+ (x1 - startx) * av.charWidth,\r
+ offset +\r
+ AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+ av.charWidth, av.charHeight);\r
+\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
+ (x1 - startx) * av.charWidth,\r
+ offset +\r
+ AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+ av.charWidth, av.charHeight);\r
+ }\r
}\r
//\r
/////////////////////////////////////\r
}\r
\r
if (group != null)\r
+ {\r
do\r
{\r
int oldY = -1;\r
int i = 0;\r
boolean inGroup = false;\r
- int top=-1, bottom =-1;\r
+ int top = -1, bottom = -1;\r
for (i = y1; i < y2; i++)\r
{\r
sx = (group.getStartRes() - startx) * av.charWidth;\r
sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;\r
+ ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;\r
\r
if (sx < getSize().width\r
&& ex > 0\r
&& group.sequences.contains(av.alignment.getSequenceAt(i)))\r
{\r
- if (bottom == -1 && (i==av.alignment.getHeight()-1 ||\r
- !group.sequences.contains(av.alignment.getSequenceAt(i + 1))))\r
- bottom = sy + av.charHeight ;\r
+ if (bottom == -1 && (i == av.alignment.getHeight() - 1 ||\r
+ !group.sequences.contains(av.alignment.\r
+ getSequenceAt(i + 1))))\r
+ {\r
+ bottom = sy + av.charHeight;\r
+ }\r
\r
if (!inGroup)\r
{\r
- if (top == -1 && i==0 ||\r
+ if (top == -1 && i == 0 ||\r
!group.sequences.contains(av.alignment.getSequenceAt(i - 1)))\r
+ {\r
top = sy;\r
-\r
+ }\r
\r
oldY = sy;\r
inGroup = true;\r
if (group == av.getSelectionGroup())\r
{\r
- g.setColor(new Color(255,0,0));\r
+ g.setColor(new Color(255, 0, 0));\r
}\r
else\r
{\r
- g.setColor(group.getOutlineColour());\r
+ g.setColor(group.getOutlineColour());\r
}\r
}\r
}\r
{\r
if (inGroup)\r
{\r
- g.drawLine(sx, oldY, sx, sy );\r
- g.drawLine(sx+ex, oldY, sx+ex, sy );\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
\r
if (top != -1)\r
{\r
g.drawLine(sx, top, sx + ex, top);\r
- top =-1;\r
+ top = -1;\r
}\r
if (bottom != -1)\r
{\r
bottom = -1;\r
}\r
\r
-\r
inGroup = false;\r
}\r
}\r
if (inGroup)\r
{\r
\r
- if(top!=-1)\r
+ if (top != -1)\r
{\r
g.drawLine(sx, top, sx + ex, top);\r
- top =-1;\r
+ top = -1;\r
}\r
- if(bottom!=-1)\r
- {\r
- g.drawLine(sx, bottom-1, sx + ex, bottom-1);\r
- bottom = -1;\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
\r
- }\r
+ }\r
sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- g.drawLine(sx, oldY, sx, sy );\r
- g.drawLine(sx+ex, oldY, sx+ex, sy );\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
inGroup = false;\r
}\r
groupIndex++;\r
if (groupIndex >= groups.size())\r
+ {\r
break;\r
+ }\r
\r
group = (SequenceGroup) groups.elementAt(groupIndex);\r
\r
}\r
while (groupIndex < groups.size());\r
-\r
+ }\r
\r
/// Highlight search Results once all sequences have been drawn\r
//////////////////////////////////////////////////////////\r
- if(displaySearch)\r
+ if (displaySearch)\r
{\r
- for(int r=0; r<searchResults.length; r+=3)\r
+ for (int r = 0; r < searchResults.length; r += 3)\r
{\r
int searchSeq = searchResults[r];\r
\r
{\r
SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
\r
- int searchStart = seq.findIndex( searchResults[r+1] )-1;\r
- int searchEnd = seq.findIndex( searchResults[r+2] )-1;\r
+ int searchStart = seq.findIndex(searchResults[r + 1]) - 1;\r
+ int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;\r
\r
SequenceRenderer ssr = (SequenceRenderer) sr;\r
- if(searchStart<x1)\r
+ if (searchStart < x1)\r
+ {\r
searchStart = x1;\r
- if(searchEnd > x2)\r
+ }\r
+ if (searchEnd > x2)\r
+ {\r
searchEnd = x2;\r
+ }\r
\r
ssr.drawHighlightedText(seq,\r
searchStart,\r
searchEnd,\r
(searchStart - startx) * av.charWidth,\r
offset +\r
- AlignmentUtil.getPixelHeight(starty, searchSeq,\r
+ AlignmentUtil.getPixelHeight(starty,\r
+ searchSeq,\r
av.charHeight),\r
av.charWidth,\r
av.charHeight);\r
\r
}\r
\r
-\r
-\r
- public void highlightSearchResults(int [] results)\r
+ public void highlightSearchResults(int[] results)\r
{\r
// results are in the order sequence, startRes, endRes\r
- if(results==null)\r
+ if (results == null)\r
+ {\r
displaySearch = false;\r
+ }\r
else\r
+ {\r
displaySearch = true;\r
+ }\r
\r
searchResults = results;\r
\r
repaint();\r
}\r
\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
+\r
import jalview.datamodel.*;\r
-import java.util.*;\r
import jalview.schemes.*;\r
\r
-\r
-public class SeqPanel extends Panel\r
+public class SeqPanel\r
+ extends Panel\r
{\r
\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel ap;\r
+ public SeqCanvas seqCanvas;\r
+ public AlignmentPanel ap;\r
\r
protected int lastres;\r
protected int startseq;\r
- int startEdit=-1;\r
- int endEdit=-1;\r
+ int startEdit = -1;\r
+ int endEdit = -1;\r
\r
protected AlignViewport av;\r
\r
boolean editingSeqs = false;\r
boolean groupEditing = false;\r
\r
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+ {\r
+ this.av = avp;\r
\r
-\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
- this.av = avp;\r
-\r
- seqCanvas = new SeqCanvas(avp);\r
+ seqCanvas = new SeqCanvas(avp);\r
setLayout(new BorderLayout());\r
add(seqCanvas);\r
\r
ap = p;\r
\r
- seqCanvas.addMouseMotionListener( new MouseMotionAdapter()\r
+ seqCanvas.addMouseMotionListener(new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- doMouseMoved(evt); }\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+ doMouseMoved(evt);\r
+ }\r
\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if( editingSeqs )\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+ if (editingSeqs)\r
+ {\r
doMouseDragged(evt);\r
+ }\r
else\r
+ {\r
doMouseDraggedDefineMode(evt);\r
+ }\r
}\r
});\r
\r
- seqCanvas.addMouseListener( new MouseAdapter()\r
+ seqCanvas.addMouseListener(new MouseAdapter()\r
{\r
public void mouseReleased(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if(editingSeqs)\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+ if (editingSeqs)\r
+ {\r
doMouseReleased(evt);\r
+ }\r
else\r
+ {\r
doMouseReleasedDefineMode(evt);\r
+ }\r
\r
}\r
+\r
public void mousePressed(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if (av.getWrapAlignment())\r
{\r
- if(evt.isAltDown() || evt.isControlDown())\r
+ return;\r
+ }\r
+ if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown() || evt.isControlDown())\r
+ {\r
groupEditing = true;\r
+ }\r
\r
editingSeqs = true;\r
doMousePressed(evt);\r
}\r
else\r
+ {\r
doMousePressedDefineMode(evt);\r
+ }\r
}\r
+\r
public void mouseExited(MouseEvent evt)\r
{\r
if (av.getWrapAlignment() || editingSeqs)\r
- return;\r
- doMouseExitedDefineMode(evt);\r
+ {\r
+ return;\r
+ }\r
+ doMouseExitedDefineMode(evt);\r
\r
}\r
+\r
public void mouseEntered(MouseEvent evt)\r
{\r
if (av.getWrapAlignment() || editingSeqs)\r
+ {\r
return;\r
+ }\r
doMouseEnteredDefineMode(evt);\r
}\r
\r
seqCanvas.repaint();\r
}\r
\r
+ public void doMouseReleased(MouseEvent evt)\r
+ {\r
\r
- public void doMouseReleased(MouseEvent evt) {\r
-\r
- if(seqEditOccurred>-1)\r
+ if (seqEditOccurred > -1)\r
+ {\r
editOccurred(seqEditOccurred);\r
+ }\r
\r
startseq = -1;\r
- lastres = -1;\r
+ lastres = -1;\r
seqEditOccurred = -1;\r
- editingSeqs = false;\r
+ editingSeqs = false;\r
groupEditing = false;\r
ap.repaint();\r
}\r
\r
- public void doMousePressed(MouseEvent evt) {\r
- ap.alignFrame.addHistoryItem( new HistoryItem(\r
- "Edit Sequence",av.alignment, HistoryItem.EDIT));\r
+ public void doMousePressed(MouseEvent evt)\r
+ {\r
+ ap.alignFrame.addHistoryItem(new HistoryItem(\r
+ "Edit Sequence", av.alignment, HistoryItem.EDIT));\r
int seq;\r
int res;\r
\r
int x = evt.getX();\r
int y = evt.getY();\r
\r
- res = x/av.getCharWidth() + av.getStartRes();\r
- seq = y/av.getCharHeight() + av.getStartSeq();\r
+ res = x / av.getCharWidth() + av.getStartRes();\r
+ seq = y / av.getCharHeight() + av.getStartSeq();\r
\r
if (seq < av.getAlignment().getHeight() &&\r
res < av.getAlignment().getSequenceAt(seq).getLength())\r
\r
public void doMouseMoved(MouseEvent evt)\r
{\r
- int res=0, seq=0;\r
+ int res = 0, seq = 0;\r
int x = evt.getX();\r
int y = evt.getY();\r
- if(av.wrapAlignment)\r
+ if (av.wrapAlignment)\r
{\r
- y -= 2*av.charHeight;\r
- int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;\r
+ y -= 2 * av.charHeight;\r
+ int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
\r
-\r
- res = (int)((y/chunkHeight)*(getSize().width/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();\r
+ res = (int) ( (y / chunkHeight) * (getSize().width / av.charWidth)) +\r
+ x / av.getCharWidth() + av.getStartRes();\r
\r
y %= chunkHeight;\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
+ seq = y / av.getCharHeight() + av.getStartSeq();\r
\r
}\r
else\r
{\r
- res = x / av.getCharWidth() + av.getStartRes();\r
+ res = x / av.getCharWidth() + av.getStartRes();\r
seq = y / av.getCharHeight() + av.getStartSeq();\r
}\r
\r
-\r
- if(seq>=av.getAlignment().getHeight())\r
+ if (seq >= av.getAlignment().getHeight())\r
+ {\r
return;\r
+ }\r
\r
SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
- if(res>sequence.getLength())\r
+ if (res > sequence.getLength())\r
+ {\r
return;\r
+ }\r
\r
- Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
+ Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
String aa = "";\r
- if(obj!=null)\r
- aa = obj.toString();\r
+ if (obj != null)\r
+ {\r
+ aa = obj.toString();\r
+ }\r
\r
- StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());\r
- if(aa!="")\r
- text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+ sequence.getName());\r
+ if (aa != "")\r
+ {\r
+ text.append(" Residue: " + aa + " (" +\r
+ av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+ }\r
\r
ap.alignFrame.statusBar.setText(text.toString());\r
\r
// use aa to see if the mouse pointer is on a\r
- if( av.showSequenceFeatures)\r
+ if (av.showSequenceFeatures)\r
{\r
Vector features = sequence.getSequenceFeatures();\r
Enumeration e = features.elements();\r
StringBuffer sbuffer = new StringBuffer();\r
\r
-\r
while (e.hasMoreElements())\r
{\r
SequenceFeature sf = (SequenceFeature) e.nextElement();\r
if (sf.getStart() <= sequence.findPosition(res) &&\r
sf.getEnd() >= sequence.findPosition(res))\r
{\r
- if(sbuffer.length()>0)\r
+ if (sbuffer.length() > 0)\r
+ {\r
sbuffer.append("; ");\r
+ }\r
sbuffer.append(sf.getType() + " " + sf.getDescription());\r
- if(sf.getStatus().length()>0)\r
- sbuffer.append(" ("+sf.getStatus()+")");\r
+ if (sf.getStatus().length() > 0)\r
+ {\r
+ sbuffer.append(" (" + sf.getStatus() + ")");\r
+ }\r
}\r
\r
}\r
}\r
\r
-\r
}\r
\r
- public void doMouseDragged(MouseEvent evt) {\r
-\r
- // If we're dragging we're editing\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if (res < 0)\r
- res = 0;\r
-\r
- if (lastres == -1 || lastres == res)\r
- return;\r
-\r
- boolean dragRight = true;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
- dragRight = false;\r
-\r
-\r
- if (res != lastres)\r
- {\r
- // Group editing\r
- if (groupEditing)\r
- {\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg==null)\r
- {\r
- lastres=-1;\r
- return;\r
- }\r
-\r
- // drag to right\r
- if(dragRight)\r
- sg.setEndRes(sg.getEndRes() + (res-lastres));\r
-\r
- // drag to left\r
- else\r
- {\r
- /// Are we able to delete?\r
- // ie are all columns blank?\r
- boolean deleteAllowed = false;\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(s);\r
- for (int j=res; j<lastres; j++)\r
- {\r
- if(seq.getSequence().length()<=j)\r
- continue;\r
-\r
- if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- res=j+1;\r
- deleteAllowed = false;\r
- continue;\r
- }\r
- deleteAllowed = true;\r
- }\r
- }\r
-\r
- if(!deleteAllowed)\r
- {\r
- lastres = -1;\r
- return;\r
- }\r
-\r
- sg.setEndRes(sg.getEndRes() - (lastres-res));\r
- }\r
-\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
-\r
- // drag to right\r
- if (dragRight)\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, k);\r
-\r
- // drag to left\r
- else\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- if(s.getLength()>j)\r
- deleteChar(res, k);\r
- }\r
- }\r
- }\r
- }\r
- else /////Editing a single sequence///////////\r
- {\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- {\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, startseq);\r
- }\r
- else if (res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- // dragging to the left\r
- for (int j = lastres; j > res; j--)\r
- {\r
- if( jalview.util.Comparison.isGap(\r
- av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
-\r
- deleteChar(res, startseq);\r
- else\r
- {\r
-\r
- break;\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
-\r
- endEdit = res;\r
- lastres = res;\r
- seqCanvas.repaint();\r
+ public void doMouseDragged(MouseEvent evt)\r
+ {\r
+\r
+ // If we're dragging we're editing\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
+\r
+ if (lastres == -1 || lastres == res)\r
+ {\r
+ return;\r
+ }\r
+\r
+ boolean dragRight = true;\r
+ if (res < av.getAlignment().getWidth() && res < lastres)\r
+ {\r
+ dragRight = false;\r
+ }\r
+\r
+ if (res != lastres)\r
+ {\r
+ // Group editing\r
+ if (groupEditing)\r
+ {\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ lastres = -1;\r
+ return;\r
+ }\r
+\r
+ // drag to right\r
+ if (dragRight)\r
+ {\r
+ sg.setEndRes(sg.getEndRes() + (res - lastres));\r
+ }\r
+\r
+ // drag to left\r
+ else\r
+ {\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+ boolean deleteAllowed = false;\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(s);\r
+ for (int j = res; j < lastres; j++)\r
+ {\r
+ if (seq.getSequence().length() <= j)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ res = j + 1;\r
+ deleteAllowed = false;\r
+ continue;\r
+ }\r
+ deleteAllowed = true;\r
+ }\r
+ }\r
+\r
+ if (!deleteAllowed)\r
+ {\r
+ lastres = -1;\r
+ return;\r
+ }\r
+\r
+ sg.setEndRes(sg.getEndRes() - (lastres - res));\r
+ }\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI s = sg.getSequenceAt(i);\r
+ int k = av.alignment.findIndex(s);\r
+\r
+ // drag to right\r
+ if (dragRight)\r
+ {\r
+ for (int j = lastres; j < res; j++)\r
+ {\r
+ insertChar(j, k);\r
+ }\r
+ }\r
+\r
+ // drag to left\r
+ else\r
+ {\r
+ for (int j = res; j < lastres; j++)\r
+ {\r
+ if (s.getLength() > j)\r
+ {\r
+ deleteChar(res, k);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else /////Editing a single sequence///////////\r
+ {\r
+ if (res < av.getAlignment().getWidth() && res > lastres)\r
+ {\r
+ // dragging to the right\r
+ for (int j = lastres; j < res; j++)\r
+ {\r
+ insertChar(j, startseq);\r
+ }\r
+ }\r
+ else if (res < av.getAlignment().getWidth() && res < lastres)\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > res; j--)\r
+ {\r
+ if (jalview.util.Comparison.isGap(\r
+ av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
+ {\r
+\r
+ deleteChar(res, startseq);\r
+ }\r
+ else\r
+ {\r
+\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ endEdit = res;\r
+ lastres = res;\r
+ seqCanvas.repaint();\r
}\r
\r
- public void drawChars(int seqstart, int seqend, int start) {\r
- seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);\r
+ public void drawChars(int seqstart, int seqend, int start)\r
+ {\r
+ seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,\r
+ av.getStartRes(), av.getStartSeq(), 0);\r
seqCanvas.repaint();\r
}\r
\r
public void insertChar(int j, int seq)\r
{\r
av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred=seq;\r
+ seqEditOccurred = seq;\r
}\r
\r
public void deleteChar(int j, int seq)\r
{\r
\r
av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
- seqEditOccurred=seq;\r
+ seqEditOccurred = seq;\r
av.alignment.getWidth();\r
repaint();\r
}\r
\r
-\r
void editOccurred(int i)\r
{\r
- if(endEdit==startEdit)\r
+ if (endEdit == startEdit)\r
{\r
ap.alignFrame.historyList.pop();\r
ap.alignFrame.updateEditMenuBar();\r
\r
// Y O Y CLUSTALX\r
ColourSchemeI cs = av.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme)\r
+ if (cs instanceof ConservationColourScheme)\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
- if(ccs.cs instanceof ClustalxColourScheme)\r
- {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
+ if (ccs.cs instanceof ClustalxColourScheme)\r
+ {\r
jalview.analysis.Conservation c = new jalview.analysis.Conservation\r
("All",\r
- ResidueProperties.propHash, 3,\r
- av.alignment.getSequences(), 0,\r
- av.alignment.getWidth() - 1);\r
+ ResidueProperties.propHash, 3,\r
+ av.alignment.getSequences(), 0,\r
+ av.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, av.ConsPercGaps);\r
\r
- ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;\r
- cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());\r
+ ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;\r
+ cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());\r
ccs = new ConservationColourScheme(c, cxs);\r
av.setGlobalColourScheme(ccs);\r
- }\r
+ }\r
}\r
\r
- if(cs instanceof ClustalxColourScheme)\r
+ if (cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
+ ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
av.setGlobalColourScheme(cs);\r
}\r
\r
-\r
}\r
\r
//////////////////////////////////////////\r
int oldSeq = -1;\r
public void doMousePressedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ int seq = evt.getY() / av.getCharHeight() + av.getStartSeq();\r
oldSeq = seq;\r
\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
\r
- if(sequence==null || res>sequence.getLength())\r
+ if (sequence == null || res > sequence.getLength())\r
+ {\r
return;\r
+ }\r
\r
stretchGroup = av.getSelectionGroup();\r
\r
- if(stretchGroup == null)\r
- {\r
- stretchGroup = av.alignment.findGroup( sequence );\r
- if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
- av.setSelectionGroup(stretchGroup);\r
- else\r
- stretchGroup = null;\r
- }\r
-\r
- else if(!stretchGroup.sequences.contains(sequence)\r
- || stretchGroup.getStartRes()>res\r
- || stretchGroup.getEndRes()<res)\r
- {\r
- stretchGroup = null;\r
-\r
- SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );\r
-\r
- if (allGroups != null)\r
- for (int i = 0; i < allGroups.length; i++)\r
- if (allGroups[i].getStartRes() <= res &&\r
- allGroups[i].getEndRes() >= res)\r
- {\r
- stretchGroup = allGroups[i];\r
- av.setSelectionGroup(stretchGroup);\r
- break;\r
- }\r
- }\r
-\r
- if(stretchGroup==null)\r
+ if (stretchGroup == null)\r
+ {\r
+ stretchGroup = av.alignment.findGroup(sequence);\r
+ if (stretchGroup != null && res > stretchGroup.getStartRes() &&\r
+ res < stretchGroup.getEndRes())\r
+ {\r
+ av.setSelectionGroup(stretchGroup);\r
+ }\r
+ else\r
+ {\r
+ stretchGroup = null;\r
+ }\r
+ }\r
+\r
+ else if (!stretchGroup.sequences.contains(sequence)\r
+ || stretchGroup.getStartRes() > res\r
+ || stretchGroup.getEndRes() < res)\r
+ {\r
+ stretchGroup = null;\r
+\r
+ SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
+\r
+ if (allGroups != null)\r
+ {\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ {\r
+ if (allGroups[i].getStartRes() <= res &&\r
+ allGroups[i].getEndRes() >= res)\r
+ {\r
+ stretchGroup = allGroups[i];\r
+ av.setSelectionGroup(stretchGroup);\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (stretchGroup == null)\r
{\r
// define a new group here\r
SequenceGroup sg = new SequenceGroup();\r
sg.setStartRes(res);\r
sg.setEndRes(res);\r
- sg.addSequence( sequence );\r
- av.setSelectionGroup( sg );\r
+ sg.addSequence(sequence);\r
+ av.setSelectionGroup(sg);\r
stretchGroup = sg;\r
\r
- if(av.getConservationSelected())\r
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
- if(av.getAbovePIDThreshold())\r
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
+ if (av.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+ if (av.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
\r
}\r
\r
// DETECT RIGHT MOUSE BUTTON IN AWT\r
- else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )\r
+ else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
+ InputEvent.BUTTON3_MASK)\r
{\r
APopupMenu popup = new APopupMenu(ap, null);\r
this.add(popup);\r
popup.show(this, evt.getX(), evt.getY());\r
}\r
\r
-\r
- if(stretchGroup!=null && stretchGroup.getEndRes()==res)\r
+ if (stretchGroup != null && stretchGroup.getEndRes() == res)\r
+ {\r
// Edit end res position of selected group\r
changeEndRes = true;\r
+ }\r
\r
- else if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
+ else if (stretchGroup != null && stretchGroup.getStartRes() == res)\r
+ {\r
// Edit end res position of selected group\r
changeStartRes = true;\r
+ }\r
\r
}\r
\r
{\r
mouseDragging = false;\r
\r
- if(stretchGroup==null)\r
+ if (stretchGroup == null)\r
+ {\r
return;\r
+ }\r
\r
- if(stretchGroup.cs instanceof ClustalxColourScheme)\r
+ if (stretchGroup.cs instanceof ClustalxColourScheme)\r
{\r
- stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
+ stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,\r
+ av.alignment.getWidth());\r
seqCanvas.repaint();\r
}\r
\r
- else if(stretchGroup.cs instanceof ConservationColourScheme)\r
+ else if (stretchGroup.cs instanceof ConservationColourScheme)\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
- stretchGroup.cs = ccs;\r
- SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
+ ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;\r
+ stretchGroup.cs = ccs;\r
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
\r
- seqCanvas.repaint();\r
+ seqCanvas.repaint();\r
}\r
else\r
{\r
- if(stretchGroup.cs !=null)\r
+ if (stretchGroup.cs != null)\r
{\r
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
}\r
\r
}\r
\r
-\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
ap.repaint();\r
}\r
\r
-\r
boolean remove = false;\r
public void doMouseDraggedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ int y = evt.getY() / av.getCharHeight() + av.getStartSeq();\r
\r
- if(stretchGroup==null)\r
+ if (stretchGroup == null)\r
+ {\r
return;\r
+ }\r
\r
- if(res>av.alignment.getWidth())\r
- res = av.alignment.getWidth()-1;\r
-\r
+ if (res > av.alignment.getWidth())\r
+ {\r
+ res = av.alignment.getWidth() - 1;\r
+ }\r
\r
- if(stretchGroup.getEndRes()==res)\r
+ if (stretchGroup.getEndRes() == res)\r
+ {\r
// Edit end res position of selected group\r
changeEndRes = true;\r
+ }\r
\r
- else if(stretchGroup.getStartRes()==res)\r
+ else if (stretchGroup.getStartRes() == res)\r
+ {\r
// Edit start res position of selected group\r
changeStartRes = true;\r
+ }\r
\r
-\r
- if(res<av.getStartRes())\r
+ if (res < av.getStartRes())\r
+ {\r
res = av.getStartRes();\r
- else if(res>av.getEndRes())\r
+ }\r
+ else if (res > av.getEndRes())\r
+ {\r
res = av.getEndRes();\r
+ }\r
\r
- if(changeEndRes)\r
+ if (changeEndRes)\r
{\r
- if(res>stretchGroup.getStartRes()-1)\r
- stretchGroup.setEndRes( res );\r
+ if (res > stretchGroup.getStartRes() - 1)\r
+ {\r
+ stretchGroup.setEndRes(res);\r
+ }\r
}\r
- else if(changeStartRes)\r
+ else if (changeStartRes)\r
{\r
- if(res<stretchGroup.getEndRes()+1)\r
- stretchGroup.setStartRes( res );\r
+ if (res < stretchGroup.getEndRes() + 1)\r
+ {\r
+ stretchGroup.setStartRes(res);\r
+ }\r
}\r
\r
int dragDirection = 0;\r
if (y > oldSeq)\r
+ {\r
dragDirection = 1;\r
+ }\r
else if (y < oldSeq)\r
+ {\r
dragDirection = -1;\r
+ }\r
\r
- while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())\r
+ while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())\r
{\r
// This routine ensures we don't skip any sequences, as the\r
// selection is quite slow.\r
}\r
else\r
{\r
- if(seq!=null)\r
- stretchGroup.addSequence(seq);\r
+ if (seq != null)\r
+ {\r
+ stretchGroup.addSequence(seq);\r
+ }\r
stretchGroup.addSequence(nextSeq);\r
}\r
}\r
oldSeq = y;\r
mouseDragging = true;\r
- if(scrollThread!=null)\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.setEvent(evt);\r
+ }\r
\r
seqCanvas.repaint();\r
}\r
public void doMouseEnteredDefineMode(MouseEvent e)\r
{\r
if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
}\r
\r
public void doMouseExitedDefineMode(MouseEvent e)\r
{\r
if (av.getWrapAlignment())\r
+ {\r
return;\r
+ }\r
\r
- if(mouseDragging)\r
+ if (mouseDragging)\r
+ {\r
scrollThread = new ScrollThread();\r
+ }\r
\r
}\r
+\r
// this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread extends Thread\r
+ class ScrollThread\r
+ extends Thread\r
{\r
MouseEvent evt;\r
boolean running = false;\r
running = true;\r
while (running)\r
{\r
- if(evt!=null)\r
+ if (evt != null)\r
{\r
\r
if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+ {\r
running = ap.scrollUp(true);\r
+ }\r
\r
if (mouseDragging && evt.getY() >= getSize().height &&\r
av.alignment.getHeight() > av.getEndSeq())\r
+ {\r
running = ap.scrollUp(false);\r
+ }\r
\r
if (mouseDragging && evt.getX() < 0)\r
+ {\r
running = ap.scrollRight(true);\r
+ }\r
\r
else if (mouseDragging && evt.getX() >= getSize().width)\r
+ {\r
running = ap.scrollRight(false);\r
+ }\r
}\r
\r
try\r
{}\r
}\r
}\r
-}\r
-\r
-\r
+ }\r
\r
}\r
-\r
-\r
-\r
-\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
+import java.awt.*;\r
+\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import java.awt.*;\r
\r
public class SequenceRenderer\r
{\r
FontMetrics fm;\r
boolean renderGaps = true;\r
SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
+ SequenceGroup[] allGroups = null;\r
Color resBoxColour;\r
Graphics graphics;\r
\r
this.av = av;\r
}\r
\r
-\r
public void renderGaps(boolean b)\r
{\r
renderGaps = b;\r
\r
void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
{\r
- if (cs != null)\r
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
- else\r
- resBoxColour = Color.white;\r
+ if (cs != null)\r
+ {\r
+ resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
+ }\r
+ else\r
+ {\r
+ resBoxColour = Color.white;\r
+ }\r
}\r
\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)\r
+ public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int x1, int y1, int width,\r
+ int height)\r
{\r
allGroups = sg;\r
\r
drawBoxes(seq, start, end, x1, y1, (int) width, height);\r
\r
fm = g.getFontMetrics();\r
- drawText(seq,start,end,x1,y1,(int)width,height);\r
+ drawText(seq, start, end, x1, y1, (int) width, height);\r
\r
}\r
\r
- public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height) {\r
- int i = start;\r
+ public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,\r
+ int width, int height)\r
+ {\r
+ int i = start;\r
int length = seq.getLength();\r
\r
int curStart = -1;\r
Color tempColour = null;\r
while (i <= end && i < length)\r
{\r
- if(inCurrentSequenceGroup(i))\r
+ if (inCurrentSequenceGroup(i))\r
{\r
- if( currentSequenceGroup.getDisplayBoxes())\r
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
else\r
- resBoxColour = Color.white;\r
+ {\r
+ resBoxColour = Color.white;\r
+ }\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.getGlobalColourScheme(), seq, i);\r
}\r
- else if(av.getShowBoxes())\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
else\r
+ {\r
resBoxColour = Color.white;\r
-\r
+ }\r
\r
if (resBoxColour != tempColour)\r
{\r
- if(tempColour!=null)\r
- graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
+ if (tempColour != null)\r
+ {\r
+ graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,\r
+ height);\r
+ }\r
graphics.setColor(resBoxColour);\r
\r
curStart = i;\r
\r
}\r
else\r
+ {\r
curWidth += width;\r
+ }\r
\r
i++;\r
}\r
\r
-\r
- graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
+ graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);\r
}\r
\r
- public void drawText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r
+ public void drawText(SequenceI seq, int start, int end, int x1, int y1,\r
+ int width, int height)\r
{\r
- int pady = height/5;\r
- int charOffset=0;\r
+ int pady = height / 5;\r
+ int charOffset = 0;\r
char s;\r
// Need to find the sequence position here.\r
\r
- String sequence = seq.getSequence();\r
+ String sequence = seq.getSequence();\r
for (int i = start; i <= end; i++)\r
{\r
- graphics.setColor(Color.black);\r
- if(i<sequence.length())\r
- s = sequence.charAt(i);\r
- else\r
- s = ' ';\r
+ graphics.setColor(Color.black);\r
+ if (i < sequence.length())\r
+ {\r
+ s = sequence.charAt(i);\r
+ }\r
+ else\r
+ {\r
+ s = ' ';\r
+ }\r
\r
- if(!renderGaps && jalview.util.Comparison.isGap(s))\r
- continue;\r
+ if (!renderGaps && jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (!currentSequenceGroup.getDisplayText())\r
+ {\r
+ continue;\r
+ }\r
\r
- if (inCurrentSequenceGroup(i))\r
+ if (currentSequenceGroup.getColourText())\r
{\r
- if(!currentSequenceGroup.getDisplayText())\r
- continue;\r
-\r
- if (currentSequenceGroup.getColourText())\r
- {\r
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
- graphics.setColor(resBoxColour.darker());\r
- }\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ graphics.setColor(resBoxColour.darker());\r
}\r
- else\r
+ }\r
+ else\r
+ {\r
+ if (!av.getShowText())\r
{\r
- if(!av.getShowText())\r
- continue;\r
-\r
- if(av.getColourText())\r
- {\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
- if(av.getShowBoxes())\r
- graphics.setColor(resBoxColour.darker());\r
- else\r
- graphics.setColor(resBoxColour);\r
- }\r
+ continue;\r
}\r
\r
- charOffset = (width - fm.charWidth(s))/2;\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i - start),\r
- y1 + height - pady);\r
+ if (av.getColourText())\r
+ {\r
+ getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+ if (av.getShowBoxes())\r
+ {\r
+ graphics.setColor(resBoxColour.darker());\r
+ }\r
+ else\r
+ {\r
+ graphics.setColor(resBoxColour);\r
+ }\r
}\r
+ }\r
\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1 + width * (i - start),\r
+ y1 + height - pady);\r
+ }\r
\r
}\r
\r
boolean inCurrentSequenceGroup(int res)\r
{\r
- if(allGroups ==null)\r
+ if (allGroups == null)\r
+ {\r
return false;\r
+ }\r
\r
- for(int i=0; i<allGroups.length; i++)\r
- if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ {\r
+ if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)\r
{\r
- currentSequenceGroup = allGroups[i];\r
- return true;\r
+ currentSequenceGroup = allGroups[i];\r
+ return true;\r
}\r
+ }\r
\r
return false;\r
}\r
\r
- public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1,\r
+ int y1, int width, int height)\r
{\r
- int pady = height/5;\r
- int charOffset=0;\r
+ int pady = height / 5;\r
+ int charOffset = 0;\r
graphics.setColor(Color.black);\r
- graphics.fillRect(x1,y1,width*(end-start+1),height);\r
+ graphics.fillRect(x1, y1, width * (end - start + 1), height);\r
graphics.setColor(Color.white);\r
\r
- char s='~';\r
+ char s = '~';\r
// Need to find the sequence position here.\r
for (int i = start; i <= end; i++)\r
{\r
- if(i<seq.getLength())\r
- s = seq.getSequence().charAt(i);\r
+ if (i < seq.getLength())\r
+ {\r
+ s = seq.getSequence().charAt(i);\r
+ }\r
\r
- charOffset = (width - fm.charWidth(s))/2;\r
- graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1 + width * (i - start),\r
+ y1 + height - pady);\r
}\r
}\r
\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.*;\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
-public class SliderPanel extends GSliderPanel\r
+import jalview.datamodel.*;\r
+import jalview.jbappletgui.*;\r
+import jalview.schemes.*;\r
+\r
+public class SliderPanel\r
+ extends GSliderPanel\r
{\r
AlignmentPanel ap;\r
boolean forConservation = true;\r
static Frame conservationSlider;\r
static Frame PIDSlider;\r
\r
- public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs, String source)\r
+ public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs,\r
+ String source)\r
{\r
SliderPanel sp = null;\r
- ConservationColourScheme ccs = (ConservationColourScheme)cs;\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
\r
- if(conservationSlider == null)\r
+ if (conservationSlider == null)\r
{\r
sp = new SliderPanel(ap, ccs.inc, true, cs);\r
conservationSlider = new Frame();\r
}\r
else\r
{\r
- sp = (SliderPanel)conservationSlider.getComponent(0);\r
- sp.cs = cs;\r
+ sp = (SliderPanel) conservationSlider.getComponent(0);\r
+ sp.cs = cs;\r
}\r
\r
- conservationSlider.setTitle("Conservation Colour Increment ("+source+")");\r
- if(ap.av.alignment.getGroups()!=null)\r
- sp.setAllGroupsCheckEnabled( true );\r
+ conservationSlider.setTitle("Conservation Colour Increment (" + source +\r
+ ")");\r
+ if (ap.av.alignment.getGroups() != null)\r
+ {\r
+ sp.setAllGroupsCheckEnabled(true);\r
+ }\r
else\r
- sp.setAllGroupsCheckEnabled( false);\r
+ {\r
+ sp.setAllGroupsCheckEnabled(false);\r
+ }\r
\r
return sp.getValue();\r
}\r
\r
public static void showConservationSlider()\r
{\r
- try{\r
+ try\r
+ {\r
PIDSlider.setVisible(false);\r
PIDSlider = null;\r
- }catch(Exception ex){}\r
-\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
\r
- if(!conservationSlider.isVisible())\r
+ if (!conservationSlider.isVisible())\r
{\r
- jalview.bin.JalviewLite.addFrame(conservationSlider, conservationSlider.getTitle(), 420, 100);\r
+ jalview.bin.JalviewLite.addFrame(conservationSlider,\r
+ conservationSlider.getTitle(), 420, 100);\r
conservationSlider.addWindowListener(new WindowAdapter()\r
{\r
public void windowClosing(WindowEvent e)\r
\r
}\r
\r
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
- {\r
- SliderPanel pid = null;\r
- if(PIDSlider == null)\r
- {\r
- pid = new SliderPanel(ap, 50, false, cs);\r
- PIDSlider = new Frame();\r
- PIDSlider.add(pid);\r
- }\r
- else\r
- {\r
- pid = (SliderPanel)PIDSlider.getComponent(0);\r
- pid.cs = cs;\r
- }\r
- PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
-\r
- if (ap.av.alignment.getGroups() != null)\r
- pid.setAllGroupsCheckEnabled(true);\r
- else\r
- pid.setAllGroupsCheckEnabled(false);\r
-\r
- return pid.getValue();\r
-\r
- }\r
-\r
- public static void showPIDSlider()\r
- {\r
- try{\r
- conservationSlider.setVisible(false);\r
- conservationSlider = null;\r
- }catch(Exception ex){}\r
-\r
- if(!PIDSlider.isVisible())\r
- {\r
- jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420, 100);\r
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,\r
+ String source)\r
+ {\r
+ SliderPanel pid = null;\r
+ if (PIDSlider == null)\r
+ {\r
+ pid = new SliderPanel(ap, 50, false, cs);\r
+ PIDSlider = new Frame();\r
+ PIDSlider.add(pid);\r
+ }\r
+ else\r
+ {\r
+ pid = (SliderPanel) PIDSlider.getComponent(0);\r
+ pid.cs = cs;\r
+ }\r
+ PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");\r
+\r
+ if (ap.av.alignment.getGroups() != null)\r
+ {\r
+ pid.setAllGroupsCheckEnabled(true);\r
+ }\r
+ else\r
+ {\r
+ pid.setAllGroupsCheckEnabled(false);\r
+ }\r
+\r
+ return pid.getValue();\r
+\r
+ }\r
+\r
+ public static void showPIDSlider()\r
+ {\r
+ try\r
+ {\r
+ conservationSlider.setVisible(false);\r
+ conservationSlider = null;\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+\r
+ if (!PIDSlider.isVisible())\r
+ {\r
+ jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420,\r
+ 100);\r
PIDSlider.addWindowListener(new WindowAdapter()\r
{\r
public void windowClosing(WindowEvent e)\r
});\r
}\r
\r
- }\r
-\r
+ }\r
\r
- public SliderPanel(AlignmentPanel ap, int value, boolean forConserve, ColourSchemeI cs)\r
+ public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,\r
+ ColourSchemeI cs)\r
{\r
this.ap = ap;\r
this.cs = cs;\r
forConservation = forConserve;\r
undoButton.setVisible(false);\r
applyButton.setVisible(false);\r
- if(forConservation)\r
+ if (forConservation)\r
{\r
label.setText("Modify conservation visibility");\r
slider.setMinimum(0);\r
- slider.setMaximum(50+slider.getVisibleAmount());\r
+ slider.setMaximum(50 + slider.getVisibleAmount());\r
slider.setUnitIncrement(1);\r
}\r
else\r
{\r
label.setText("Colour residues above % occurence");\r
slider.setMinimum(0);\r
- slider.setMaximum(100+slider.getVisibleAmount());\r
+ slider.setMaximum(100 + slider.getVisibleAmount());\r
slider.setBlockIncrement(1);\r
}\r
\r
-\r
- slider.addAdjustmentListener( new AdjustmentListener()\r
+ slider.addAdjustmentListener(new AdjustmentListener()\r
{\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
- valueChanged( slider.getValue() );\r
+ valueField.setText(slider.getValue() + "");\r
+ valueChanged(slider.getValue());\r
}\r
});\r
\r
slider.setValue(value);\r
- valueField.setText(value+"");\r
+ valueField.setText(value + "");\r
}\r
\r
public void valueChanged(int i)\r
{\r
- if(cs == null)\r
+ if (cs == null)\r
+ {\r
return;\r
+ }\r
\r
ColourSchemeI toChange = null;\r
Vector allGroups = null;\r
int groupIndex = 0;\r
\r
- if(allGroupsCheck.getState())\r
+ if (allGroupsCheck.getState())\r
{\r
allGroups = ap.av.alignment.getGroups();\r
- groupIndex = allGroups.size()-1;\r
+ groupIndex = allGroups.size() - 1;\r
}\r
else\r
+ {\r
toChange = cs;\r
+ }\r
\r
-\r
- while( groupIndex > -1 )\r
+ while (groupIndex > -1)\r
{\r
- if(allGroups!=null)\r
- toChange = ((SequenceGroup)allGroups.elementAt(groupIndex)).cs;\r
+ if (allGroups != null)\r
+ {\r
+ toChange = ( (SequenceGroup) allGroups.elementAt(groupIndex)).cs;\r
+ }\r
\r
if (forConservation)\r
{\r
if (toChange instanceof ConservationColourScheme)\r
+ {\r
( (ConservationColourScheme) toChange).inc = i;\r
+ }\r
}\r
else\r
{\r
- ( (ResidueColourScheme) toChange).setThreshold(i);\r
+ ( (ResidueColourScheme) toChange).setThreshold(i);\r
}\r
\r
groupIndex--;\r
allGroupsCheck.setEnabled(b);\r
}\r
\r
-\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
int i = Integer.parseInt(valueField.getText());\r
slider.setValue(i);\r
}\r
- catch(Exception ex)\r
+ catch (Exception ex)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
+ valueField.setText(slider.getValue() + "");\r
}\r
}\r
\r
{\r
slider.setValue(value);\r
}\r
+\r
public int getValue()\r
{\r
return Integer.parseInt(valueField.getText());\r
}\r
\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
+import java.util.*;\r
\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-import jalview.schemes.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+import jalview.util.*;\r
\r
-public class TreeCanvas extends Panel implements MouseListener\r
+public class TreeCanvas\r
+ extends Panel implements MouseListener\r
{\r
NJTree tree;\r
ScrollPane scrollPane;\r
AlignViewport av;\r
- public static final String PLACEHOLDER=" * ";\r
+ public static final String PLACEHOLDER = " * ";\r
Font font;\r
- int fontSize = 12;\r
+ int fontSize = 12;\r
\r
boolean fitToWindow = true;\r
boolean showDistances = false;\r
float threshold;\r
\r
String longestName;\r
- int labelLength=-1;\r
+ int labelLength = -1;\r
\r
//RubberbandRectangle rubberband;\r
\r
- Vector listeners;\r
+ Vector listeners;\r
\r
Hashtable nameHash = new Hashtable();\r
Hashtable nodeHash = new Hashtable();\r
\r
- public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller, String label)\r
+ public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,\r
+ String label)\r
{\r
this.av = av;\r
- this.tree = tree;\r
+ this.tree = tree;\r
scrollPane = scroller;\r
addMouseListener(this);\r
tree.findHeight(tree.getTopNode());\r
\r
PaintRefresher.Register(this);\r
}\r
+\r
public void TreeSelectionChanged(Sequence sequence)\r
- {\r
+ {\r
SequenceGroup selected = av.getSelectionGroup();\r
- if(selected == null)\r
+ if (selected == null)\r
{\r
selected = new SequenceGroup();\r
av.setSelectionGroup(selected);\r
selected.setEndRes(av.alignment.getWidth());\r
selected.addOrRemove(sequence);\r
\r
-\r
PaintRefresher.Refresh(this);\r
repaint();\r
- }\r
-\r
-\r
+ }\r
\r
- public void setTree(NJTree tree) {\r
+ public void setTree(NJTree tree)\r
+ {\r
this.tree = tree;\r
tree.findHeight(tree.getTopNode());\r
}\r
\r
- public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {\r
- if (node == null) {\r
+ public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,\r
+ int width, int offx, int offy)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if (node.left() == null && node.right() == null) {\r
+ if (node.left() == null && node.right() == null)\r
+ {\r
// Drawing leaf node\r
\r
float height = node.height;\r
- float dist = node.dist;\r
+ float dist = node.dist;\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\r
+ int xstart = (int) ( (height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
\r
- int ypos = (int)(node.ycount * chunk) + offy;\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
\r
if (node.element() instanceof SequenceI)\r
{\r
- if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() == Color.white)\r
- {\r
- g.setColor(Color.black);\r
- }\r
- else\r
- g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().\r
- darker());\r
+ if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() ==\r
+ Color.white)\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
+ else\r
+ {\r
+ g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().\r
+ darker());\r
+ }\r
\r
}\r
else\r
- g.setColor(Color.black);\r
-\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
\r
// Draw horizontal line\r
- g.drawLine(xstart,ypos,xend,ypos);\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
\r
String nodeLabel = "";\r
- if (showDistances && node.dist > 0) {\r
+ if (showDistances && node.dist > 0)\r
+ {\r
nodeLabel = new Format("%5.2f").form(node.dist);\r
}\r
- if (showBootstrap) {\r
- if (showDistances) {\r
+ if (showBootstrap)\r
+ {\r
+ if (showDistances)\r
+ {\r
nodeLabel = nodeLabel + " : ";\r
}\r
nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
}\r
- if (! nodeLabel.equals("")) {\r
- g.drawString(nodeLabel,xstart,ypos - 10);\r
+ if (!nodeLabel.equals(""))\r
+ {\r
+ g.drawString(nodeLabel, xstart, ypos - 10);\r
}\r
\r
- String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER+node.getName()) : node.getName();\r
+ String name = (markPlaceholders && node.isPlaceholder()) ?\r
+ (PLACEHOLDER + node.getName()) : node.getName();\r
FontMetrics fm = g.getFontMetrics(font);\r
- int charWidth = fm.stringWidth(name) + 3;\r
+ int charWidth = fm.stringWidth(name) + 3;\r
int charHeight = fm.getHeight();\r
\r
- Rectangle rect = new Rectangle(xend+20,ypos-charHeight,\r
- charWidth,charHeight);\r
+ Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,\r
+ charWidth, charHeight);\r
\r
- nameHash.put((SequenceI)node.element(),rect);\r
+ nameHash.put( (SequenceI) node.element(), rect);\r
\r
// Colour selected leaves differently\r
SequenceGroup selected = av.getSelectionGroup();\r
- if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {\r
+ if (selected != null &&\r
+ selected.sequences.contains( (SequenceI) node.element()))\r
+ {\r
g.setColor(Color.gray);\r
\r
- g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);\r
+ g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight);\r
g.setColor(Color.white);\r
}\r
- g.drawString(name,xend+10,ypos);\r
+ g.drawString(name, xend + 10, ypos);\r
g.setColor(Color.black);\r
- } else {\r
- drawNode(g,(SequenceNode)node.left(), chunk,scale,width,offx,offy);\r
- drawNode(g,(SequenceNode)node.right(),chunk,scale,width,offx,offy);\r
+ }\r
+ else\r
+ {\r
+ drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, offy);\r
+ drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, offy);\r
\r
float height = node.height;\r
- float dist = node.dist;\r
+ float dist = node.dist;\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height *scale) + offx;\r
- int ypos = (int)(node.ycount *chunk) + offy;\r
+ int xstart = (int) ( (height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
\r
- g.setColor(((SequenceNode)node).color.darker());\r
+ g.setColor( ( (SequenceNode) node).color.darker());\r
\r
// Draw horizontal line\r
- g.drawLine(xstart,ypos,xend,ypos);\r
- g.fillRect(xend-2, ypos-2, 4,4);\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
+ g.fillRect(xend - 2, ypos - 2, 4, 4);\r
\r
- int ystart = (int)(((SequenceNode)node.left()) .ycount * chunk) + offy;\r
- int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;\r
+ int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) + offy;\r
+ int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) + offy;\r
\r
- Rectangle pos = new Rectangle(xend-2,ypos-2,5,5);\r
- nodeHash.put(node,pos);\r
+ Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);\r
+ nodeHash.put(node, pos);\r
\r
- g.drawLine((int)(height*scale) + offx, ystart,\r
- (int)(height*scale) + offx, yend);\r
+ g.drawLine( (int) (height * scale) + offx, ystart,\r
+ (int) (height * scale) + offx, yend);\r
\r
- if (showDistances && node.dist > 0) {\r
- g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);\r
+ if (showDistances && node.dist > 0)\r
+ {\r
+ g.drawString(new Format("%5.2f").form(node.dist), xstart, ypos - 5);\r
}\r
\r
}\r
}\r
- public Object findElement(int x, int y) {\r
- Enumeration keys = nameHash.keys();\r
\r
- while (keys.hasMoreElements()) {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle)nameHash.get(ob);\r
+ public Object findElement(int x, int y)\r
+ {\r
+ Enumeration keys = nameHash.keys();\r
\r
- if (x >= rect.x && x <= (rect.x + rect.width) &&\r
- y >= rect.y && y <= (rect.y + rect.height)) {\r
- return ob;\r
- }\r
- }\r
- keys = nodeHash.keys();\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nameHash.get(ob);\r
+\r
+ if (x >= rect.x && x <= (rect.x + rect.width) &&\r
+ y >= rect.y && y <= (rect.y + rect.height))\r
+ {\r
+ return ob;\r
+ }\r
+ }\r
+ keys = nodeHash.keys();\r
\r
- while (keys.hasMoreElements()) {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle)nodeHash.get(ob);\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nodeHash.get(ob);\r
\r
- if (x >= rect.x && x <= (rect.x + rect.width) &&\r
- y >= rect.y && y <= (rect.y + rect.height)) {\r
- return ob;\r
- }\r
+ if (x >= rect.x && x <= (rect.x + rect.width) &&\r
+ y >= rect.y && y <= (rect.y + rect.height))\r
+ {\r
+ return ob;\r
+ }\r
}\r
- return null;\r
+ return null;\r
\r
}\r
\r
- public void pickNodes(Rectangle pickBox) {\r
- int width = getSize().width;\r
+ public void pickNodes(Rectangle pickBox)\r
+ {\r
+ int width = getSize().width;\r
int height = getSize().height;\r
\r
SequenceNode top = tree.getTopNode();\r
\r
- float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()\r
-;\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
+ float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight()\r
+ ;\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ( (SequenceNode) top.left()).count +\r
+ ( (SequenceNode) top.right()).count;\r
}\r
- float chunk = (float)(height-offy*2)/top.count;\r
+ float chunk = (float) (height - offy * 2) / top.count;\r
\r
- pickNode(pickBox,top,chunk,wscale,width,offx,offy);\r
+ pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
}\r
\r
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {\r
- if (node == null) {\r
+ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,\r
+ float scale, int width, int offx, int offy)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if (node.left() == null && node.right() == null) {\r
+ if (node.left() == null && node.right() == null)\r
+ {\r
float height = node.height;\r
- float dist = node.dist;\r
+ float dist = node.dist;\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\r
+ int xstart = (int) ( (height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
\r
- int ypos = (int)(node.ycount * chunk) + offy;\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
\r
- if (pickBox.contains(new Point(xend,ypos))) {\r
- if (node.element() instanceof SequenceI) {\r
- SequenceI seq = (SequenceI)node.element();\r
+ if (pickBox.contains(new Point(xend, ypos)))\r
+ {\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ SequenceI seq = (SequenceI) node.element();\r
SequenceGroup sg = av.getSelectionGroup();\r
- if(sg!=null)\r
+ if (sg != null)\r
+ {\r
sg.addOrRemove(seq);\r
+ }\r
}\r
}\r
- } else {\r
- pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);\r
- pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);\r
+ }\r
+ else\r
+ {\r
+ pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, offx,\r
+ offy);\r
+ pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, offx,\r
+ offy);\r
}\r
}\r
\r
public void setColor(SequenceNode node, Color c)\r
{\r
if (node == null)\r
+ {\r
return;\r
+ }\r
\r
if (node.left() == null && node.right() == null)\r
{\r
node.color = c;\r
\r
if (node.element() instanceof SequenceI)\r
- ((SequenceI)node.element()).setColor(c);\r
- } else\r
+ {\r
+ ( (SequenceI) node.element()).setColor(c);\r
+ }\r
+ }\r
+ else\r
{\r
node.color = c;\r
- setColor((SequenceNode)node.left(),c);\r
- setColor((SequenceNode)node.right(),c);\r
+ setColor( (SequenceNode) node.left(), c);\r
+ setColor( (SequenceNode) node.right(), c);\r
}\r
}\r
\r
-\r
public void paint(Graphics g)\r
{\r
\r
- font = new Font("Verdana",Font.PLAIN,fontSize);\r
+ font = new Font("Verdana", Font.PLAIN, fontSize);\r
g.setFont(font);\r
\r
FontMetrics fm = g.getFontMetrics(font);\r
\r
- if(nameHash.size()==0)\r
+ if (nameHash.size() == 0)\r
+ {\r
repaint();\r
+ }\r
\r
-\r
- if( fitToWindow || (!fitToWindow && scrollPane.getSize().height > fm.getHeight() * nameHash.size()+offy ) )\r
- {\r
- draw(g,scrollPane.getSize().width,scrollPane.getSize().height);\r
- }\r
+ if (fitToWindow ||\r
+ (!fitToWindow &&\r
+ scrollPane.getSize().height > fm.getHeight() * nameHash.size() + offy))\r
+ {\r
+ draw(g, scrollPane.getSize().width, scrollPane.getSize().height);\r
+ }\r
else\r
- {\r
- setSize(new Dimension(scrollPane.getSize().width, fm.getHeight() * nameHash.size()));\r
- draw( g,scrollPane.getSize().width, fm.getHeight() * nameHash.size());\r
- }\r
+ {\r
+ setSize(new Dimension(scrollPane.getSize().width,\r
+ fm.getHeight() * nameHash.size()));\r
+ draw(g, scrollPane.getSize().width, fm.getHeight() * nameHash.size());\r
+ }\r
\r
scrollPane.validate();\r
}\r
- public int getFontSize() {\r
- return fontSize;\r
- }\r
- public void setFontSize(int fontSize) {\r
- this.fontSize = fontSize;\r
- repaint();\r
- }\r
- public void draw(Graphics g, int width, int height) {\r
\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,width,height);\r
+ public int getFontSize()\r
+ {\r
+ return fontSize;\r
+ }\r
\r
+ public void setFontSize(int fontSize)\r
+ {\r
+ this.fontSize = fontSize;\r
+ repaint();\r
+ }\r
\r
- labelLength = g.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar\r
+ public void draw(Graphics g, int width, int height)\r
+ {\r
\r
- float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, width, height);\r
\r
- SequenceNode top = tree.getTopNode();\r
+ labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar\r
\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
- }\r
- float chunk = (float)(height-offy*2)/top.count ;\r
+ float wscale = (float) (width - labelLength - offx * 2) / tree.getMaxHeight();\r
\r
- drawNode(g,tree.getTopNode(),chunk,wscale,width,offx,offy);\r
+ SequenceNode top = tree.getTopNode();\r
\r
- if (threshold != 0)\r
- {\r
- if(av.getCurrentTree() == tree)\r
- g.setColor(Color.red);\r
- else\r
- g.setColor(Color.gray);\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ( (SequenceNode) top.left()).count +\r
+ ( (SequenceNode) top.right()).count;\r
+ }\r
+ float chunk = (float) (height - offy * 2) / top.count;\r
\r
- int x = (int)( threshold * (float)(getSize().width-labelLength - 2*offx) +offx ) ;\r
+ drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
\r
- g.drawLine(x,0,x,getSize().height);\r
+ if (threshold != 0)\r
+ {\r
+ if (av.getCurrentTree() == tree)\r
+ {\r
+ g.setColor(Color.red);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(Color.gray);\r
}\r
\r
- }\r
-\r
- public void mouseReleased(MouseEvent e) { }\r
- public void mouseEntered(MouseEvent e) { }\r
- public void mouseExited(MouseEvent e) { }\r
- public void mouseClicked(MouseEvent e) {\r
- }\r
-\r
- public void mousePressed(MouseEvent e) {\r
+ int x = (int) (threshold *\r
+ (float) (getSize().width - labelLength - 2 * offx) + offx);\r
\r
- av.setCurrentTree(tree);\r
+ g.drawLine(x, 0, x, getSize().height);\r
+ }\r
\r
- int x = e.getX();\r
- int y = e.getY();\r
+ }\r
\r
- Object ob = findElement(x,y);\r
+ public void mouseReleased(MouseEvent e)\r
+ {}\r
\r
- if (ob instanceof SequenceI)\r
- {\r
- TreeSelectionChanged((Sequence)ob);\r
- repaint();\r
- return;\r
+ public void mouseEntered(MouseEvent e)\r
+ {}\r
\r
- } else if (ob instanceof SequenceNode) {\r
- SequenceNode tmpnode = (SequenceNode)ob;\r
- tree.swapNodes(tmpnode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- } else {\r
- // Find threshold\r
+ public void mouseExited(MouseEvent e)\r
+ {}\r
\r
- if (tree.getMaxHeight() != 0) {\r
- threshold = (float)(x - offx)/(float)(getSize().width-labelLength - 2*offx);\r
+ public void mouseClicked(MouseEvent e)\r
+ {\r
+ }\r
\r
- tree.getGroups().removeAllElements();\r
- tree.groupNodes(tree.getTopNode(),threshold);\r
- setColor(tree.getTopNode(),Color.black);\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
\r
- av.setSelectionGroup(null);\r
- av.alignment.deleteAllGroups();\r
+ av.setCurrentTree(tree);\r
\r
- for (int i=0; i < tree.getGroups().size(); i++)\r
- {\r
+ int x = e.getX();\r
+ int y = e.getY();\r
\r
- Color col = new Color((int)(Math.random()*255),\r
- (int)(Math.random()*255),\r
- (int)(Math.random()*255));\r
- setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());\r
+ Object ob = findElement(x, y);\r
\r
- Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());\r
- SequenceGroup sg = null;\r
- for (int j = 0; j < l.size(); j++)\r
- {\r
- SequenceNode sn = (SequenceNode) l.elementAt(j);\r
- if(sg==null)\r
- sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());\r
+ if (ob instanceof SequenceI)\r
+ {\r
+ TreeSelectionChanged( (Sequence) ob);\r
+ repaint();\r
+ return;\r
\r
- sg.addSequence( (Sequence) sn.element());\r
- }\r
+ }\r
+ else if (ob instanceof SequenceNode)\r
+ {\r
+ SequenceNode tmpnode = (SequenceNode) ob;\r
+ tree.swapNodes(tmpnode);\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+ }\r
+ else\r
+ {\r
+ // Find threshold\r
\r
- if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, sg.getStartRes(),\r
- sg.getEndRes());\r
+ if (tree.getMaxHeight() != 0)\r
+ {\r
+ threshold = (float) (x - offx) /\r
+ (float) (getSize().width - labelLength - 2 * offx);\r
+\r
+ tree.getGroups().removeAllElements();\r
+ tree.groupNodes(tree.getTopNode(), threshold);\r
+ setColor(tree.getTopNode(), Color.black);\r
+\r
+ av.setSelectionGroup(null);\r
+ av.alignment.deleteAllGroups();\r
+\r
+ for (int i = 0; i < tree.getGroups().size(); i++)\r
+ {\r
+\r
+ Color col = new Color( (int) (Math.random() * 255),\r
+ (int) (Math.random() * 255),\r
+ (int) (Math.random() * 255));\r
+ setColor( (SequenceNode) tree.getGroups().elementAt(i), col.brighter());\r
+\r
+ Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(\r
+ i), new Vector());\r
+ SequenceGroup sg = null;\r
+ for (int j = 0; j < l.size(); j++)\r
+ {\r
+ SequenceNode sn = (SequenceNode) l.elementAt(j);\r
+ if (sg == null)\r
+ {\r
+ sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true, false,\r
+ 0, av.alignment.getWidth());\r
+ }\r
\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
+ sg.addSequence( (Sequence) sn.element());\r
+ }\r
\r
- sg.cs = ccs;\r
+ if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) av.\r
+ getGlobalColourScheme();\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, sg.getStartRes(),\r
+ sg.getEndRes());\r
\r
- }\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
\r
+ sg.cs = ccs;\r
\r
+ }\r
\r
- av.alignment.addGroup(sg);\r
+ av.alignment.addGroup(sg);\r
\r
- }\r
- }\r
+ }\r
}\r
+ }\r
\r
- PaintRefresher.Refresh(this);\r
- repaint();\r
+ PaintRefresher.Refresh(this);\r
+ repaint();\r
\r
}\r
\r
- public void setShowDistances(boolean state) {\r
- this.showDistances = state;\r
- repaint();\r
- }\r
+ public void setShowDistances(boolean state)\r
+ {\r
+ this.showDistances = state;\r
+ repaint();\r
+ }\r
\r
- public void setShowBootstrap(boolean state) {\r
- this.showBootstrap = state;\r
- repaint();\r
- }\r
- public void setMarkPlaceholders(boolean state) {\r
- this.markPlaceholders = state;\r
- repaint();\r
- }\r
+ public void setShowBootstrap(boolean state)\r
+ {\r
+ this.showBootstrap = state;\r
+ repaint();\r
+ }\r
\r
-}\r
+ public void setMarkPlaceholders(boolean state)\r
+ {\r
+ this.markPlaceholders = state;\r
+ repaint();\r
+ }\r
\r
+}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.io.NewickFile;\r
-import jalview.analysis.*;\r
-import jalview.jbappletgui.GTreePanel;\r
-import java.awt.event.*;\r
import java.util.*;\r
-import jalview.io.NewickFile;\r
\r
+import java.awt.event.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbappletgui.*;\r
\r
-public class TreePanel extends GTreePanel\r
+public class TreePanel\r
+ extends GTreePanel\r
{\r
SequenceI[] seq;\r
String type;\r
return tree;\r
}\r
\r
- public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
+ public TreePanel(AlignViewport av, Vector seqVector, String type,\r
+ String pwtype, int s, int e)\r
{\r
super();\r
\r
end = e;\r
\r
String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ seq = new Sequence[seqVector.size()];\r
+ for (int i = 0; i < seqVector.size(); i++)\r
{\r
seq[i] = (Sequence) seqVector.elementAt(i);\r
- if(seq[i].getName().length()>longestName.length())\r
+ if (seq[i].getName().length() > longestName.length())\r
+ {\r
longestName = seq[i].getName();\r
+ }\r
}\r
\r
tree = new NJTree(seq, type, pwtype, start, end);\r
scrollPane.add(treeCanvas);\r
\r
}\r
+\r
public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
String type, String pwtype)\r
- {\r
- super();\r
- // These are probably only arbitrary strings reflecting source of tree\r
- this.type = type;\r
- this.pwtype = pwtype;\r
+ {\r
+ super();\r
+ // These are probably only arbitrary strings reflecting source of tree\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
\r
- start = 0;\r
- end = seqVector.size();\r
+ start = 0;\r
+ end = seqVector.size();\r
+\r
+ String longestName = "";\r
+ seq = new Sequence[seqVector.size()];\r
+ for (int i = 0; i < seqVector.size(); i++)\r
+ {\r
+ seq[i] = (Sequence) seqVector.elementAt(i);\r
+ }\r
+ // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
+ tree = new NJTree(seq, newtree);\r
+ // Now have to calculate longest name based on the leaves\r
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ if (longestName.length() <\r
+ ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().\r
+ length())\r
{\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).\r
+ getName();\r
}\r
- // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
- tree = new NJTree(seq, newtree);\r
- // Now have to calculate longest name based on the leaves\r
- Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());\r
-\r
- for (int i=0;i < leaves.size();i++)\r
- if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())\r
- longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();\r
-\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
-\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- distanceMenu.setState(newtree.HasDistances());\r
- bootstrapMenu.setState(newtree.HasBootstrap());\r
- if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
- placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
- scrollPane.add(treeCanvas);\r
+ }\r
+\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
\r
+ treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+ treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
+ treeCanvas.setShowDistances(newtree.HasDistances());\r
+ distanceMenu.setState(newtree.HasDistances());\r
+ bootstrapMenu.setState(newtree.HasBootstrap());\r
+ if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
+ {\r
+ placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
}\r
+ scrollPane.add(treeCanvas);\r
\r
-public String getText(String format) {\r
- return null;\r
-}\r
+ }\r
+\r
+ public String getText(String format)\r
+ {\r
+ return null;\r
+ }\r
\r
protected void fitToWindow_actionPerformed(ActionEvent e)\r
{\r
cap.setText(output);\r
java.awt.Frame frame = new java.awt.Frame();\r
frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,100);\r
+ jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);\r
}\r
\r
-\r
-\r
protected void fontSize_actionPerformed(ActionEvent e)\r
{\r
- /* if( treeCanvas==null )\r
- return;\r
-\r
- String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);\r
-\r
- Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Select font size",\r
- "Font size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
- ,"Font Size - "+size);\r
- if(selection!=null)\r
- {\r
- fontSize.setText("Font Size - " + selection);\r
-\r
- int i = Integer.parseInt(selection.toString());\r
- treeCanvas.setFontSize(i);\r
- }\r
- scrollPane.setViewportView(treeCanvas);\r
-*/\r
+ /* if( treeCanvas==null )\r
+ return;\r
+\r
+ String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);\r
+\r
+ Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Select font size",\r
+ "Font size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
+ ,"Font Size - "+size);\r
+ if(selection!=null)\r
+ {\r
+ fontSize.setText("Font Size - " + selection);\r
+\r
+ int i = Integer.parseInt(selection.toString());\r
+ treeCanvas.setFontSize(i);\r
+ }\r
+ scrollPane.setViewportView(treeCanvas);\r
+ */\r
}\r
\r
protected void distanceMenu_actionPerformed(ActionEvent e)\r
\r
protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
{\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
}\r
\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GUserDefinedColours;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.io.*;\r
import java.io.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.jbappletgui.*;\r
+import jalview.schemes.*;\r
\r
-public class UserDefinedColours extends GUserDefinedColours\r
+public class UserDefinedColours\r
+ extends GUserDefinedColours\r
{\r
\r
AlignmentPanel ap;\r
super();\r
frame = new Frame();\r
frame.add(this);\r
- jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420,345 );\r
-\r
- if(sg!=null)\r
- frame.setTitle( frame.getTitle()+ " ("+sg.getName()+")");\r
+ jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);\r
\r
+ if (sg != null)\r
+ {\r
+ frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");\r
+ }\r
\r
this.ap = ap;\r
seqGroup = sg;\r
\r
+ if (seqGroup != null)\r
+ {\r
+ oldColourScheme = seqGroup.cs;\r
+ }\r
+ else\r
+ {\r
+ oldColourScheme = ap.av.getGlobalColourScheme();\r
+ }\r
\r
- if (seqGroup != null)\r
- oldColourScheme = seqGroup.cs;\r
- else\r
- oldColourScheme = ap.av.getGlobalColourScheme();\r
-\r
- for (int i = 0; i < 20; i++)\r
- makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
- "", ResidueProperties.aa[i]);\r
+ for (int i = 0; i < 20; i++)\r
+ {\r
+ makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
+ "", ResidueProperties.aa[i]);\r
+ }\r
\r
- makeButton("B", "B");\r
- makeButton("Z", "Z");\r
- makeButton("X", "X");\r
- makeButton("Gap", "'.','-',' '");\r
+ makeButton("B", "B");\r
+ makeButton("Z", "Z");\r
+ makeButton("X", "X");\r
+ makeButton("Gap", "'.','-',' '");\r
\r
}\r
\r
- protected void rText_actionPerformed(ActionEvent e) {\r
- try{\r
+ protected void rText_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
int i = Integer.parseInt(rText.getText());\r
rScroller.setValue(i);\r
- }catch(NumberFormatException ex){}\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {}\r
}\r
\r
- protected void gText_actionPerformed(ActionEvent e) {\r
- try{\r
+ protected void gText_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
int i = Integer.parseInt(gText.getText());\r
gScroller.setValue(i);\r
- }catch(NumberFormatException ex){}\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {}\r
\r
}\r
\r
- protected void bText_actionPerformed(ActionEvent e) {\r
- try{\r
+ protected void bText_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
int i = Integer.parseInt(bText.getText());\r
bScroller.setValue(i);\r
- }catch(NumberFormatException ex){}\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {}\r
\r
}\r
\r
-\r
- protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
+ protected void rScroller_adjustmentValueChanged(AdjustmentEvent e)\r
+ {\r
R = rScroller.getValue();\r
- rText.setText(R+"");\r
+ rText.setText(R + "");\r
colourChanged();\r
}\r
\r
- protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
+ protected void gScroller_adjustmentValueChanged(AdjustmentEvent e)\r
+ {\r
G = gScroller.getValue();\r
- gText.setText(G+"");\r
+ gText.setText(G + "");\r
colourChanged();\r
}\r
\r
- protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
+ protected void bScroller_adjustmentValueChanged(AdjustmentEvent e)\r
+ {\r
B = bScroller.getValue();\r
- bText.setText(B+"");\r
+ bText.setText(B + "");\r
colourChanged();\r
}\r
\r
- public void colourChanged()\r
- {\r
- Color col = new Color(R,G,B);\r
- target.setBackground( col );\r
+ public void colourChanged()\r
+ {\r
+ Color col = new Color(R, G, B);\r
+ target.setBackground(col);\r
\r
- if(selectedButton!=null)\r
- selectedButton.setBackground( col );\r
- }\r
+ if (selectedButton != null)\r
+ {\r
+ selectedButton.setBackground(col);\r
+ }\r
+ }\r
\r
public void colourButtonPressed(MouseEvent e)\r
{\r
- selectedButton = (Button)e.getSource();\r
- Color col = selectedButton.getBackground();\r
- R = col.getRed();\r
- G = col.getGreen();\r
- B = col.getBlue();\r
- rScroller.setValue(R);\r
- gScroller.setValue(G);\r
- bScroller.setValue(B);\r
- rText.setText(R+"");\r
- gText.setText(G+"");\r
- bText.setText(B+"");\r
-\r
- colourChanged();\r
+ selectedButton = (Button) e.getSource();\r
+ Color col = selectedButton.getBackground();\r
+ R = col.getRed();\r
+ G = col.getGreen();\r
+ B = col.getBlue();\r
+ rScroller.setValue(R);\r
+ gScroller.setValue(G);\r
+ bScroller.setValue(B);\r
+ rText.setText(R + "");\r
+ gText.setText(G + "");\r
+ bText.setText(B + "");\r
+\r
+ colourChanged();\r
}\r
\r
void makeButton(String label, String aa)\r
final Button button = new Button();\r
Color col = Color.white;\r
\r
-\r
- try{\r
+ try\r
+ {\r
col = oldColourScheme.findColour(aa, -1);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
\r
- button.setBackground( col );\r
- oldColours.addElement( col );\r
- button.setLabel( label );\r
- button.setForeground( col.darker().darker().darker() );\r
+ button.setBackground(col);\r
+ oldColours.addElement(col);\r
+ button.setLabel(label);\r
+ button.setForeground(col.darker().darker().darker());\r
button.setFont(new java.awt.Font("Verdana", 1, 10));\r
button.addMouseListener(new java.awt.event.MouseAdapter()\r
{\r
buttonPanel.add(button, null);\r
}\r
\r
-\r
protected void okButton_actionPerformed(ActionEvent e)\r
{\r
applyButton_actionPerformed(null);\r
- frame.setVisible(false);\r
+ frame.setVisible(false);\r
}\r
\r
protected void applyButton_actionPerformed(ActionEvent e)\r
{\r
\r
- Color [] newColours = new Color[24];\r
- for(int i=0; i<24; i++)\r
+ Color[] newColours = new Color[24];\r
+ for (int i = 0; i < 24; i++)\r
{\r
- Button button = (Button)buttonPanel.getComponent(i);\r
- newColours[i] = button.getBackground();\r
+ Button button = (Button) buttonPanel.getComponent(i);\r
+ newColours[i] = button.getBackground();\r
}\r
\r
- UserColourScheme ucs = new UserColourScheme( newColours );\r
+ UserColourScheme ucs = new UserColourScheme(newColours);\r
ucs.setThreshold(0);\r
\r
- if(seqGroup!=null)\r
+ if (seqGroup != null)\r
+ {\r
seqGroup.cs = ucs;\r
+ }\r
else\r
+ {\r
ap.av.setGlobalColourScheme(ucs);\r
+ }\r
\r
ap.repaint();\r
}\r
\r
-\r
public static UserColourScheme loadDefaultColours(String file)\r
{\r
UserColourScheme ucs = null;\r
try\r
{\r
BufferedReader in = new BufferedReader(new FileReader(file));\r
- Color [] newColours = new Color[24];\r
+ Color[] newColours = new Color[24];\r
for (int i = 0; i < 24; i++)\r
{\r
newColours[i] = new Color(Integer.parseInt(in.readLine()));\r
return ucs;\r
}\r
\r
-\r
protected void cancelButton_actionPerformed(ActionEvent e)\r
{\r
\r
- Color [] newColours = new Color[24];\r
- for(int i=0; i<24; i++)\r
+ Color[] newColours = new Color[24];\r
+ for (int i = 0; i < 24; i++)\r
{\r
- newColours[i] = (Color)oldColours.elementAt(i);\r
- buttonPanel.getComponent(i).setBackground(newColours[i]);\r
+ newColours[i] = (Color) oldColours.elementAt(i);\r
+ buttonPanel.getComponent(i).setBackground(newColours[i]);\r
}\r
\r
- UserColourScheme ucs = new UserColourScheme( newColours );\r
+ UserColourScheme ucs = new UserColourScheme(newColours);\r
\r
if (seqGroup != null)\r
+ {\r
seqGroup.cs = ucs;\r
+ }\r
else\r
+ {\r
ap.av.setGlobalColourScheme(ucs);\r
+ }\r
\r
ap.repaint();\r
\r
frame.setVisible(false);\r
}\r
\r
-\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.bin;\r
-import java.util.*;\r
+\r
import java.io.*;\r
\r
+import java.util.*;\r
import java.util.jar.*;\r
-public class Cache\r
-{\r
- public static String VERSION = "Release 2.0";\r
- public static String BUILD_DATE = "";\r
-\r
- public static Properties applicationProperties;\r
- // Current properties include:\r
- //\r
- // LAST_DIRECTORY , use this to cache record of where the user looked to find a file\r
- // UNIPROT_CACHE\r
- // USER_DEFINED_COLOUR - file describing last user set colours\r
- // FONT_NAME\r
- // FONT_STYLE\r
- // FONT_SIZE\r
- // logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)\r
- // jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.\r
- public static void loadProperties()\r
- {\r
- // get last build time.\r
- long date = 0;\r
- try{\r
- String localFile = Cache.class.getProtectionDomain().getCodeSource().getLocation().toString();\r
- localFile = localFile.concat("!/");\r
- String tmpString = "jar:";\r
- String localJarFileString = tmpString.concat(localFile);\r
- java.net.URL localJarFileURL = new java.net.URL(localJarFileString);\r
- java.net.JarURLConnection localJarFile = (java.net.JarURLConnection)localJarFileURL.openConnection();\r
- date = localJarFile.getLastModified();\r
- }catch(Exception ex){ex.printStackTrace();}\r
- if(date==0)\r
- {\r
- // this is called for unpackaged class files, ie not in a Jar file\r
- // InstallAnywhere version will find build date this way\r
- // not entirely accurate as it only tells you when Cache.class was last compiled\r
-\r
-\r
- java.io.File f = new java.io.File(System.getProperty("user.dir") + "/jalview/bin/Cache.class" );\r
- date = f.lastModified();\r
- }\r
-\r
- if(date!=0)\r
- BUILD_DATE = new Date( date ).toString();\r
\r
- applicationProperties = new Properties();\r
\r
- try\r
- {\r
- FileInputStream in = new FileInputStream(System.getProperty("user.home") +\r
- "/.jalview_properties");\r
- applicationProperties = new Properties();\r
- applicationProperties.load(in);\r
- in.close();\r
+public class Cache {\r
+ public static String VERSION = "Release 2.0";\r
+ public static String BUILD_DATE = "";\r
+ public static Properties applicationProperties;\r
+\r
+ // Current properties include:\r
+ //\r
+ // LAST_DIRECTORY , use this to cache record of where the user looked to find a file\r
+ // UNIPROT_CACHE\r
+ // USER_DEFINED_COLOUR - file describing last user set colours\r
+ // FONT_NAME\r
+ // FONT_STYLE\r
+ // FONT_SIZE\r
+ // logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)\r
+ // jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.\r
+ public static void loadProperties() {\r
+ // get last build time.\r
+ long date = 0;\r
+\r
+ try {\r
+ String localFile = Cache.class.getProtectionDomain().getCodeSource()\r
+ .getLocation().toString();\r
+ localFile = localFile.concat("!/");\r
+\r
+ String tmpString = "jar:";\r
+ String localJarFileString = tmpString.concat(localFile);\r
+ java.net.URL localJarFileURL = new java.net.URL(localJarFileString);\r
+ java.net.JarURLConnection localJarFile = (java.net.JarURLConnection) localJarFileURL.openConnection();\r
+ date = localJarFile.getLastModified();\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if (date == 0) {\r
+ // this is called for unpackaged class files, ie not in a Jar file\r
+ // InstallAnywhere version will find build date this way\r
+ // not entirely accurate as it only tells you when Cache.class was last compiled\r
+ java.io.File f = new java.io.File(System.getProperty("user.dir") +\r
+ "/jalview/bin/Cache.class");\r
+ date = f.lastModified();\r
+ }\r
+\r
+ if (date != 0) {\r
+ BUILD_DATE = new Date(date).toString();\r
+ }\r
+\r
+ applicationProperties = new Properties();\r
+\r
+ try {\r
+ FileInputStream in = new FileInputStream(System.getProperty(\r
+ "user.home") + "/.jalview_properties");\r
+ applicationProperties = new Properties();\r
+ applicationProperties.load(in);\r
+ in.close();\r
+ } catch (Exception ex) {\r
+ }\r
}\r
- catch (Exception ex)\r
- { }\r
- }\r
-\r
- public static String getProperty(String key)\r
- {\r
- return applicationProperties.getProperty(key);\r
- }\r
-\r
- public static String setProperty(String key, String obj)\r
- {\r
- try\r
- {\r
- FileOutputStream out = new FileOutputStream(System.getProperty(\r
- "user.home") + "/.jalview_properties");\r
-\r
- applicationProperties.setProperty(key, obj);\r
-\r
- applicationProperties.store(out, "---JalviewX Properties File---");\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- return obj;\r
-\r
- }\r
\r
+ public static String getProperty(String key) {\r
+ return applicationProperties.getProperty(key);\r
+ }\r
\r
+ public static String setProperty(String key, String obj) {\r
+ try {\r
+ FileOutputStream out = new FileOutputStream(System.getProperty(\r
+ "user.home") + "/.jalview_properties");\r
\r
+ applicationProperties.setProperty(key, obj);\r
\r
+ applicationProperties.store(out, "---JalviewX Properties File---");\r
+ out.close();\r
+ } catch (Exception ex) {\r
+ }\r
\r
+ return obj;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.bin;\r
\r
import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
+\r
import jalview.io.*;\r
\r
import org.apache.log4j.*;\r
\r
-public class Jalview extends JApplet\r
-{\r
- public static JApplet applet;\r
- Desktop frame;\r
- public void init()\r
- {\r
- applet = this;\r
- Cache.loadProperties();\r
- jalview.gui.Preferences.initPreferences();\r
-\r
- frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
- frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);\r
- frame.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- applet.stop();\r
- applet.destroy();\r
- }\r
- });\r
-\r
- String file = getParameter("alignment");\r
-\r
- if(file!=null)\r
- {\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);\r
- String protocol = "File";\r
- if (file.indexOf("http:") > -1)\r
- protocol = "URL";\r
-\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
-\r
- frame.LoadFile(file, protocol, format);\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+\r
+\r
+public class Jalview extends JApplet {\r
+ public static JApplet applet;\r
+ Desktop frame;\r
+\r
+ public void init() {\r
+ applet = this;\r
+ Cache.loadProperties();\r
+ jalview.gui.Preferences.initPreferences();\r
+\r
+ frame = new Desktop();\r
+ frame.setResizable(true);\r
+ frame.setVisible(true);\r
+ frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);\r
+ frame.addWindowListener(new WindowAdapter() {\r
+ public void windowClosing(WindowEvent e) {\r
+ applet.stop();\r
+ applet.destroy();\r
+ }\r
+ });\r
+\r
+ String file = getParameter("alignment");\r
+\r
+ if (file != null) {\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);\r
+\r
+ String protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1) {\r
+ protocol = "URL";\r
+ }\r
+\r
+ String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+\r
+ frame.LoadFile(file, protocol, format);\r
+ }\r
}\r
- }\r
-\r
- public void destroy()\r
- {\r
- if(applet!=null)\r
- applet.stop();\r
- else\r
- System.exit(0);\r
- frame.setVisible(false);\r
- }\r
-\r
- private static void initLogger() {\r
- Logger l = Logger.getLogger("org.apache.axis");\r
- if (Cache.getProperty("logs.Axis.Level")==null) {\r
- Cache.setProperty("logs.Axis.Level", Level.INFO.toString());\r
+\r
+ public void destroy() {\r
+ if (applet != null) {\r
+ applet.stop();\r
+ } else {\r
+ System.exit(0);\r
+ }\r
+\r
+ frame.setVisible(false);\r
}\r
\r
- l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));\r
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),"System.err");\r
- ap.setName("Axis");\r
- l.addAppender(ap);\r
- }\r
- public static void main(String[] args) {\r
-\r
- Cache.loadProperties();\r
- jalview.gui.Preferences.initPreferences();\r
- try {\r
- initLogger();\r
- } catch (Exception e) {\r
- System.err.println("Problems initializing the log4j system\n");\r
- e.printStackTrace();\r
+ private static void initLogger() {\r
+ Logger l = Logger.getLogger("org.apache.axis");\r
+\r
+ if (Cache.getProperty("logs.Axis.Level") == null) {\r
+ Cache.setProperty("logs.Axis.Level", Level.INFO.toString());\r
+ }\r
+\r
+ l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));\r
+\r
+ ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),\r
+ "System.err");\r
+ ap.setName("Axis");\r
+ l.addAppender(ap);\r
}\r
- try{\r
- UIManager.setLookAndFeel(\r
- // "javax.swing.plaf.metal.MetalLookAndFeel"\r
- // "javax.swing.plaf.multi.MultiLookAndFeel"\r
- UIManager.getSystemLookAndFeelClassName()\r
- // UIManager.getCrossPlatformLookAndFeelClassName()\r
- // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
- // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
- // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
- );\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- Desktop frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
-\r
-\r
-\r
- if(args!=null && args.length>0)\r
- {\r
- String file=null;\r
- if(args[0].equals("-open"))\r
- file = args[1];\r
- else\r
- file = args[0];\r
-\r
- String protocol = "File";\r
- if(file.indexOf("http:")>-1)\r
- protocol = "URL";\r
-\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
-\r
- frame.LoadFile(file, protocol, format);\r
- }\r
-\r
- if(jalview.gui.Preferences.showStartupFile &&\r
- jalview.gui.Preferences.startupFile!=null)\r
- {\r
- String file = jalview.gui.Preferences.startupFile;\r
- String protocol = "File";\r
- if (file.indexOf("http:") > -1)\r
- protocol = "URL";\r
-\r
- if(file.endsWith(".jar"))\r
- Jalview2XML.LoadJalviewAlign(file);\r
- else\r
- {\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
- frame.LoadFile(file, protocol, format);\r
- }\r
- }\r
-\r
-\r
-\r
- }\r
\r
+ public static void main(String[] args) {\r
+ Cache.loadProperties();\r
+ jalview.gui.Preferences.initPreferences();\r
+\r
+ try {\r
+ initLogger();\r
+ } catch (Exception e) {\r
+ System.err.println("Problems initializing the log4j system\n");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ try {\r
+ UIManager.setLookAndFeel(\r
+ // "javax.swing.plaf.metal.MetalLookAndFeel"\r
+ // "javax.swing.plaf.multi.MultiLookAndFeel"\r
+ UIManager.getSystemLookAndFeelClassName());\r
+ } catch (Exception ex) {\r
+ }\r
+\r
+ Desktop frame = new Desktop();\r
+ frame.setResizable(true);\r
+ frame.setVisible(true);\r
+\r
+ if ((args != null) && (args.length > 0)) {\r
+ String file = null;\r
+\r
+ if (args[0].equals("-open")) {\r
+ file = args[1];\r
+ } else {\r
+ file = args[0];\r
+ }\r
+\r
+ String protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1) {\r
+ protocol = "URL";\r
+ }\r
+\r
+ String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+\r
+ frame.LoadFile(file, protocol, format);\r
+ }\r
+\r
+ if (jalview.gui.Preferences.showStartupFile &&\r
+ (jalview.gui.Preferences.startupFile != null)) {\r
+ String file = jalview.gui.Preferences.startupFile;\r
+ String protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1) {\r
+ protocol = "URL";\r
+ }\r
+\r
+ if (file.endsWith(".jar")) {\r
+ Jalview2XML.LoadJalviewAlign(file);\r
+ } else {\r
+ String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+ frame.LoadFile(file, protocol, format);\r
+ }\r
+ }\r
+ }\r
}\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.bin;\r
\r
+import jalview.appletgui.AlignFrame;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import jalview.io.*;\r
+\r
import java.applet.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.appletgui.AlignFrame;\r
\r
-public class JalviewLite extends Applet\r
-{\r
- static int lastFrameX = 200;\r
- static int lastFrameY = 200;\r
- static Applet applet;\r
- boolean fileFound = true;\r
- String file = "No file";\r
- Button launcher = new Button("Start Jalview");\r
-\r
- public void init()\r
- {\r
- applet = this;\r
- this.setBackground(Color.white);\r
-\r
- file = getParameter("file");\r
- if (file != null)\r
- {\r
- add(launcher);\r
- file = applet.getCodeBase() + file;\r
- launcher.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- String format = jalview.io.IdentifyFile.Identify( file, "URL");\r
- LoadFile(file, "URL", format);\r
- }\r
- });\r
+\r
+public class JalviewLite extends Applet {\r
+ static int lastFrameX = 200;\r
+ static int lastFrameY = 200;\r
+ static Applet applet;\r
+ boolean fileFound = true;\r
+ String file = "No file";\r
+ Button launcher = new Button("Start Jalview");\r
+\r
+ public void init() {\r
+ applet = this;\r
+ this.setBackground(Color.white);\r
+\r
+ file = getParameter("file");\r
+\r
+ if (file != null) {\r
+ add(launcher);\r
+ file = applet.getCodeBase() + file;\r
+ launcher.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ String format = jalview.io.IdentifyFile.Identify(file,\r
+ "URL");\r
+ LoadFile(file, "URL", format);\r
+ }\r
+ });\r
+ } else {\r
+ file = "NO FILE";\r
+ fileFound = false;\r
+ }\r
+ }\r
+\r
+ public static void showURL(String url) {\r
+ try {\r
+ applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ "HELP_WINDOW");\r
+ } catch (Exception ex) {\r
+ }\r
}\r
- else\r
- {\r
- file = "NO FILE";\r
- fileFound = false;\r
- }\r
- }\r
-\r
-\r
- public static void showURL(String url)\r
- {\r
- try{\r
- applet.getAppletContext().showDocument(new java.net.URL(url), "HELP_WINDOW");\r
- }catch(Exception ex){}\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format, this);\r
- loader.start();\r
- }\r
-\r
- public static void addFrame(final Frame frame, String title, int width, int height)\r
- {\r
- frame.setLocation(lastFrameX,lastFrameY);\r
- lastFrameX+=40; lastFrameY+=40;\r
- frame.setSize(width,height);\r
- frame.setTitle(title);\r
- frame.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- frame.dispose();\r
- }\r
- });\r
- frame.setVisible(true);\r
- }\r
-\r
-\r
- public void paint(Graphics g)\r
- {\r
- if(!fileFound)\r
- {\r
- g.setColor(new Color(200,200,200));\r
- g.setColor(Color.cyan);\r
- g.fillRect(0,0,getSize().width, getSize().height);\r
- g.setColor(Color.red);\r
- g.drawString("Jalview can't open file", 5, 15);\r
- g.drawString("\""+ file+"\"", 5, 30);\r
- }\r
- }\r
-\r
- class LoadingThread extends Thread\r
- {\r
- String file, protocol, format;\r
- JalviewLite jlapplet;\r
-\r
- public LoadingThread(String file, String protocol, String format, JalviewLite applet)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- this.jlapplet = applet;\r
- }\r
- public void run()\r
- {\r
- SequenceI [] sequences = null;\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
-\r
- if (sequences != null && sequences.length>0)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences), jlapplet );\r
- addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully loaded file " + file);\r
- }\r
- else\r
- {\r
- fileFound = false;\r
- remove(launcher);\r
- repaint();\r
- }\r
- }\r
- }\r
-}\r
\r
+ public void LoadFile(String file, String protocol, String format) {\r
+ LoadingThread loader = new LoadingThread(file, protocol, format, this);\r
+ loader.start();\r
+ }\r
\r
+ public static void addFrame(final Frame frame, String title, int width,\r
+ int height) {\r
+ frame.setLocation(lastFrameX, lastFrameY);\r
+ lastFrameX += 40;\r
+ lastFrameY += 40;\r
+ frame.setSize(width, height);\r
+ frame.setTitle(title);\r
+ frame.addWindowListener(new WindowAdapter() {\r
+ public void windowClosing(WindowEvent e) {\r
+ frame.dispose();\r
+ }\r
+ });\r
+ frame.setVisible(true);\r
+ }\r
+\r
+ public void paint(Graphics g) {\r
+ if (!fileFound) {\r
+ g.setColor(new Color(200, 200, 200));\r
+ g.setColor(Color.cyan);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setColor(Color.red);\r
+ g.drawString("Jalview can't open file", 5, 15);\r
+ g.drawString("\"" + file + "\"", 5, 30);\r
+ }\r
+ }\r
+\r
+ class LoadingThread extends Thread {\r
+ String file;\r
+ String protocol;\r
+ String format;\r
+ JalviewLite jlapplet;\r
+\r
+ public LoadingThread(String file, String protocol, String format,\r
+ JalviewLite applet) {\r
+ this.file = file;\r
+ this.protocol = protocol;\r
+ this.format = format;\r
+ this.jlapplet = applet;\r
+ }\r
+\r
+ public void run() {\r
+ SequenceI[] sequences = null;\r
+ sequences = FormatAdapter.readFile(file, protocol, format);\r
+\r
+ if ((sequences != null) && (sequences.length > 0)) {\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences),\r
+ jlapplet);\r
+ addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.statusBar.setText("Successfully loaded file " + file);\r
+ } else {\r
+ fileFound = false;\r
+ remove(launcher);\r
+ repaint();\r
+ }\r
+ }\r
+ }\r
+}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class Alignment.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class Alignment implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.SequenceSet _sequenceSet;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public Alignment() {\r
super();\r
- } //-- jalview.binding.Alignment()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.Alignment()\r
+ //-----------/\r
\r
- /**\r
- * Returns the value of field 'annotation'.\r
- *\r
- * @return Annotation\r
- * @return the value of field 'annotation'.\r
- */\r
- public jalview.binding.Annotation getAnnotation()\r
- {\r
+ public jalview.binding.Annotation getAnnotation() {\r
return this._annotation;\r
- } //-- jalview.binding.Annotation getAnnotation()\r
+ }\r
+ //-- jalview.binding.Annotation getAnnotation()\r
\r
/**\r
* Returns the value of field 'sequenceSet'.\r
* @return SequenceSet\r
* @return the value of field 'sequenceSet'.\r
*/\r
- public jalview.binding.SequenceSet getSequenceSet()\r
- {\r
+ public jalview.binding.SequenceSet getSequenceSet() {\r
return this._sequenceSet;\r
- } //-- jalview.binding.SequenceSet getSequenceSet()\r
+ }\r
+ //-- jalview.binding.SequenceSet getSequenceSet()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'annotation'.\r
*\r
* @param annotation the value of field 'annotation'.\r
*/\r
- public void setAnnotation(jalview.binding.Annotation annotation)\r
- {\r
+ public void setAnnotation(jalview.binding.Annotation annotation) {\r
this._annotation = annotation;\r
- } //-- void setAnnotation(jalview.binding.Annotation)\r
+ }\r
+ //-- void setAnnotation(jalview.binding.Annotation)\r
\r
/**\r
* Sets the value of field 'sequenceSet'.\r
*\r
* @param sequenceSet the value of field 'sequenceSet'.\r
*/\r
- public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)\r
- {\r
+ public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) {\r
this._sequenceSet = sequenceSet;\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet)\r
+ }\r
+ //-- void setSequenceSet(jalview.binding.SequenceSet)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+\r
+import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class Annotation.\r
* @version $Revision$ $Date$\r
*/\r
public class Annotation implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.lang.String _description;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public Annotation() {\r
super();\r
_annotationElementList = new Vector();\r
- } //-- jalview.binding.Annotation()\r
-\r
+ }\r
+ //-- jalview.binding.Annotation()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotationElement\r
- *\r
- *\r
- *\r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addAnnotationElement(\r
+ jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
+ }\r
+ //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
\r
/**\r
* Method addAnnotationElement\r
* @param index\r
* @param vAnnotationElement\r
*/\r
- public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addAnnotationElement(int index,\r
+ jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)\r
+ }\r
+ //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)\r
\r
/**\r
* Method deleteGraph\r
*\r
*/\r
- public void deleteGraph()\r
- {\r
- this._has_graph= false;\r
- } //-- void deleteGraph()\r
+ public void deleteGraph() {\r
+ this._has_graph = false;\r
+ }\r
+ //-- void deleteGraph()\r
\r
/**\r
* Method enumerateAnnotationElement\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
+ public java.util.Enumeration enumerateAnnotationElement() {\r
return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement()\r
+ }\r
+ //-- java.util.Enumeration enumerateAnnotationElement()\r
\r
/**\r
* Method getAnnotationElement\r
* @return AnnotationElement\r
*/\r
public jalview.binding.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationElementList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
+ }\r
+ //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
\r
/**\r
* Method getAnnotationElement\r
*\r
* @return AnnotationElement\r
*/\r
- public jalview.binding.AnnotationElement[] getAnnotationElement()\r
- {\r
+ public jalview.binding.AnnotationElement[] getAnnotationElement() {\r
int size = _annotationElementList.size();\r
jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.AnnotationElement[] getAnnotationElement()\r
+ }\r
+ //-- jalview.binding.AnnotationElement[] getAnnotationElement()\r
\r
/**\r
* Method getAnnotationElementCount\r
*\r
* @return int\r
*/\r
- public int getAnnotationElementCount()\r
- {\r
+ public int getAnnotationElementCount() {\r
return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount()\r
+ }\r
+ //-- int getAnnotationElementCount()\r
\r
/**\r
* Returns the value of field 'description'.\r
* @return String\r
* @return the value of field 'description'.\r
*/\r
- public java.lang.String getDescription()\r
- {\r
+ public java.lang.String getDescription() {\r
return this._description;\r
- } //-- java.lang.String getDescription()\r
+ }\r
+ //-- java.lang.String getDescription()\r
\r
/**\r
* Returns the value of field 'graph'.\r
* @return boolean\r
* @return the value of field 'graph'.\r
*/\r
- public boolean getGraph()\r
- {\r
+ public boolean getGraph() {\r
return this._graph;\r
- } //-- boolean getGraph()\r
+ }\r
+ //-- boolean getGraph()\r
\r
/**\r
* Returns the value of field 'label'.\r
* @return String\r
* @return the value of field 'label'.\r
*/\r
- public java.lang.String getLabel()\r
- {\r
+ public java.lang.String getLabel() {\r
return this._label;\r
- } //-- java.lang.String getLabel()\r
+ }\r
+ //-- java.lang.String getLabel()\r
\r
/**\r
* Method hasGraph\r
*\r
* @return boolean\r
*/\r
- public boolean hasGraph()\r
- {\r
+ public boolean hasGraph() {\r
return this._has_graph;\r
- } //-- boolean hasGraph()\r
+ }\r
+ //-- boolean hasGraph()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllAnnotationElement\r
*\r
*/\r
- public void removeAllAnnotationElement()\r
- {\r
+ public void removeAllAnnotationElement() {\r
_annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement()\r
+ }\r
+ //-- void removeAllAnnotationElement()\r
\r
/**\r
* Method removeAnnotationElement\r
* @param index\r
* @return AnnotationElement\r
*/\r
- public jalview.binding.AnnotationElement removeAnnotationElement(int index)\r
- {\r
+ public jalview.binding.AnnotationElement removeAnnotationElement(int index) {\r
java.lang.Object obj = _annotationElementList.elementAt(index);\r
_annotationElementList.removeElementAt(index);\r
+\r
return (jalview.binding.AnnotationElement) obj;\r
- } //-- jalview.binding.AnnotationElement removeAnnotationElement(int)\r
+ }\r
+ //-- jalview.binding.AnnotationElement removeAnnotationElement(int)\r
\r
/**\r
* Method setAnnotationElement\r
* @param index\r
* @param vAnnotationElement\r
*/\r
- public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void setAnnotationElement(int index,\r
+ jalview.binding.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationElementList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)\r
+ }\r
+ //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)\r
\r
/**\r
* Method setAnnotationElement\r
*\r
* @param annotationElementArray\r
*/\r
- public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)\r
- {\r
+ public void setAnnotationElement(\r
+ jalview.binding.AnnotationElement[] annotationElementArray) {\r
//-- copy array\r
_annotationElementList.removeAllElements();\r
+\r
for (int i = 0; i < annotationElementArray.length; i++) {\r
_annotationElementList.addElement(annotationElementArray[i]);\r
}\r
- } //-- void setAnnotationElement(jalview.binding.AnnotationElement)\r
+ }\r
+ //-- void setAnnotationElement(jalview.binding.AnnotationElement)\r
\r
/**\r
* Sets the value of field 'description'.\r
*\r
* @param description the value of field 'description'.\r
*/\r
- public void setDescription(java.lang.String description)\r
- {\r
+ public void setDescription(java.lang.String description) {\r
this._description = description;\r
- } //-- void setDescription(java.lang.String)\r
+ }\r
+ //-- void setDescription(java.lang.String)\r
\r
/**\r
* Sets the value of field 'graph'.\r
*\r
* @param graph the value of field 'graph'.\r
*/\r
- public void setGraph(boolean graph)\r
- {\r
+ public void setGraph(boolean graph) {\r
this._graph = graph;\r
this._has_graph = true;\r
- } //-- void setGraph(boolean)\r
+ }\r
+ //-- void setGraph(boolean)\r
\r
/**\r
* Sets the value of field 'label'.\r
*\r
* @param label the value of field 'label'.\r
*/\r
- public void setLabel(java.lang.String label)\r
- {\r
+ public void setLabel(java.lang.String label) {\r
this._label = label;\r
- } //-- void setLabel(java.lang.String)\r
+ }\r
+ //-- void setLabel(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class AnnotationElement.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class AnnotationElement implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private boolean _has_value;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public AnnotationElement() {\r
super();\r
- } //-- jalview.binding.AnnotationElement()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.AnnotationElement()\r
+ //-----------/\r
\r
- /**\r
- * Method deletePosition\r
- *\r
- */\r
- public void deletePosition()\r
- {\r
- this._has_position= false;\r
- } //-- void deletePosition()\r
+ public void deletePosition() {\r
+ this._has_position = false;\r
+ }\r
+ //-- void deletePosition()\r
\r
/**\r
* Method deleteValue\r
*\r
*/\r
- public void deleteValue()\r
- {\r
- this._has_value= false;\r
- } //-- void deleteValue()\r
+ public void deleteValue() {\r
+ this._has_value = false;\r
+ }\r
+ //-- void deleteValue()\r
\r
/**\r
* Returns the value of field 'description'.\r
* @return String\r
* @return the value of field 'description'.\r
*/\r
- public java.lang.String getDescription()\r
- {\r
+ public java.lang.String getDescription() {\r
return this._description;\r
- } //-- java.lang.String getDescription()\r
+ }\r
+ //-- java.lang.String getDescription()\r
\r
/**\r
* Returns the value of field 'displayCharacter'.\r
* @return String\r
* @return the value of field 'displayCharacter'.\r
*/\r
- public java.lang.String getDisplayCharacter()\r
- {\r
+ public java.lang.String getDisplayCharacter() {\r
return this._displayCharacter;\r
- } //-- java.lang.String getDisplayCharacter()\r
+ }\r
+ //-- java.lang.String getDisplayCharacter()\r
\r
/**\r
* Returns the value of field 'position'.\r
* @return int\r
* @return the value of field 'position'.\r
*/\r
- public int getPosition()\r
- {\r
+ public int getPosition() {\r
return this._position;\r
- } //-- int getPosition()\r
+ }\r
+ //-- int getPosition()\r
\r
/**\r
* Returns the value of field 'secondaryStructure'.\r
* @return String\r
* @return the value of field 'secondaryStructure'.\r
*/\r
- public java.lang.String getSecondaryStructure()\r
- {\r
+ public java.lang.String getSecondaryStructure() {\r
return this._secondaryStructure;\r
- } //-- java.lang.String getSecondaryStructure()\r
+ }\r
+ //-- java.lang.String getSecondaryStructure()\r
\r
/**\r
* Returns the value of field 'value'.\r
* @return float\r
* @return the value of field 'value'.\r
*/\r
- public float getValue()\r
- {\r
+ public float getValue() {\r
return this._value;\r
- } //-- float getValue()\r
+ }\r
+ //-- float getValue()\r
\r
/**\r
* Method hasPosition\r
*\r
* @return boolean\r
*/\r
- public boolean hasPosition()\r
- {\r
+ public boolean hasPosition() {\r
return this._has_position;\r
- } //-- boolean hasPosition()\r
+ }\r
+ //-- boolean hasPosition()\r
\r
/**\r
* Method hasValue\r
*\r
* @return boolean\r
*/\r
- public boolean hasValue()\r
- {\r
+ public boolean hasValue() {\r
return this._has_value;\r
- } //-- boolean hasValue()\r
+ }\r
+ //-- boolean hasValue()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'description'.\r
*\r
* @param description the value of field 'description'.\r
*/\r
- public void setDescription(java.lang.String description)\r
- {\r
+ public void setDescription(java.lang.String description) {\r
this._description = description;\r
- } //-- void setDescription(java.lang.String)\r
+ }\r
+ //-- void setDescription(java.lang.String)\r
\r
/**\r
* Sets the value of field 'displayCharacter'.\r
*\r
* @param displayCharacter the value of field 'displayCharacter'\r
*/\r
- public void setDisplayCharacter(java.lang.String displayCharacter)\r
- {\r
+ public void setDisplayCharacter(java.lang.String displayCharacter) {\r
this._displayCharacter = displayCharacter;\r
- } //-- void setDisplayCharacter(java.lang.String)\r
+ }\r
+ //-- void setDisplayCharacter(java.lang.String)\r
\r
/**\r
* Sets the value of field 'position'.\r
*\r
* @param position the value of field 'position'.\r
*/\r
- public void setPosition(int position)\r
- {\r
+ public void setPosition(int position) {\r
this._position = position;\r
this._has_position = true;\r
- } //-- void setPosition(int)\r
+ }\r
+ //-- void setPosition(int)\r
\r
/**\r
* Sets the value of field 'secondaryStructure'.\r
* @param secondaryStructure the value of field\r
* 'secondaryStructure'.\r
*/\r
- public void setSecondaryStructure(java.lang.String secondaryStructure)\r
- {\r
+ public void setSecondaryStructure(java.lang.String secondaryStructure) {\r
this._secondaryStructure = secondaryStructure;\r
- } //-- void setSecondaryStructure(java.lang.String)\r
+ }\r
+ //-- void setSecondaryStructure(java.lang.String)\r
\r
/**\r
* Sets the value of field 'value'.\r
*\r
* @param value the value of field 'value'.\r
*/\r
- public void setValue(float value)\r
- {\r
+ public void setValue(float value) {\r
this._value = value;\r
this._has_value = true;\r
- } //-- void setValue(float)\r
+ }\r
+ //-- void setValue(float)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class Colour.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class Colour implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.lang.String _RGB;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public Colour() {\r
super();\r
- } //-- jalview.binding.Colour()\r
-\r
+ }\r
+ //-- jalview.binding.Colour()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- *\r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName() {\r
return this._name;\r
- } //-- java.lang.String getName()\r
+ }\r
+ //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'RGB'.\r
* @return String\r
* @return the value of field 'RGB'.\r
*/\r
- public java.lang.String getRGB()\r
- {\r
+ public java.lang.String getRGB() {\r
return this._RGB;\r
- } //-- java.lang.String getRGB()\r
+ }\r
+ //-- java.lang.String getRGB()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'name'.\r
*\r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String)\r
+ }\r
+ //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'RGB'.\r
*\r
* @param RGB the value of field 'RGB'.\r
*/\r
- public void setRGB(java.lang.String RGB)\r
- {\r
+ public void setRGB(java.lang.String RGB) {\r
this._RGB = RGB;\r
- } //-- void setRGB(java.lang.String)\r
+ }\r
+ //-- void setRGB(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+\r
+import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class JGroup.\r
* @version $Revision$ $Date$\r
*/\r
public class JGroup implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _seqList;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public JGroup() {\r
super();\r
_seqList = new Vector();\r
- } //-- jalview.binding.JGroup()\r
-\r
+ }\r
+ //-- jalview.binding.JGroup()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addSeq\r
- *\r
- *\r
- *\r
- * @param vSeq\r
- */\r
- public void addSeq(int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addSeq(int vSeq) throws java.lang.IndexOutOfBoundsException {\r
_seqList.addElement(new java.lang.Integer(vSeq));\r
- } //-- void addSeq(int)\r
+ }\r
+ //-- void addSeq(int)\r
\r
/**\r
* Method addSeq\r
* @param vSeq\r
*/\r
public void addSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void addSeq(int, int)\r
+ }\r
+ //-- void addSeq(int, int)\r
\r
/**\r
* Method deleteColourText\r
*\r
*/\r
- public void deleteColourText()\r
- {\r
- this._has_colourText= false;\r
- } //-- void deleteColourText()\r
+ public void deleteColourText() {\r
+ this._has_colourText = false;\r
+ }\r
+ //-- void deleteColourText()\r
\r
/**\r
* Method deleteConsThreshold\r
*\r
*/\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold()\r
+ public void deleteConsThreshold() {\r
+ this._has_consThreshold = false;\r
+ }\r
+ //-- void deleteConsThreshold()\r
\r
/**\r
* Method deleteDisplayBoxes\r
*\r
*/\r
- public void deleteDisplayBoxes()\r
- {\r
- this._has_displayBoxes= false;\r
- } //-- void deleteDisplayBoxes()\r
+ public void deleteDisplayBoxes() {\r
+ this._has_displayBoxes = false;\r
+ }\r
+ //-- void deleteDisplayBoxes()\r
\r
/**\r
* Method deleteDisplayText\r
*\r
*/\r
- public void deleteDisplayText()\r
- {\r
- this._has_displayText= false;\r
- } //-- void deleteDisplayText()\r
+ public void deleteDisplayText() {\r
+ this._has_displayText = false;\r
+ }\r
+ //-- void deleteDisplayText()\r
\r
/**\r
* Method deleteEnd\r
*\r
*/\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd()\r
+ public void deleteEnd() {\r
+ this._has_end = false;\r
+ }\r
+ //-- void deleteEnd()\r
\r
/**\r
* Method deleteOutlineColour\r
*\r
*/\r
- public void deleteOutlineColour()\r
- {\r
- this._has_outlineColour= false;\r
- } //-- void deleteOutlineColour()\r
+ public void deleteOutlineColour() {\r
+ this._has_outlineColour = false;\r
+ }\r
+ //-- void deleteOutlineColour()\r
\r
/**\r
* Method deletePidThreshold\r
*\r
*/\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold()\r
+ public void deletePidThreshold() {\r
+ this._has_pidThreshold = false;\r
+ }\r
+ //-- void deletePidThreshold()\r
\r
/**\r
* Method deleteStart\r
*\r
*/\r
- public void deleteStart()\r
- {\r
- this._has_start= false;\r
- } //-- void deleteStart()\r
+ public void deleteStart() {\r
+ this._has_start = false;\r
+ }\r
+ //-- void deleteStart()\r
\r
/**\r
* Method enumerateSeq\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateSeq()\r
- {\r
+ public java.util.Enumeration enumerateSeq() {\r
return _seqList.elements();\r
- } //-- java.util.Enumeration enumerateSeq()\r
+ }\r
+ //-- java.util.Enumeration enumerateSeq()\r
\r
/**\r
* Returns the value of field 'colour'.\r
* @return String\r
* @return the value of field 'colour'.\r
*/\r
- public java.lang.String getColour()\r
- {\r
+ public java.lang.String getColour() {\r
return this._colour;\r
- } //-- java.lang.String getColour()\r
+ }\r
+ //-- java.lang.String getColour()\r
\r
/**\r
* Returns the value of field 'colourText'.\r
* @return boolean\r
* @return the value of field 'colourText'.\r
*/\r
- public boolean getColourText()\r
- {\r
+ public boolean getColourText() {\r
return this._colourText;\r
- } //-- boolean getColourText()\r
+ }\r
+ //-- boolean getColourText()\r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
* @return int\r
* @return the value of field 'consThreshold'.\r
*/\r
- public int getConsThreshold()\r
- {\r
+ public int getConsThreshold() {\r
return this._consThreshold;\r
- } //-- int getConsThreshold()\r
+ }\r
+ //-- int getConsThreshold()\r
\r
/**\r
* Returns the value of field 'displayBoxes'.\r
* @return boolean\r
* @return the value of field 'displayBoxes'.\r
*/\r
- public boolean getDisplayBoxes()\r
- {\r
+ public boolean getDisplayBoxes() {\r
return this._displayBoxes;\r
- } //-- boolean getDisplayBoxes()\r
+ }\r
+ //-- boolean getDisplayBoxes()\r
\r
/**\r
* Returns the value of field 'displayText'.\r
* @return boolean\r
* @return the value of field 'displayText'.\r
*/\r
- public boolean getDisplayText()\r
- {\r
+ public boolean getDisplayText() {\r
return this._displayText;\r
- } //-- boolean getDisplayText()\r
+ }\r
+ //-- boolean getDisplayText()\r
\r
/**\r
* Returns the value of field 'end'.\r
* @return int\r
* @return the value of field 'end'.\r
*/\r
- public int getEnd()\r
- {\r
+ public int getEnd() {\r
return this._end;\r
- } //-- int getEnd()\r
+ }\r
+ //-- int getEnd()\r
\r
/**\r
* Returns the value of field 'name'.\r
* @return String\r
* @return the value of field 'name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName() {\r
return this._name;\r
- } //-- java.lang.String getName()\r
+ }\r
+ //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'outlineColour'.\r
* @return int\r
* @return the value of field 'outlineColour'.\r
*/\r
- public int getOutlineColour()\r
- {\r
+ public int getOutlineColour() {\r
return this._outlineColour;\r
- } //-- int getOutlineColour()\r
+ }\r
+ //-- int getOutlineColour()\r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
* @return int\r
* @return the value of field 'pidThreshold'.\r
*/\r
- public int getPidThreshold()\r
- {\r
+ public int getPidThreshold() {\r
return this._pidThreshold;\r
- } //-- int getPidThreshold()\r
+ }\r
+ //-- int getPidThreshold()\r
\r
/**\r
* Method getSeq\r
* @param index\r
* @return int\r
*/\r
- public int getSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public int getSeq(int index) throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _seqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
- return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
- } //-- int getSeq(int)\r
+ return ((java.lang.Integer) _seqList.elementAt(index)).intValue();\r
+ }\r
+ //-- int getSeq(int)\r
\r
/**\r
* Method getSeq\r
*\r
* @return int\r
*/\r
- public int[] getSeq()\r
- {\r
+ public int[] getSeq() {\r
int size = _seqList.size();\r
int[] mArray = new int[size];\r
+\r
for (int index = 0; index < size; index++) {\r
- mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
+ mArray[index] = ((java.lang.Integer) _seqList.elementAt(index)).intValue();\r
}\r
+\r
return mArray;\r
- } //-- int[] getSeq()\r
+ }\r
+ //-- int[] getSeq()\r
\r
/**\r
* Method getSeqCount\r
*\r
* @return int\r
*/\r
- public int getSeqCount()\r
- {\r
+ public int getSeqCount() {\r
return _seqList.size();\r
- } //-- int getSeqCount()\r
+ }\r
+ //-- int getSeqCount()\r
\r
/**\r
* Returns the value of field 'start'.\r
* @return int\r
* @return the value of field 'start'.\r
*/\r
- public int getStart()\r
- {\r
+ public int getStart() {\r
return this._start;\r
- } //-- int getStart()\r
+ }\r
+ //-- int getStart()\r
\r
/**\r
* Method hasColourText\r
*\r
* @return boolean\r
*/\r
- public boolean hasColourText()\r
- {\r
+ public boolean hasColourText() {\r
return this._has_colourText;\r
- } //-- boolean hasColourText()\r
+ }\r
+ //-- boolean hasColourText()\r
\r
/**\r
* Method hasConsThreshold\r
*\r
* @return boolean\r
*/\r
- public boolean hasConsThreshold()\r
- {\r
+ public boolean hasConsThreshold() {\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold()\r
+ }\r
+ //-- boolean hasConsThreshold()\r
\r
/**\r
* Method hasDisplayBoxes\r
*\r
* @return boolean\r
*/\r
- public boolean hasDisplayBoxes()\r
- {\r
+ public boolean hasDisplayBoxes() {\r
return this._has_displayBoxes;\r
- } //-- boolean hasDisplayBoxes()\r
+ }\r
+ //-- boolean hasDisplayBoxes()\r
\r
/**\r
* Method hasDisplayText\r
*\r
* @return boolean\r
*/\r
- public boolean hasDisplayText()\r
- {\r
+ public boolean hasDisplayText() {\r
return this._has_displayText;\r
- } //-- boolean hasDisplayText()\r
+ }\r
+ //-- boolean hasDisplayText()\r
\r
/**\r
* Method hasEnd\r
*\r
* @return boolean\r
*/\r
- public boolean hasEnd()\r
- {\r
+ public boolean hasEnd() {\r
return this._has_end;\r
- } //-- boolean hasEnd()\r
+ }\r
+ //-- boolean hasEnd()\r
\r
/**\r
* Method hasOutlineColour\r
*\r
* @return boolean\r
*/\r
- public boolean hasOutlineColour()\r
- {\r
+ public boolean hasOutlineColour() {\r
return this._has_outlineColour;\r
- } //-- boolean hasOutlineColour()\r
+ }\r
+ //-- boolean hasOutlineColour()\r
\r
/**\r
* Method hasPidThreshold\r
*\r
* @return boolean\r
*/\r
- public boolean hasPidThreshold()\r
- {\r
+ public boolean hasPidThreshold() {\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold()\r
+ }\r
+ //-- boolean hasPidThreshold()\r
\r
/**\r
* Method hasStart\r
*\r
* @return boolean\r
*/\r
- public boolean hasStart()\r
- {\r
+ public boolean hasStart() {\r
return this._has_start;\r
- } //-- boolean hasStart()\r
+ }\r
+ //-- boolean hasStart()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllSeq\r
*\r
*/\r
- public void removeAllSeq()\r
- {\r
+ public void removeAllSeq() {\r
_seqList.removeAllElements();\r
- } //-- void removeAllSeq()\r
+ }\r
+ //-- void removeAllSeq()\r
\r
/**\r
* Method removeSeq\r
* @param index\r
* @return int\r
*/\r
- public int removeSeq(int index)\r
- {\r
+ public int removeSeq(int index) {\r
java.lang.Object obj = _seqList.elementAt(index);\r
_seqList.removeElementAt(index);\r
- return ((java.lang.Integer)obj).intValue();\r
- } //-- int removeSeq(int)\r
+\r
+ return ((java.lang.Integer) obj).intValue();\r
+ }\r
+ //-- int removeSeq(int)\r
\r
/**\r
* Sets the value of field 'colour'.\r
*\r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(java.lang.String colour)\r
- {\r
+ public void setColour(java.lang.String colour) {\r
this._colour = colour;\r
- } //-- void setColour(java.lang.String)\r
+ }\r
+ //-- void setColour(java.lang.String)\r
\r
/**\r
* Sets the value of field 'colourText'.\r
*\r
* @param colourText the value of field 'colourText'.\r
*/\r
- public void setColourText(boolean colourText)\r
- {\r
+ public void setColourText(boolean colourText) {\r
this._colourText = colourText;\r
this._has_colourText = true;\r
- } //-- void setColourText(boolean)\r
+ }\r
+ //-- void setColourText(boolean)\r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
*\r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
- public void setConsThreshold(int consThreshold)\r
- {\r
+ public void setConsThreshold(int consThreshold) {\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int)\r
+ }\r
+ //-- void setConsThreshold(int)\r
\r
/**\r
* Sets the value of field 'displayBoxes'.\r
*\r
* @param displayBoxes the value of field 'displayBoxes'.\r
*/\r
- public void setDisplayBoxes(boolean displayBoxes)\r
- {\r
+ public void setDisplayBoxes(boolean displayBoxes) {\r
this._displayBoxes = displayBoxes;\r
this._has_displayBoxes = true;\r
- } //-- void setDisplayBoxes(boolean)\r
+ }\r
+ //-- void setDisplayBoxes(boolean)\r
\r
/**\r
* Sets the value of field 'displayText'.\r
*\r
* @param displayText the value of field 'displayText'.\r
*/\r
- public void setDisplayText(boolean displayText)\r
- {\r
+ public void setDisplayText(boolean displayText) {\r
this._displayText = displayText;\r
this._has_displayText = true;\r
- } //-- void setDisplayText(boolean)\r
+ }\r
+ //-- void setDisplayText(boolean)\r
\r
/**\r
* Sets the value of field 'end'.\r
*\r
* @param end the value of field 'end'.\r
*/\r
- public void setEnd(int end)\r
- {\r
+ public void setEnd(int end) {\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int)\r
+ }\r
+ //-- void setEnd(int)\r
\r
/**\r
* Sets the value of field 'name'.\r
*\r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String)\r
+ }\r
+ //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'outlineColour'.\r
*\r
* @param outlineColour the value of field 'outlineColour'.\r
*/\r
- public void setOutlineColour(int outlineColour)\r
- {\r
+ public void setOutlineColour(int outlineColour) {\r
this._outlineColour = outlineColour;\r
this._has_outlineColour = true;\r
- } //-- void setOutlineColour(int)\r
+ }\r
+ //-- void setOutlineColour(int)\r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
*\r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
+ public void setPidThreshold(int pidThreshold) {\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int)\r
+ }\r
+ //-- void setPidThreshold(int)\r
\r
/**\r
* Method setSeq\r
* @param vSeq\r
*/\r
public void setSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _seqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void setSeq(int, int)\r
+ }\r
+ //-- void setSeq(int, int)\r
\r
/**\r
* Method setSeq\r
*\r
* @param seqArray\r
*/\r
- public void setSeq(int[] seqArray)\r
- {\r
+ public void setSeq(int[] seqArray) {\r
//-- copy array\r
_seqList.removeAllElements();\r
+\r
for (int i = 0; i < seqArray.length; i++) {\r
_seqList.addElement(new java.lang.Integer(seqArray[i]));\r
}\r
- } //-- void setSeq(int)\r
+ }\r
+ //-- void setSeq(int)\r
\r
/**\r
* Sets the value of field 'start'.\r
*\r
* @param start the value of field 'start'.\r
*/\r
- public void setStart(int start)\r
- {\r
+ public void setStart(int start) {\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int)\r
+ }\r
+ //-- void setStart(int)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class JSeq.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class JSeq implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private boolean _has_id;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public JSeq() {\r
super();\r
- } //-- jalview.binding.JSeq()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.JSeq()\r
+ //-----------/\r
\r
- /**\r
- * Method deleteColour\r
- *\r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour= false;\r
- } //-- void deleteColour()\r
+ public void deleteColour() {\r
+ this._has_colour = false;\r
+ }\r
+ //-- void deleteColour()\r
\r
/**\r
* Method deleteEnd\r
*\r
*/\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd()\r
+ public void deleteEnd() {\r
+ this._has_end = false;\r
+ }\r
+ //-- void deleteEnd()\r
\r
/**\r
* Method deleteId\r
*\r
*/\r
- public void deleteId()\r
- {\r
- this._has_id= false;\r
- } //-- void deleteId()\r
+ public void deleteId() {\r
+ this._has_id = false;\r
+ }\r
+ //-- void deleteId()\r
\r
/**\r
* Method deleteStart\r
*\r
*/\r
- public void deleteStart()\r
- {\r
- this._has_start= false;\r
- } //-- void deleteStart()\r
+ public void deleteStart() {\r
+ this._has_start = false;\r
+ }\r
+ //-- void deleteStart()\r
\r
/**\r
* Returns the value of field 'colour'.\r
* @return int\r
* @return the value of field 'colour'.\r
*/\r
- public int getColour()\r
- {\r
+ public int getColour() {\r
return this._colour;\r
- } //-- int getColour()\r
+ }\r
+ //-- int getColour()\r
\r
/**\r
* Returns the value of field 'end'.\r
* @return int\r
* @return the value of field 'end'.\r
*/\r
- public int getEnd()\r
- {\r
+ public int getEnd() {\r
return this._end;\r
- } //-- int getEnd()\r
+ }\r
+ //-- int getEnd()\r
\r
/**\r
* Returns the value of field 'id'.\r
* @return int\r
* @return the value of field 'id'.\r
*/\r
- public int getId()\r
- {\r
+ public int getId() {\r
return this._id;\r
- } //-- int getId()\r
+ }\r
+ //-- int getId()\r
\r
/**\r
* Returns the value of field 'start'.\r
* @return int\r
* @return the value of field 'start'.\r
*/\r
- public int getStart()\r
- {\r
+ public int getStart() {\r
return this._start;\r
- } //-- int getStart()\r
+ }\r
+ //-- int getStart()\r
\r
/**\r
* Method hasColour\r
*\r
* @return boolean\r
*/\r
- public boolean hasColour()\r
- {\r
+ public boolean hasColour() {\r
return this._has_colour;\r
- } //-- boolean hasColour()\r
+ }\r
+ //-- boolean hasColour()\r
\r
/**\r
* Method hasEnd\r
*\r
* @return boolean\r
*/\r
- public boolean hasEnd()\r
- {\r
+ public boolean hasEnd() {\r
return this._has_end;\r
- } //-- boolean hasEnd()\r
+ }\r
+ //-- boolean hasEnd()\r
\r
/**\r
* Method hasId\r
*\r
* @return boolean\r
*/\r
- public boolean hasId()\r
- {\r
+ public boolean hasId() {\r
return this._has_id;\r
- } //-- boolean hasId()\r
+ }\r
+ //-- boolean hasId()\r
\r
/**\r
* Method hasStart\r
*\r
* @return boolean\r
*/\r
- public boolean hasStart()\r
- {\r
+ public boolean hasStart() {\r
return this._has_start;\r
- } //-- boolean hasStart()\r
+ }\r
+ //-- boolean hasStart()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'colour'.\r
*\r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(int colour)\r
- {\r
+ public void setColour(int colour) {\r
this._colour = colour;\r
this._has_colour = true;\r
- } //-- void setColour(int)\r
+ }\r
+ //-- void setColour(int)\r
\r
/**\r
* Sets the value of field 'end'.\r
*\r
* @param end the value of field 'end'.\r
*/\r
- public void setEnd(int end)\r
- {\r
+ public void setEnd(int end) {\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int)\r
+ }\r
+ //-- void setEnd(int)\r
\r
/**\r
* Sets the value of field 'id'.\r
*\r
* @param id the value of field 'id'.\r
*/\r
- public void setId(int id)\r
- {\r
+ public void setId(int id) {\r
this._id = id;\r
this._has_id = true;\r
- } //-- void setId(int)\r
+ }\r
+ //-- void setId(int)\r
\r
/**\r
* Sets the value of field 'start'.\r
*\r
* @param start the value of field 'start'.\r
*/\r
- public void setStart(int start)\r
- {\r
+ public void setStart(int start) {\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int)\r
+ }\r
+ //-- void setStart(int)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+\r
+import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\r
import java.util.Date;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class JalviewModel.\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModel implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.JalviewModelSequence _jalviewModelSequence;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public JalviewModel() {\r
super();\r
- } //-- jalview.binding.JalviewModel()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.JalviewModel()\r
+ //-----------/\r
\r
- /**\r
- * Returns the value of field 'creationDate'.\r
- *\r
- * @return Date\r
- * @return the value of field 'creationDate'.\r
- */\r
- public java.util.Date getCreationDate()\r
- {\r
+ public java.util.Date getCreationDate() {\r
return this._creationDate;\r
- } //-- java.util.Date getCreationDate()\r
+ }\r
+ //-- java.util.Date getCreationDate()\r
\r
/**\r
* Returns the value of field 'jalviewModelSequence'.\r
* @return JalviewModelSequence\r
* @return the value of field 'jalviewModelSequence'.\r
*/\r
- public jalview.binding.JalviewModelSequence getJalviewModelSequence()\r
- {\r
+ public jalview.binding.JalviewModelSequence getJalviewModelSequence() {\r
return this._jalviewModelSequence;\r
- } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence()\r
+ }\r
+ //-- jalview.binding.JalviewModelSequence getJalviewModelSequence()\r
\r
/**\r
* Returns the value of field 'vamsasModel'.\r
* @return VamsasModel\r
* @return the value of field 'vamsasModel'.\r
*/\r
- public jalview.binding.VamsasModel getVamsasModel()\r
- {\r
+ public jalview.binding.VamsasModel getVamsasModel() {\r
return this._vamsasModel;\r
- } //-- jalview.binding.VamsasModel getVamsasModel()\r
+ }\r
+ //-- jalview.binding.VamsasModel getVamsasModel()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'creationDate'.\r
*\r
* @param creationDate the value of field 'creationDate'.\r
*/\r
- public void setCreationDate(java.util.Date creationDate)\r
- {\r
+ public void setCreationDate(java.util.Date creationDate) {\r
this._creationDate = creationDate;\r
- } //-- void setCreationDate(java.util.Date)\r
+ }\r
+ //-- void setCreationDate(java.util.Date)\r
\r
/**\r
* Sets the value of field 'jalviewModelSequence'.\r
* @param jalviewModelSequence the value of field\r
* 'jalviewModelSequence'.\r
*/\r
- public void setJalviewModelSequence(jalview.binding.JalviewModelSequence jalviewModelSequence)\r
- {\r
+ public void setJalviewModelSequence(\r
+ jalview.binding.JalviewModelSequence jalviewModelSequence) {\r
this._jalviewModelSequence = jalviewModelSequence;\r
- } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence)\r
+ }\r
+ //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence)\r
\r
/**\r
* Sets the value of field 'vamsasModel'.\r
*\r
* @param vamsasModel the value of field 'vamsasModel'.\r
*/\r
- public void setVamsasModel(jalview.binding.VamsasModel vamsasModel)\r
- {\r
+ public void setVamsasModel(jalview.binding.VamsasModel vamsasModel) {\r
this._vamsasModel = vamsasModel;\r
- } //-- void setVamsasModel(jalview.binding.VamsasModel)\r
+ }\r
+ //-- void setVamsasModel(jalview.binding.VamsasModel)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
\r
+import org.xml.sax.ContentHandler;\r
+\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class JalviewModelSequence.\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _userColoursList;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public JalviewModelSequence() {\r
super();\r
_JSeqList = new Vector();\r
_JGroupList = new Vector();\r
_viewportList = new Vector();\r
_userColoursList = new Vector();\r
- } //-- jalview.binding.JalviewModelSequence()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.JalviewModelSequence()\r
+ //-----------/\r
\r
- /**\r
- * Method addJGroup\r
- *\r
- *\r
- *\r
- * @param vJGroup\r
- */\r
public void addJGroup(jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_JGroupList.addElement(vJGroup);\r
- } //-- void addJGroup(jalview.binding.JGroup)\r
+ }\r
+ //-- void addJGroup(jalview.binding.JGroup)\r
\r
/**\r
* Method addJGroup\r
* @param vJGroup\r
*/\r
public void addJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_JGroupList.insertElementAt(vJGroup, index);\r
- } //-- void addJGroup(int, jalview.binding.JGroup)\r
+ }\r
+ //-- void addJGroup(int, jalview.binding.JGroup)\r
\r
/**\r
* Method addJSeq\r
* @param vJSeq\r
*/\r
public void addJSeq(jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_JSeqList.addElement(vJSeq);\r
- } //-- void addJSeq(jalview.binding.JSeq)\r
+ }\r
+ //-- void addJSeq(jalview.binding.JSeq)\r
\r
/**\r
* Method addJSeq\r
* @param vJSeq\r
*/\r
public void addJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_JSeqList.insertElementAt(vJSeq, index);\r
- } //-- void addJSeq(int, jalview.binding.JSeq)\r
+ }\r
+ //-- void addJSeq(int, jalview.binding.JSeq)\r
\r
/**\r
* Method addUserColours\r
* @param vUserColours\r
*/\r
public void addUserColours(jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_userColoursList.addElement(vUserColours);\r
- } //-- void addUserColours(jalview.binding.UserColours)\r
+ }\r
+ //-- void addUserColours(jalview.binding.UserColours)\r
\r
/**\r
* Method addUserColours\r
* @param index\r
* @param vUserColours\r
*/\r
- public void addUserColours(int index, jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addUserColours(int index,\r
+ jalview.binding.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_userColoursList.insertElementAt(vUserColours, index);\r
- } //-- void addUserColours(int, jalview.binding.UserColours)\r
+ }\r
+ //-- void addUserColours(int, jalview.binding.UserColours)\r
\r
/**\r
* Method addViewport\r
* @param vViewport\r
*/\r
public void addViewport(jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_viewportList.addElement(vViewport);\r
- } //-- void addViewport(jalview.binding.Viewport)\r
+ }\r
+ //-- void addViewport(jalview.binding.Viewport)\r
\r
/**\r
* Method addViewport\r
* @param vViewport\r
*/\r
public void addViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_viewportList.insertElementAt(vViewport, index);\r
- } //-- void addViewport(int, jalview.binding.Viewport)\r
+ }\r
+ //-- void addViewport(int, jalview.binding.Viewport)\r
\r
/**\r
* Method enumerateJGroup\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateJGroup()\r
- {\r
+ public java.util.Enumeration enumerateJGroup() {\r
return _JGroupList.elements();\r
- } //-- java.util.Enumeration enumerateJGroup()\r
+ }\r
+ //-- java.util.Enumeration enumerateJGroup()\r
\r
/**\r
* Method enumerateJSeq\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateJSeq()\r
- {\r
+ public java.util.Enumeration enumerateJSeq() {\r
return _JSeqList.elements();\r
- } //-- java.util.Enumeration enumerateJSeq()\r
+ }\r
+ //-- java.util.Enumeration enumerateJSeq()\r
\r
/**\r
* Method enumerateUserColours\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateUserColours()\r
- {\r
+ public java.util.Enumeration enumerateUserColours() {\r
return _userColoursList.elements();\r
- } //-- java.util.Enumeration enumerateUserColours()\r
+ }\r
+ //-- java.util.Enumeration enumerateUserColours()\r
\r
/**\r
* Method enumerateViewport\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateViewport()\r
- {\r
+ public java.util.Enumeration enumerateViewport() {\r
return _viewportList.elements();\r
- } //-- java.util.Enumeration enumerateViewport()\r
+ }\r
+ //-- java.util.Enumeration enumerateViewport()\r
\r
/**\r
* Method getJGroup\r
* @return JGroup\r
*/\r
public jalview.binding.JGroup getJGroup(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JGroupList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- } //-- jalview.binding.JGroup getJGroup(int)\r
+ }\r
+ //-- jalview.binding.JGroup getJGroup(int)\r
\r
/**\r
* Method getJGroup\r
*\r
* @return JGroup\r
*/\r
- public jalview.binding.JGroup[] getJGroup()\r
- {\r
+ public jalview.binding.JGroup[] getJGroup() {\r
int size = _JGroupList.size();\r
jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.JGroup[] getJGroup()\r
+ }\r
+ //-- jalview.binding.JGroup[] getJGroup()\r
\r
/**\r
* Method getJGroupCount\r
*\r
* @return int\r
*/\r
- public int getJGroupCount()\r
- {\r
+ public int getJGroupCount() {\r
return _JGroupList.size();\r
- } //-- int getJGroupCount()\r
+ }\r
+ //-- int getJGroupCount()\r
\r
/**\r
* Method getJSeq\r
* @return JSeq\r
*/\r
public jalview.binding.JSeq getJSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JSeqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- } //-- jalview.binding.JSeq getJSeq(int)\r
+ }\r
+ //-- jalview.binding.JSeq getJSeq(int)\r
\r
/**\r
* Method getJSeq\r
*\r
* @return JSeq\r
*/\r
- public jalview.binding.JSeq[] getJSeq()\r
- {\r
+ public jalview.binding.JSeq[] getJSeq() {\r
int size = _JSeqList.size();\r
jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.JSeq[] getJSeq()\r
+ }\r
+ //-- jalview.binding.JSeq[] getJSeq()\r
\r
/**\r
* Method getJSeqCount\r
*\r
* @return int\r
*/\r
- public int getJSeqCount()\r
- {\r
+ public int getJSeqCount() {\r
return _JSeqList.size();\r
- } //-- int getJSeqCount()\r
+ }\r
+ //-- int getJSeqCount()\r
\r
/**\r
* Method getUserColours\r
* @return UserColours\r
*/\r
public jalview.binding.UserColours getUserColours(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _userColoursList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
- } //-- jalview.binding.UserColours getUserColours(int)\r
+ }\r
+ //-- jalview.binding.UserColours getUserColours(int)\r
\r
/**\r
* Method getUserColours\r
*\r
* @return UserColours\r
*/\r
- public jalview.binding.UserColours[] getUserColours()\r
- {\r
+ public jalview.binding.UserColours[] getUserColours() {\r
int size = _userColoursList.size();\r
jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.UserColours[] getUserColours()\r
+ }\r
+ //-- jalview.binding.UserColours[] getUserColours()\r
\r
/**\r
* Method getUserColoursCount\r
*\r
* @return int\r
*/\r
- public int getUserColoursCount()\r
- {\r
+ public int getUserColoursCount() {\r
return _userColoursList.size();\r
- } //-- int getUserColoursCount()\r
+ }\r
+ //-- int getUserColoursCount()\r
\r
/**\r
* Method getViewport\r
* @return Viewport\r
*/\r
public jalview.binding.Viewport getViewport(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _viewportList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- } //-- jalview.binding.Viewport getViewport(int)\r
+ }\r
+ //-- jalview.binding.Viewport getViewport(int)\r
\r
/**\r
* Method getViewport\r
*\r
* @return Viewport\r
*/\r
- public jalview.binding.Viewport[] getViewport()\r
- {\r
+ public jalview.binding.Viewport[] getViewport() {\r
int size = _viewportList.size();\r
jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.Viewport[] getViewport()\r
+ }\r
+ //-- jalview.binding.Viewport[] getViewport()\r
\r
/**\r
* Method getViewportCount\r
*\r
* @return int\r
*/\r
- public int getViewportCount()\r
- {\r
+ public int getViewportCount() {\r
return _viewportList.size();\r
- } //-- int getViewportCount()\r
+ }\r
+ //-- int getViewportCount()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllJGroup\r
*\r
*/\r
- public void removeAllJGroup()\r
- {\r
+ public void removeAllJGroup() {\r
_JGroupList.removeAllElements();\r
- } //-- void removeAllJGroup()\r
+ }\r
+ //-- void removeAllJGroup()\r
\r
/**\r
* Method removeAllJSeq\r
*\r
*/\r
- public void removeAllJSeq()\r
- {\r
+ public void removeAllJSeq() {\r
_JSeqList.removeAllElements();\r
- } //-- void removeAllJSeq()\r
+ }\r
+ //-- void removeAllJSeq()\r
\r
/**\r
* Method removeAllUserColours\r
*\r
*/\r
- public void removeAllUserColours()\r
- {\r
+ public void removeAllUserColours() {\r
_userColoursList.removeAllElements();\r
- } //-- void removeAllUserColours()\r
+ }\r
+ //-- void removeAllUserColours()\r
\r
/**\r
* Method removeAllViewport\r
*\r
*/\r
- public void removeAllViewport()\r
- {\r
+ public void removeAllViewport() {\r
_viewportList.removeAllElements();\r
- } //-- void removeAllViewport()\r
+ }\r
+ //-- void removeAllViewport()\r
\r
/**\r
* Method removeJGroup\r
* @param index\r
* @return JGroup\r
*/\r
- public jalview.binding.JGroup removeJGroup(int index)\r
- {\r
+ public jalview.binding.JGroup removeJGroup(int index) {\r
java.lang.Object obj = _JGroupList.elementAt(index);\r
_JGroupList.removeElementAt(index);\r
+\r
return (jalview.binding.JGroup) obj;\r
- } //-- jalview.binding.JGroup removeJGroup(int)\r
+ }\r
+ //-- jalview.binding.JGroup removeJGroup(int)\r
\r
/**\r
* Method removeJSeq\r
* @param index\r
* @return JSeq\r
*/\r
- public jalview.binding.JSeq removeJSeq(int index)\r
- {\r
+ public jalview.binding.JSeq removeJSeq(int index) {\r
java.lang.Object obj = _JSeqList.elementAt(index);\r
_JSeqList.removeElementAt(index);\r
+\r
return (jalview.binding.JSeq) obj;\r
- } //-- jalview.binding.JSeq removeJSeq(int)\r
+ }\r
+ //-- jalview.binding.JSeq removeJSeq(int)\r
\r
/**\r
* Method removeUserColours\r
* @param index\r
* @return UserColours\r
*/\r
- public jalview.binding.UserColours removeUserColours(int index)\r
- {\r
+ public jalview.binding.UserColours removeUserColours(int index) {\r
java.lang.Object obj = _userColoursList.elementAt(index);\r
_userColoursList.removeElementAt(index);\r
+\r
return (jalview.binding.UserColours) obj;\r
- } //-- jalview.binding.UserColours removeUserColours(int)\r
+ }\r
+ //-- jalview.binding.UserColours removeUserColours(int)\r
\r
/**\r
* Method removeViewport\r
* @param index\r
* @return Viewport\r
*/\r
- public jalview.binding.Viewport removeViewport(int index)\r
- {\r
+ public jalview.binding.Viewport removeViewport(int index) {\r
java.lang.Object obj = _viewportList.elementAt(index);\r
_viewportList.removeElementAt(index);\r
+\r
return (jalview.binding.Viewport) obj;\r
- } //-- jalview.binding.Viewport removeViewport(int)\r
+ }\r
+ //-- jalview.binding.Viewport removeViewport(int)\r
\r
/**\r
* Method setJGroup\r
* @param vJGroup\r
*/\r
public void setJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JGroupList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_JGroupList.setElementAt(vJGroup, index);\r
- } //-- void setJGroup(int, jalview.binding.JGroup)\r
+ }\r
+ //-- void setJGroup(int, jalview.binding.JGroup)\r
\r
/**\r
* Method setJGroup\r
*\r
* @param JGroupArray\r
*/\r
- public void setJGroup(jalview.binding.JGroup[] JGroupArray)\r
- {\r
+ public void setJGroup(jalview.binding.JGroup[] JGroupArray) {\r
//-- copy array\r
_JGroupList.removeAllElements();\r
+\r
for (int i = 0; i < JGroupArray.length; i++) {\r
_JGroupList.addElement(JGroupArray[i]);\r
}\r
- } //-- void setJGroup(jalview.binding.JGroup)\r
+ }\r
+ //-- void setJGroup(jalview.binding.JGroup)\r
\r
/**\r
* Method setJSeq\r
* @param vJSeq\r
*/\r
public void setJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _JSeqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_JSeqList.setElementAt(vJSeq, index);\r
- } //-- void setJSeq(int, jalview.binding.JSeq)\r
+ }\r
+ //-- void setJSeq(int, jalview.binding.JSeq)\r
\r
/**\r
* Method setJSeq\r
*\r
* @param JSeqArray\r
*/\r
- public void setJSeq(jalview.binding.JSeq[] JSeqArray)\r
- {\r
+ public void setJSeq(jalview.binding.JSeq[] JSeqArray) {\r
//-- copy array\r
_JSeqList.removeAllElements();\r
+\r
for (int i = 0; i < JSeqArray.length; i++) {\r
_JSeqList.addElement(JSeqArray[i]);\r
}\r
- } //-- void setJSeq(jalview.binding.JSeq)\r
+ }\r
+ //-- void setJSeq(jalview.binding.JSeq)\r
\r
/**\r
* Method setUserColours\r
* @param index\r
* @param vUserColours\r
*/\r
- public void setUserColours(int index, jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void setUserColours(int index,\r
+ jalview.binding.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _userColoursList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_userColoursList.setElementAt(vUserColours, index);\r
- } //-- void setUserColours(int, jalview.binding.UserColours)\r
+ }\r
+ //-- void setUserColours(int, jalview.binding.UserColours)\r
\r
/**\r
* Method setUserColours\r
*\r
* @param userColoursArray\r
*/\r
- public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
- {\r
+ public void setUserColours(jalview.binding.UserColours[] userColoursArray) {\r
//-- copy array\r
_userColoursList.removeAllElements();\r
+\r
for (int i = 0; i < userColoursArray.length; i++) {\r
_userColoursList.addElement(userColoursArray[i]);\r
}\r
- } //-- void setUserColours(jalview.binding.UserColours)\r
+ }\r
+ //-- void setUserColours(jalview.binding.UserColours)\r
\r
/**\r
* Method setViewport\r
* @param vViewport\r
*/\r
public void setViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _viewportList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_viewportList.setElementAt(vViewport, index);\r
- } //-- void setViewport(int, jalview.binding.Viewport)\r
+ }\r
+ //-- void setViewport(int, jalview.binding.Viewport)\r
\r
/**\r
* Method setViewport\r
*\r
* @param viewportArray\r
*/\r
- public void setViewport(jalview.binding.Viewport[] viewportArray)\r
- {\r
+ public void setViewport(jalview.binding.Viewport[] viewportArray) {\r
//-- copy array\r
_viewportList.removeAllElements();\r
+\r
for (int i = 0; i < viewportArray.length; i++) {\r
_viewportList.addElement(viewportArray[i]);\r
}\r
- } //-- void setViewport(jalview.binding.Viewport)\r
+ }\r
+ //-- void setViewport(jalview.binding.Viewport)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+\r
+import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class JalviewModelSequence2.\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence2 implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _items;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public JalviewModelSequence2() {\r
super();\r
_items = new Vector();\r
- } //-- jalview.binding.JalviewModelSequence2()\r
-\r
+ }\r
+ //-- jalview.binding.JalviewModelSequence2()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
- * @param vJalviewModelSequence2Item\r
- */\r
- public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addJalviewModelSequence2Item(\r
+ jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_items.addElement(vJalviewModelSequence2Item);\r
- } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)\r
+ }\r
+ //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)\r
\r
/**\r
* Method addJalviewModelSequence2Item\r
* @param index\r
* @param vJalviewModelSequence2Item\r
*/\r
- public void addJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addJalviewModelSequence2Item(int index,\r
+ jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_items.insertElementAt(vJalviewModelSequence2Item, index);\r
- } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item)\r
+ }\r
+ //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item)\r
\r
/**\r
* Method enumerateJalviewModelSequence2Item\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateJalviewModelSequence2Item()\r
- {\r
+ public java.util.Enumeration enumerateJalviewModelSequence2Item() {\r
return _items.elements();\r
- } //-- java.util.Enumeration enumerateJalviewModelSequence2Item()\r
+ }\r
+ //-- java.util.Enumeration enumerateJalviewModelSequence2Item()\r
\r
/**\r
* Method getJalviewModelSequence2Item\r
* @param index\r
* @return JalviewModelSequence2Item\r
*/\r
- public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(\r
+ int index) throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _items.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
- } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int)\r
+ }\r
+ //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int)\r
\r
/**\r
* Method getJalviewModelSequence2Item\r
*\r
* @return JalviewModelSequence2Item\r
*/\r
- public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
- {\r
+ public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() {\r
int size = _items.size();\r
jalview.binding.JalviewModelSequence2Item[] mArray = new jalview.binding.JalviewModelSequence2Item[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
+ }\r
+ //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
\r
/**\r
* Method getJalviewModelSequence2ItemCount\r
*\r
* @return int\r
*/\r
- public int getJalviewModelSequence2ItemCount()\r
- {\r
+ public int getJalviewModelSequence2ItemCount() {\r
return _items.size();\r
- } //-- int getJalviewModelSequence2ItemCount()\r
+ }\r
+ //-- int getJalviewModelSequence2ItemCount()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllJalviewModelSequence2Item\r
*\r
*/\r
- public void removeAllJalviewModelSequence2Item()\r
- {\r
+ public void removeAllJalviewModelSequence2Item() {\r
_items.removeAllElements();\r
- } //-- void removeAllJalviewModelSequence2Item()\r
+ }\r
+ //-- void removeAllJalviewModelSequence2Item()\r
\r
/**\r
* Method removeJalviewModelSequence2Item\r
* @param index\r
* @return JalviewModelSequence2Item\r
*/\r
- public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int index)\r
- {\r
+ public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(\r
+ int index) {\r
java.lang.Object obj = _items.elementAt(index);\r
_items.removeElementAt(index);\r
+\r
return (jalview.binding.JalviewModelSequence2Item) obj;\r
- } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int)\r
+ }\r
+ //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int)\r
\r
/**\r
* Method setJalviewModelSequence2Item\r
* @param index\r
* @param vJalviewModelSequence2Item\r
*/\r
- public void setJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void setJalviewModelSequence2Item(int index,\r
+ jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _items.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_items.setElementAt(vJalviewModelSequence2Item, index);\r
- } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item)\r
+ }\r
+ //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item)\r
\r
/**\r
* Method setJalviewModelSequence2Item\r
*\r
* @param jalviewModelSequence2ItemArray\r
*/\r
- public void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray)\r
- {\r
+ public void setJalviewModelSequence2Item(\r
+ jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray) {\r
//-- copy array\r
_items.removeAllElements();\r
+\r
for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) {\r
_items.addElement(jalviewModelSequence2ItemArray[i]);\r
}\r
- } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)\r
+ }\r
+ //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.Serializable;\r
+\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
+\r
\r
/**\r
* Class JalviewModelSequence2Item.\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence2Item implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _userColourSchemeList;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public JalviewModelSequence2Item() {\r
super();\r
_userColourSchemeList = new Vector();\r
- } //-- jalview.binding.JalviewModelSequence2Item()\r
-\r
+ }\r
+ //-- jalview.binding.JalviewModelSequence2Item()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addUserColourScheme\r
- *\r
- *\r
- *\r
- * @param vUserColourScheme\r
- */\r
- public void addUserColourScheme(jalview.binding.UserColourScheme vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addUserColourScheme(\r
+ jalview.binding.UserColourScheme vUserColourScheme)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_userColourSchemeList.addElement(vUserColourScheme);\r
- } //-- void addUserColourScheme(jalview.binding.UserColourScheme)\r
+ }\r
+ //-- void addUserColourScheme(jalview.binding.UserColourScheme)\r
\r
/**\r
* Method addUserColourScheme\r
* @param index\r
* @param vUserColourScheme\r
*/\r
- public void addUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addUserColourScheme(int index,\r
+ jalview.binding.UserColourScheme vUserColourScheme)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_userColourSchemeList.insertElementAt(vUserColourScheme, index);\r
- } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme)\r
+ }\r
+ //-- void addUserColourScheme(int, jalview.binding.UserColourScheme)\r
\r
/**\r
* Method enumerateUserColourScheme\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateUserColourScheme()\r
- {\r
+ public java.util.Enumeration enumerateUserColourScheme() {\r
return _userColourSchemeList.elements();\r
- } //-- java.util.Enumeration enumerateUserColourScheme()\r
+ }\r
+ //-- java.util.Enumeration enumerateUserColourScheme()\r
\r
/**\r
* Method getUserColourScheme\r
* @return UserColourScheme\r
*/\r
public jalview.binding.UserColourScheme getUserColourScheme(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _userColourSchemeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme(int)\r
+ }\r
+ //-- jalview.binding.UserColourScheme getUserColourScheme(int)\r
\r
/**\r
* Method getUserColourScheme\r
*\r
* @return UserColourScheme\r
*/\r
- public jalview.binding.UserColourScheme[] getUserColourScheme()\r
- {\r
+ public jalview.binding.UserColourScheme[] getUserColourScheme() {\r
int size = _userColourSchemeList.size();\r
jalview.binding.UserColourScheme[] mArray = new jalview.binding.UserColourScheme[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.UserColourScheme[] getUserColourScheme()\r
+ }\r
+ //-- jalview.binding.UserColourScheme[] getUserColourScheme()\r
\r
/**\r
* Method getUserColourSchemeCount\r
*\r
* @return int\r
*/\r
- public int getUserColourSchemeCount()\r
- {\r
+ public int getUserColourSchemeCount() {\r
return _userColourSchemeList.size();\r
- } //-- int getUserColourSchemeCount()\r
+ }\r
+ //-- int getUserColourSchemeCount()\r
\r
/**\r
* Method removeAllUserColourScheme\r
*\r
*/\r
- public void removeAllUserColourScheme()\r
- {\r
+ public void removeAllUserColourScheme() {\r
_userColourSchemeList.removeAllElements();\r
- } //-- void removeAllUserColourScheme()\r
+ }\r
+ //-- void removeAllUserColourScheme()\r
\r
/**\r
* Method removeUserColourScheme\r
* @param index\r
* @return UserColourScheme\r
*/\r
- public jalview.binding.UserColourScheme removeUserColourScheme(int index)\r
- {\r
+ public jalview.binding.UserColourScheme removeUserColourScheme(int index) {\r
java.lang.Object obj = _userColourSchemeList.elementAt(index);\r
_userColourSchemeList.removeElementAt(index);\r
+\r
return (jalview.binding.UserColourScheme) obj;\r
- } //-- jalview.binding.UserColourScheme removeUserColourScheme(int)\r
+ }\r
+ //-- jalview.binding.UserColourScheme removeUserColourScheme(int)\r
\r
/**\r
* Method setUserColourScheme\r
* @param index\r
* @param vUserColourScheme\r
*/\r
- public void setUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void setUserColourScheme(int index,\r
+ jalview.binding.UserColourScheme vUserColourScheme)\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _userColourSchemeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_userColourSchemeList.setElementAt(vUserColourScheme, index);\r
- } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme)\r
+ }\r
+ //-- void setUserColourScheme(int, jalview.binding.UserColourScheme)\r
\r
/**\r
* Method setUserColourScheme\r
*\r
* @param userColourSchemeArray\r
*/\r
- public void setUserColourScheme(jalview.binding.UserColourScheme[] userColourSchemeArray)\r
- {\r
+ public void setUserColourScheme(\r
+ jalview.binding.UserColourScheme[] userColourSchemeArray) {\r
//-- copy array\r
_userColourSchemeList.removeAllElements();\r
+\r
for (int i = 0; i < userColourSchemeArray.length; i++) {\r
_userColourSchemeList.addElement(userColourSchemeArray[i]);\r
}\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
-\r
+ }\r
+ //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+\r
+import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class JalviewUserColours.\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewUserColours implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _colourList;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public JalviewUserColours() {\r
super();\r
_colourList = new Vector();\r
- } //-- jalview.binding.JalviewUserColours()\r
-\r
+ }\r
+ //-- jalview.binding.JalviewUserColours()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addColour\r
- *\r
- *\r
- *\r
- * @param vColour\r
- */\r
public void addColour(jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_colourList.addElement(vColour);\r
- } //-- void addColour(jalview.binding.Colour)\r
+ }\r
+ //-- void addColour(jalview.binding.Colour)\r
\r
/**\r
* Method addColour\r
* @param vColour\r
*/\r
public void addColour(int index, jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_colourList.insertElementAt(vColour, index);\r
- } //-- void addColour(int, jalview.binding.Colour)\r
+ }\r
+ //-- void addColour(int, jalview.binding.Colour)\r
\r
/**\r
* Method enumerateColour\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateColour()\r
- {\r
+ public java.util.Enumeration enumerateColour() {\r
return _colourList.elements();\r
- } //-- java.util.Enumeration enumerateColour()\r
+ }\r
+ //-- java.util.Enumeration enumerateColour()\r
\r
/**\r
* Method getColour\r
* @return Colour\r
*/\r
public jalview.binding.Colour getColour(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _colourList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.Colour) _colourList.elementAt(index);\r
- } //-- jalview.binding.Colour getColour(int)\r
+ }\r
+ //-- jalview.binding.Colour getColour(int)\r
\r
/**\r
* Method getColour\r
*\r
* @return Colour\r
*/\r
- public jalview.binding.Colour[] getColour()\r
- {\r
+ public jalview.binding.Colour[] getColour() {\r
int size = _colourList.size();\r
jalview.binding.Colour[] mArray = new jalview.binding.Colour[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.Colour[] getColour()\r
+ }\r
+ //-- jalview.binding.Colour[] getColour()\r
\r
/**\r
* Method getColourCount\r
*\r
* @return int\r
*/\r
- public int getColourCount()\r
- {\r
+ public int getColourCount() {\r
return _colourList.size();\r
- } //-- int getColourCount()\r
+ }\r
+ //-- int getColourCount()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllColour\r
*\r
*/\r
- public void removeAllColour()\r
- {\r
+ public void removeAllColour() {\r
_colourList.removeAllElements();\r
- } //-- void removeAllColour()\r
+ }\r
+ //-- void removeAllColour()\r
\r
/**\r
* Method removeColour\r
* @param index\r
* @return Colour\r
*/\r
- public jalview.binding.Colour removeColour(int index)\r
- {\r
+ public jalview.binding.Colour removeColour(int index) {\r
java.lang.Object obj = _colourList.elementAt(index);\r
_colourList.removeElementAt(index);\r
+\r
return (jalview.binding.Colour) obj;\r
- } //-- jalview.binding.Colour removeColour(int)\r
+ }\r
+ //-- jalview.binding.Colour removeColour(int)\r
\r
/**\r
* Method setColour\r
* @param vColour\r
*/\r
public void setColour(int index, jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _colourList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_colourList.setElementAt(vColour, index);\r
- } //-- void setColour(int, jalview.binding.Colour)\r
+ }\r
+ //-- void setColour(int, jalview.binding.Colour)\r
\r
/**\r
* Method setColour\r
*\r
* @param colourArray\r
*/\r
- public void setColour(jalview.binding.Colour[] colourArray)\r
- {\r
+ public void setColour(jalview.binding.Colour[] colourArray) {\r
//-- copy array\r
_colourList.removeAllElements();\r
+\r
for (int i = 0; i < colourArray.length; i++) {\r
_colourList.addElement(colourArray[i]);\r
}\r
- } //-- void setColour(jalview.binding.Colour)\r
+ }\r
+ //-- void setColour(jalview.binding.Colour)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.Serializable;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.Serializable;\r
+\r
+\r
/**\r
* Class JalviewUserColoursItem.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewUserColoursItem implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.Colour _colour;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public JalviewUserColoursItem() {\r
super();\r
- } //-- jalview.binding.JalviewUserColoursItem()\r
-\r
+ }\r
+ //-- jalview.binding.JalviewUserColoursItem()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- *\r
- * @return Colour\r
- * @return the value of field 'colour'.\r
- */\r
- public jalview.binding.Colour getColour()\r
- {\r
+ public jalview.binding.Colour getColour() {\r
return this._colour;\r
- } //-- jalview.binding.Colour getColour()\r
+ }\r
+ //-- jalview.binding.Colour getColour()\r
\r
/**\r
* Sets the value of field 'colour'.\r
*\r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(jalview.binding.Colour colour)\r
- {\r
+ public void setColour(jalview.binding.Colour colour) {\r
this._colour = colour;\r
- } //-- void setColour(jalview.binding.Colour)\r
-\r
+ }\r
+ //-- void setColour(jalview.binding.Colour)\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class Residue.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class Residue implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private boolean _has_RGB;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public Residue() {\r
super();\r
- } //-- jalview.binding.Residue()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.Residue()\r
+ //-----------/\r
\r
- /**\r
- * Method deleteRGB\r
- *\r
- */\r
- public void deleteRGB()\r
- {\r
- this._has_RGB= false;\r
- } //-- void deleteRGB()\r
+ public void deleteRGB() {\r
+ this._has_RGB = false;\r
+ }\r
+ //-- void deleteRGB()\r
\r
/**\r
* Returns the value of field 'name'.\r
* @return String\r
* @return the value of field 'name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName() {\r
return this._name;\r
- } //-- java.lang.String getName()\r
+ }\r
+ //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'RGB'.\r
* @return int\r
* @return the value of field 'RGB'.\r
*/\r
- public int getRGB()\r
- {\r
+ public int getRGB() {\r
return this._RGB;\r
- } //-- int getRGB()\r
+ }\r
+ //-- int getRGB()\r
\r
/**\r
* Method hasRGB\r
*\r
* @return boolean\r
*/\r
- public boolean hasRGB()\r
- {\r
+ public boolean hasRGB() {\r
return this._has_RGB;\r
- } //-- boolean hasRGB()\r
+ }\r
+ //-- boolean hasRGB()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'name'.\r
*\r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String)\r
+ }\r
+ //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'RGB'.\r
*\r
* @param RGB the value of field 'RGB'.\r
*/\r
- public void setRGB(int RGB)\r
- {\r
+ public void setRGB(int RGB) {\r
this._RGB = RGB;\r
this._has_RGB = true;\r
- } //-- void setRGB(int)\r
+ }\r
+ //-- void setRGB(int)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class Sequence.\r
*\r
* @version $Revision$ $Date$\r
*/\r
-public class Sequence extends SequenceType\r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
+public class Sequence extends SequenceType implements java.io.Serializable {\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
-\r
public Sequence() {\r
super();\r
- } //-- jalview.binding.Sequence()\r
+ }\r
+ //-- jalview.binding.Sequence()\r
+ //-----------/\r
\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+\r
+import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class SequenceSet.\r
* @version $Revision$ $Date$\r
*/\r
public class SequenceSet implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _annotationList;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public SequenceSet() {\r
super();\r
_sequenceList = new Vector();\r
_annotationList = new Vector();\r
- } //-- jalview.binding.SequenceSet()\r
+ }\r
+ //-- jalview.binding.SequenceSet()\r
+ //-----------/\r
\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotation\r
- *\r
- *\r
- *\r
- * @param vAnnotation\r
- */\r
public void addAnnotation(jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_annotationList.addElement(vAnnotation);\r
- } //-- void addAnnotation(jalview.binding.Annotation)\r
+ }\r
+ //-- void addAnnotation(jalview.binding.Annotation)\r
\r
/**\r
* Method addAnnotation\r
* @param vAnnotation\r
*/\r
public void addAnnotation(int index, jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_annotationList.insertElementAt(vAnnotation, index);\r
- } //-- void addAnnotation(int, jalview.binding.Annotation)\r
+ }\r
+ //-- void addAnnotation(int, jalview.binding.Annotation)\r
\r
/**\r
* Method addSequence\r
* @param vSequence\r
*/\r
public void addSequence(jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_sequenceList.addElement(vSequence);\r
- } //-- void addSequence(jalview.binding.Sequence)\r
+ }\r
+ //-- void addSequence(jalview.binding.Sequence)\r
\r
/**\r
* Method addSequence\r
* @param vSequence\r
*/\r
public void addSequence(int index, jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_sequenceList.insertElementAt(vSequence, index);\r
- } //-- void addSequence(int, jalview.binding.Sequence)\r
+ }\r
+ //-- void addSequence(int, jalview.binding.Sequence)\r
\r
/**\r
* Method deleteAligned\r
*\r
*/\r
- public void deleteAligned()\r
- {\r
- this._has_aligned= false;\r
- } //-- void deleteAligned()\r
+ public void deleteAligned() {\r
+ this._has_aligned = false;\r
+ }\r
+ //-- void deleteAligned()\r
\r
/**\r
* Method enumerateAnnotation\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateAnnotation()\r
- {\r
+ public java.util.Enumeration enumerateAnnotation() {\r
return _annotationList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotation()\r
+ }\r
+ //-- java.util.Enumeration enumerateAnnotation()\r
\r
/**\r
* Method enumerateSequence\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateSequence()\r
- {\r
+ public java.util.Enumeration enumerateSequence() {\r
return _sequenceList.elements();\r
- } //-- java.util.Enumeration enumerateSequence()\r
+ }\r
+ //-- java.util.Enumeration enumerateSequence()\r
\r
/**\r
* Returns the value of field 'aligned'.\r
* @return boolean\r
* @return the value of field 'aligned'.\r
*/\r
- public boolean getAligned()\r
- {\r
+ public boolean getAligned() {\r
return this._aligned;\r
- } //-- boolean getAligned()\r
+ }\r
+ //-- boolean getAligned()\r
\r
/**\r
* Method getAnnotation\r
* @return Annotation\r
*/\r
public jalview.binding.Annotation getAnnotation(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.Annotation) _annotationList.elementAt(index);\r
- } //-- jalview.binding.Annotation getAnnotation(int)\r
+ }\r
+ //-- jalview.binding.Annotation getAnnotation(int)\r
\r
/**\r
* Method getAnnotation\r
*\r
* @return Annotation\r
*/\r
- public jalview.binding.Annotation[] getAnnotation()\r
- {\r
+ public jalview.binding.Annotation[] getAnnotation() {\r
int size = _annotationList.size();\r
jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.Annotation[] getAnnotation()\r
+ }\r
+ //-- jalview.binding.Annotation[] getAnnotation()\r
\r
/**\r
* Method getAnnotationCount\r
*\r
* @return int\r
*/\r
- public int getAnnotationCount()\r
- {\r
+ public int getAnnotationCount() {\r
return _annotationList.size();\r
- } //-- int getAnnotationCount()\r
+ }\r
+ //-- int getAnnotationCount()\r
\r
/**\r
* Returns the value of field 'gapChar'.\r
* @return String\r
* @return the value of field 'gapChar'.\r
*/\r
- public java.lang.String getGapChar()\r
- {\r
+ public java.lang.String getGapChar() {\r
return this._gapChar;\r
- } //-- java.lang.String getGapChar()\r
+ }\r
+ //-- java.lang.String getGapChar()\r
\r
/**\r
* Method getSequence\r
* @return Sequence\r
*/\r
public jalview.binding.Sequence getSequence(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
- } //-- jalview.binding.Sequence getSequence(int)\r
+ }\r
+ //-- jalview.binding.Sequence getSequence(int)\r
\r
/**\r
* Method getSequence\r
*\r
* @return Sequence\r
*/\r
- public jalview.binding.Sequence[] getSequence()\r
- {\r
+ public jalview.binding.Sequence[] getSequence() {\r
int size = _sequenceList.size();\r
jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.Sequence[] getSequence()\r
+ }\r
+ //-- jalview.binding.Sequence[] getSequence()\r
\r
/**\r
* Method getSequenceCount\r
*\r
* @return int\r
*/\r
- public int getSequenceCount()\r
- {\r
+ public int getSequenceCount() {\r
return _sequenceList.size();\r
- } //-- int getSequenceCount()\r
+ }\r
+ //-- int getSequenceCount()\r
\r
/**\r
* Method hasAligned\r
*\r
* @return boolean\r
*/\r
- public boolean hasAligned()\r
- {\r
+ public boolean hasAligned() {\r
return this._has_aligned;\r
- } //-- boolean hasAligned()\r
+ }\r
+ //-- boolean hasAligned()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllAnnotation\r
*\r
*/\r
- public void removeAllAnnotation()\r
- {\r
+ public void removeAllAnnotation() {\r
_annotationList.removeAllElements();\r
- } //-- void removeAllAnnotation()\r
+ }\r
+ //-- void removeAllAnnotation()\r
\r
/**\r
* Method removeAllSequence\r
*\r
*/\r
- public void removeAllSequence()\r
- {\r
+ public void removeAllSequence() {\r
_sequenceList.removeAllElements();\r
- } //-- void removeAllSequence()\r
+ }\r
+ //-- void removeAllSequence()\r
\r
/**\r
* Method removeAnnotation\r
* @param index\r
* @return Annotation\r
*/\r
- public jalview.binding.Annotation removeAnnotation(int index)\r
- {\r
+ public jalview.binding.Annotation removeAnnotation(int index) {\r
java.lang.Object obj = _annotationList.elementAt(index);\r
_annotationList.removeElementAt(index);\r
+\r
return (jalview.binding.Annotation) obj;\r
- } //-- jalview.binding.Annotation removeAnnotation(int)\r
+ }\r
+ //-- jalview.binding.Annotation removeAnnotation(int)\r
\r
/**\r
* Method removeSequence\r
* @param index\r
* @return Sequence\r
*/\r
- public jalview.binding.Sequence removeSequence(int index)\r
- {\r
+ public jalview.binding.Sequence removeSequence(int index) {\r
java.lang.Object obj = _sequenceList.elementAt(index);\r
_sequenceList.removeElementAt(index);\r
+\r
return (jalview.binding.Sequence) obj;\r
- } //-- jalview.binding.Sequence removeSequence(int)\r
+ }\r
+ //-- jalview.binding.Sequence removeSequence(int)\r
\r
/**\r
* Sets the value of field 'aligned'.\r
*\r
* @param aligned the value of field 'aligned'.\r
*/\r
- public void setAligned(boolean aligned)\r
- {\r
+ public void setAligned(boolean aligned) {\r
this._aligned = aligned;\r
this._has_aligned = true;\r
- } //-- void setAligned(boolean)\r
+ }\r
+ //-- void setAligned(boolean)\r
\r
/**\r
* Method setAnnotation\r
* @param vAnnotation\r
*/\r
public void setAnnotation(int index, jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_annotationList.setElementAt(vAnnotation, index);\r
- } //-- void setAnnotation(int, jalview.binding.Annotation)\r
+ }\r
+ //-- void setAnnotation(int, jalview.binding.Annotation)\r
\r
/**\r
* Method setAnnotation\r
*\r
* @param annotationArray\r
*/\r
- public void setAnnotation(jalview.binding.Annotation[] annotationArray)\r
- {\r
+ public void setAnnotation(jalview.binding.Annotation[] annotationArray) {\r
//-- copy array\r
_annotationList.removeAllElements();\r
+\r
for (int i = 0; i < annotationArray.length; i++) {\r
_annotationList.addElement(annotationArray[i]);\r
}\r
- } //-- void setAnnotation(jalview.binding.Annotation)\r
+ }\r
+ //-- void setAnnotation(jalview.binding.Annotation)\r
\r
/**\r
* Sets the value of field 'gapChar'.\r
*\r
* @param gapChar the value of field 'gapChar'.\r
*/\r
- public void setGapChar(java.lang.String gapChar)\r
- {\r
+ public void setGapChar(java.lang.String gapChar) {\r
this._gapChar = gapChar;\r
- } //-- void setGapChar(java.lang.String)\r
+ }\r
+ //-- void setGapChar(java.lang.String)\r
\r
/**\r
* Method setSequence\r
* @param vSequence\r
*/\r
public void setSequence(int index, jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_sequenceList.setElementAt(vSequence, index);\r
- } //-- void setSequence(int, jalview.binding.Sequence)\r
+ }\r
+ //-- void setSequence(int, jalview.binding.Sequence)\r
\r
/**\r
* Method setSequence\r
*\r
* @param sequenceArray\r
*/\r
- public void setSequence(jalview.binding.Sequence[] sequenceArray)\r
- {\r
+ public void setSequence(jalview.binding.Sequence[] sequenceArray) {\r
//-- copy array\r
_sequenceList.removeAllElements();\r
+\r
for (int i = 0; i < sequenceArray.length; i++) {\r
_sequenceList.addElement(sequenceArray[i]);\r
}\r
- } //-- void setSequence(jalview.binding.Sequence)\r
+ }\r
+ //-- void setSequence(jalview.binding.Sequence)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class SequenceType.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class SequenceType implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.lang.String _name;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public SequenceType() {\r
super();\r
- } //-- jalview.binding.SequenceType()\r
-\r
+ }\r
+ //-- jalview.binding.SequenceType()\r
+ //-----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- *\r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
+ public java.lang.String getId() {\r
return this._id;\r
- } //-- java.lang.String getId()\r
+ }\r
+ //-- java.lang.String getId()\r
\r
/**\r
* Returns the value of field 'name'.\r
* @return String\r
* @return the value of field 'name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName() {\r
return this._name;\r
- } //-- java.lang.String getName()\r
+ }\r
+ //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'sequence'.\r
* @return String\r
* @return the value of field 'sequence'.\r
*/\r
- public java.lang.String getSequence()\r
- {\r
+ public java.lang.String getSequence() {\r
return this._sequence;\r
- } //-- java.lang.String getSequence()\r
+ }\r
+ //-- java.lang.String getSequence()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'id'.\r
*\r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id)\r
- {\r
+ public void setId(java.lang.String id) {\r
this._id = id;\r
- } //-- void setId(java.lang.String)\r
+ }\r
+ //-- void setId(java.lang.String)\r
\r
/**\r
* Sets the value of field 'name'.\r
*\r
* @param name the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
- {\r
+ public void setName(java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String)\r
+ }\r
+ //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'sequence'.\r
*\r
* @param sequence the value of field 'sequence'.\r
*/\r
- public void setSequence(java.lang.String sequence)\r
- {\r
+ public void setSequence(java.lang.String sequence) {\r
this._sequence = sequence;\r
- } //-- void setSequence(java.lang.String)\r
+ }\r
+ //-- void setSequence(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class UserColour.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class UserColour implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.UserColourScheme _userColourScheme;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public UserColour() {\r
super();\r
- } //-- jalview.binding.UserColour()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.UserColour()\r
+ //-----------/\r
\r
- /**\r
- * Method deleteId\r
- *\r
- */\r
- public void deleteId()\r
- {\r
- this._has_id= false;\r
- } //-- void deleteId()\r
+ public void deleteId() {\r
+ this._has_id = false;\r
+ }\r
+ //-- void deleteId()\r
\r
/**\r
* Returns the value of field 'id'.\r
* @return int\r
* @return the value of field 'id'.\r
*/\r
- public int getId()\r
- {\r
+ public int getId() {\r
return this._id;\r
- } //-- int getId()\r
+ }\r
+ //-- int getId()\r
\r
/**\r
* Returns the value of field 'userColourScheme'.\r
* @return UserColourScheme\r
* @return the value of field 'userColourScheme'.\r
*/\r
- public jalview.binding.UserColourScheme getUserColourScheme()\r
- {\r
+ public jalview.binding.UserColourScheme getUserColourScheme() {\r
return this._userColourScheme;\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme()\r
+ }\r
+ //-- jalview.binding.UserColourScheme getUserColourScheme()\r
\r
/**\r
* Method hasId\r
*\r
* @return boolean\r
*/\r
- public boolean hasId()\r
- {\r
+ public boolean hasId() {\r
return this._has_id;\r
- } //-- boolean hasId()\r
+ }\r
+ //-- boolean hasId()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'id'.\r
*\r
* @param id the value of field 'id'.\r
*/\r
- public void setId(int id)\r
- {\r
+ public void setId(int id) {\r
this._id = id;\r
this._has_id = true;\r
- } //-- void setId(int)\r
+ }\r
+ //-- void setId(int)\r
\r
/**\r
* Sets the value of field 'userColourScheme'.\r
*\r
* @param userColourScheme the value of field 'userColourScheme'\r
*/\r
- public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
- {\r
+ public void setUserColourScheme(\r
+ jalview.binding.UserColourScheme userColourScheme) {\r
this._userColourScheme = userColourScheme;\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
+ }\r
+ //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class UserColourScheme.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class UserColourScheme extends JalviewUserColours\r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
+ implements java.io.Serializable {\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
-\r
public UserColourScheme() {\r
super();\r
- } //-- jalview.binding.UserColourScheme()\r
+ }\r
+ //-- jalview.binding.UserColourScheme()\r
+ //-----------/\r
\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class UserColours.\r
*\r
* @version $Revision$ $Date$\r
*/\r
public class UserColours implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private jalview.binding.UserColourScheme _userColourScheme;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public UserColours() {\r
super();\r
- } //-- jalview.binding.UserColours()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.UserColours()\r
+ //-----------/\r
\r
- /**\r
- * Returns the value of field 'id'.\r
- *\r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
+ public java.lang.String getId() {\r
return this._id;\r
- } //-- java.lang.String getId()\r
+ }\r
+ //-- java.lang.String getId()\r
\r
/**\r
* Returns the value of field 'userColourScheme'.\r
* @return UserColourScheme\r
* @return the value of field 'userColourScheme'.\r
*/\r
- public jalview.binding.UserColourScheme getUserColourScheme()\r
- {\r
+ public jalview.binding.UserColourScheme getUserColourScheme() {\r
return this._userColourScheme;\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme()\r
+ }\r
+ //-- jalview.binding.UserColourScheme getUserColourScheme()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'id'.\r
*\r
* @param id the value of field 'id'.\r
*/\r
- public void setId(java.lang.String id)\r
- {\r
+ public void setId(java.lang.String id) {\r
this._id = id;\r
- } //-- void setId(java.lang.String)\r
+ }\r
+ //-- void setId(java.lang.String)\r
\r
/**\r
* Sets the value of field 'userColourScheme'.\r
*\r
* @param userColourScheme the value of field 'userColourScheme'\r
*/\r
- public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
- {\r
+ public void setUserColourScheme(\r
+ jalview.binding.UserColourScheme userColourScheme) {\r
this._userColourScheme = userColourScheme;\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
+ }\r
+ //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
\r
+import org.xml.sax.ContentHandler;\r
+\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+\r
import java.util.Enumeration;\r
import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class VAMSAS.\r
* @version $Revision$ $Date$\r
*/\r
public class VAMSAS implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _sequenceSetList;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public VAMSAS() {\r
super();\r
_alignmentList = new Vector();\r
_treeList = new Vector();\r
_sequenceSetList = new Vector();\r
- } //-- jalview.binding.VAMSAS()\r
+ }\r
+ //-- jalview.binding.VAMSAS()\r
+ //-----------/\r
\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAlignment\r
- *\r
- *\r
- *\r
- * @param vAlignment\r
- */\r
public void addAlignment(jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_alignmentList.addElement(vAlignment);\r
- } //-- void addAlignment(jalview.binding.Alignment)\r
+ }\r
+ //-- void addAlignment(jalview.binding.Alignment)\r
\r
/**\r
* Method addAlignment\r
* @param vAlignment\r
*/\r
public void addAlignment(int index, jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_alignmentList.insertElementAt(vAlignment, index);\r
- } //-- void addAlignment(int, jalview.binding.Alignment)\r
+ }\r
+ //-- void addAlignment(int, jalview.binding.Alignment)\r
\r
/**\r
* Method addSequenceSet\r
* @param vSequenceSet\r
*/\r
public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_sequenceSetList.addElement(vSequenceSet);\r
- } //-- void addSequenceSet(jalview.binding.SequenceSet)\r
+ }\r
+ //-- void addSequenceSet(jalview.binding.SequenceSet)\r
\r
/**\r
* Method addSequenceSet\r
* @param index\r
* @param vSequenceSet\r
*/\r
- public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void addSequenceSet(int index,\r
+ jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException {\r
_sequenceSetList.insertElementAt(vSequenceSet, index);\r
- } //-- void addSequenceSet(int, jalview.binding.SequenceSet)\r
+ }\r
+ //-- void addSequenceSet(int, jalview.binding.SequenceSet)\r
\r
/**\r
* Method addTree\r
* @param vTree\r
*/\r
public void addTree(java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_treeList.addElement(vTree);\r
- } //-- void addTree(java.lang.String)\r
+ }\r
+ //-- void addTree(java.lang.String)\r
\r
/**\r
* Method addTree\r
* @param vTree\r
*/\r
public void addTree(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
_treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, java.lang.String)\r
+ }\r
+ //-- void addTree(int, java.lang.String)\r
\r
/**\r
* Method enumerateAlignment\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateAlignment()\r
- {\r
+ public java.util.Enumeration enumerateAlignment() {\r
return _alignmentList.elements();\r
- } //-- java.util.Enumeration enumerateAlignment()\r
+ }\r
+ //-- java.util.Enumeration enumerateAlignment()\r
\r
/**\r
* Method enumerateSequenceSet\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateSequenceSet()\r
- {\r
+ public java.util.Enumeration enumerateSequenceSet() {\r
return _sequenceSetList.elements();\r
- } //-- java.util.Enumeration enumerateSequenceSet()\r
+ }\r
+ //-- java.util.Enumeration enumerateSequenceSet()\r
\r
/**\r
* Method enumerateTree\r
*\r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateTree()\r
- {\r
+ public java.util.Enumeration enumerateTree() {\r
return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree()\r
+ }\r
+ //-- java.util.Enumeration enumerateTree()\r
\r
/**\r
* Method getAlignment\r
* @return Alignment\r
*/\r
public jalview.binding.Alignment getAlignment(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _alignmentList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
- } //-- jalview.binding.Alignment getAlignment(int)\r
+ }\r
+ //-- jalview.binding.Alignment getAlignment(int)\r
\r
/**\r
* Method getAlignment\r
*\r
* @return Alignment\r
*/\r
- public jalview.binding.Alignment[] getAlignment()\r
- {\r
+ public jalview.binding.Alignment[] getAlignment() {\r
int size = _alignmentList.size();\r
jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.Alignment[] getAlignment()\r
+ }\r
+ //-- jalview.binding.Alignment[] getAlignment()\r
\r
/**\r
* Method getAlignmentCount\r
*\r
* @return int\r
*/\r
- public int getAlignmentCount()\r
- {\r
+ public int getAlignmentCount() {\r
return _alignmentList.size();\r
- } //-- int getAlignmentCount()\r
+ }\r
+ //-- int getAlignmentCount()\r
\r
/**\r
* Method getSequenceSet\r
* @return SequenceSet\r
*/\r
public jalview.binding.SequenceSet getSequenceSet(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _sequenceSetList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
- } //-- jalview.binding.SequenceSet getSequenceSet(int)\r
+ }\r
+ //-- jalview.binding.SequenceSet getSequenceSet(int)\r
\r
/**\r
* Method getSequenceSet\r
*\r
* @return SequenceSet\r
*/\r
- public jalview.binding.SequenceSet[] getSequenceSet()\r
- {\r
+ public jalview.binding.SequenceSet[] getSequenceSet() {\r
int size = _sequenceSetList.size();\r
jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];\r
+\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- jalview.binding.SequenceSet[] getSequenceSet()\r
+ }\r
+ //-- jalview.binding.SequenceSet[] getSequenceSet()\r
\r
/**\r
* Method getSequenceSetCount\r
*\r
* @return int\r
*/\r
- public int getSequenceSetCount()\r
- {\r
+ public int getSequenceSetCount() {\r
return _sequenceSetList.size();\r
- } //-- int getSequenceSetCount()\r
+ }\r
+ //-- int getSequenceSetCount()\r
\r
/**\r
* Method getTree\r
* @return String\r
*/\r
public java.lang.String getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _treeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
\r
- return (String)_treeList.elementAt(index);\r
- } //-- java.lang.String getTree(int)\r
+ return (String) _treeList.elementAt(index);\r
+ }\r
+ //-- java.lang.String getTree(int)\r
\r
/**\r
* Method getTree\r
*\r
* @return String\r
*/\r
- public java.lang.String[] getTree()\r
- {\r
+ public java.lang.String[] getTree() {\r
int size = _treeList.size();\r
java.lang.String[] mArray = new java.lang.String[size];\r
+\r
for (int index = 0; index < size; index++) {\r
- mArray[index] = (String)_treeList.elementAt(index);\r
+ mArray[index] = (String) _treeList.elementAt(index);\r
}\r
+\r
return mArray;\r
- } //-- java.lang.String[] getTree()\r
+ }\r
+ //-- java.lang.String[] getTree()\r
\r
/**\r
* Method getTreeCount\r
*\r
* @return int\r
*/\r
- public int getTreeCount()\r
- {\r
+ public int getTreeCount() {\r
return _treeList.size();\r
- } //-- int getTreeCount()\r
+ }\r
+ //-- int getTreeCount()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAlignment\r
* @param index\r
* @return Alignment\r
*/\r
- public jalview.binding.Alignment removeAlignment(int index)\r
- {\r
+ public jalview.binding.Alignment removeAlignment(int index) {\r
java.lang.Object obj = _alignmentList.elementAt(index);\r
_alignmentList.removeElementAt(index);\r
+\r
return (jalview.binding.Alignment) obj;\r
- } //-- jalview.binding.Alignment removeAlignment(int)\r
+ }\r
+ //-- jalview.binding.Alignment removeAlignment(int)\r
\r
/**\r
* Method removeAllAlignment\r
*\r
*/\r
- public void removeAllAlignment()\r
- {\r
+ public void removeAllAlignment() {\r
_alignmentList.removeAllElements();\r
- } //-- void removeAllAlignment()\r
+ }\r
+ //-- void removeAllAlignment()\r
\r
/**\r
* Method removeAllSequenceSet\r
*\r
*/\r
- public void removeAllSequenceSet()\r
- {\r
+ public void removeAllSequenceSet() {\r
_sequenceSetList.removeAllElements();\r
- } //-- void removeAllSequenceSet()\r
+ }\r
+ //-- void removeAllSequenceSet()\r
\r
/**\r
* Method removeAllTree\r
*\r
*/\r
- public void removeAllTree()\r
- {\r
+ public void removeAllTree() {\r
_treeList.removeAllElements();\r
- } //-- void removeAllTree()\r
+ }\r
+ //-- void removeAllTree()\r
\r
/**\r
* Method removeSequenceSet\r
* @param index\r
* @return SequenceSet\r
*/\r
- public jalview.binding.SequenceSet removeSequenceSet(int index)\r
- {\r
+ public jalview.binding.SequenceSet removeSequenceSet(int index) {\r
java.lang.Object obj = _sequenceSetList.elementAt(index);\r
_sequenceSetList.removeElementAt(index);\r
+\r
return (jalview.binding.SequenceSet) obj;\r
- } //-- jalview.binding.SequenceSet removeSequenceSet(int)\r
+ }\r
+ //-- jalview.binding.SequenceSet removeSequenceSet(int)\r
\r
/**\r
* Method removeTree\r
* @param index\r
* @return String\r
*/\r
- public java.lang.String removeTree(int index)\r
- {\r
+ public java.lang.String removeTree(int index) {\r
java.lang.Object obj = _treeList.elementAt(index);\r
_treeList.removeElementAt(index);\r
- return (String)obj;\r
- } //-- java.lang.String removeTree(int)\r
+\r
+ return (String) obj;\r
+ }\r
+ //-- java.lang.String removeTree(int)\r
\r
/**\r
* Method setAlignment\r
* @param vAlignment\r
*/\r
public void setAlignment(int index, jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _alignmentList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_alignmentList.setElementAt(vAlignment, index);\r
- } //-- void setAlignment(int, jalview.binding.Alignment)\r
+ }\r
+ //-- void setAlignment(int, jalview.binding.Alignment)\r
\r
/**\r
* Method setAlignment\r
*\r
* @param alignmentArray\r
*/\r
- public void setAlignment(jalview.binding.Alignment[] alignmentArray)\r
- {\r
+ public void setAlignment(jalview.binding.Alignment[] alignmentArray) {\r
//-- copy array\r
_alignmentList.removeAllElements();\r
+\r
for (int i = 0; i < alignmentArray.length; i++) {\r
_alignmentList.addElement(alignmentArray[i]);\r
}\r
- } //-- void setAlignment(jalview.binding.Alignment)\r
+ }\r
+ //-- void setAlignment(jalview.binding.Alignment)\r
\r
/**\r
* Method setSequenceSet\r
* @param index\r
* @param vSequenceSet\r
*/\r
- public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ public void setSequenceSet(int index,\r
+ jalview.binding.SequenceSet vSequenceSet)\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _sequenceSetList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_sequenceSetList.setElementAt(vSequenceSet, index);\r
- } //-- void setSequenceSet(int, jalview.binding.SequenceSet)\r
+ }\r
+ //-- void setSequenceSet(int, jalview.binding.SequenceSet)\r
\r
/**\r
* Method setSequenceSet\r
*\r
* @param sequenceSetArray\r
*/\r
- public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
- {\r
+ public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) {\r
//-- copy array\r
_sequenceSetList.removeAllElements();\r
+\r
for (int i = 0; i < sequenceSetArray.length; i++) {\r
_sequenceSetList.addElement(sequenceSetArray[i]);\r
}\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet)\r
+ }\r
+ //-- void setSequenceSet(jalview.binding.SequenceSet)\r
\r
/**\r
* Method setTree\r
* @param vTree\r
*/\r
public void setTree(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
+ throws java.lang.IndexOutOfBoundsException {\r
//-- check bounds for index\r
if ((index < 0) || (index > _treeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
+\r
_treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, java.lang.String)\r
+ }\r
+ //-- void setTree(int, java.lang.String)\r
\r
/**\r
* Method setTree\r
*\r
* @param treeArray\r
*/\r
- public void setTree(java.lang.String[] treeArray)\r
- {\r
+ public void setTree(java.lang.String[] treeArray) {\r
//-- copy array\r
_treeList.removeAllElements();\r
+\r
for (int i = 0; i < treeArray.length; i++) {\r
_treeList.addElement(treeArray[i]);\r
}\r
- } //-- void setTree(java.lang.String)\r
+ }\r
+ //-- void setTree(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* Schema.\r
* $Id$\r
*/\r
-\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.binding;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
import org.exolab.castor.xml.ValidationException;\r
+\r
import org.xml.sax.ContentHandler;\r
\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+\r
+\r
/**\r
* Class VamsasModel.\r
*\r
* @version $Revision$ $Date$\r
*/\r
-public class VamsasModel extends VAMSAS\r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
+public class VamsasModel extends VAMSAS implements java.io.Serializable {\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
-\r
public VamsasModel() {\r
super();\r
- } //-- jalview.binding.VamsasModel()\r
+ }\r
+ //-- jalview.binding.VamsasModel()\r
+ //-----------/\r
\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
/*\r
* This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
+package jalview.binding;\r
\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
\r
-package jalview.binding;\r
+import org.xml.sax.ContentHandler;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
//---------------------------------/\r
-\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
import java.io.IOException;\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
+\r
\r
/**\r
* Class Viewport.\r
* @version $Revision$ $Date$\r
*/\r
public class Viewport implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private boolean _has_fontStyle;\r
\r
-\r
- //----------------/\r
- //- Constructors -/\r
//----------------/\r
-\r
+ //- Constructors -/\r
+ //----------------/\r
public Viewport() {\r
super();\r
- } //-- jalview.binding.Viewport()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ }\r
+ //-- jalview.binding.Viewport()\r
+ //-----------/\r
\r
- /**\r
- * Method deleteConsThreshold\r
- *\r
- */\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold()\r
+ public void deleteConsThreshold() {\r
+ this._has_consThreshold = false;\r
+ }\r
+ //-- void deleteConsThreshold()\r
\r
/**\r
* Method deleteConservationSelected\r
*\r
*/\r
- public void deleteConservationSelected()\r
- {\r
- this._has_conservationSelected= false;\r
- } //-- void deleteConservationSelected()\r
+ public void deleteConservationSelected() {\r
+ this._has_conservationSelected = false;\r
+ }\r
+ //-- void deleteConservationSelected()\r
\r
/**\r
* Method deleteFontSize\r
*\r
*/\r
- public void deleteFontSize()\r
- {\r
- this._has_fontSize= false;\r
- } //-- void deleteFontSize()\r
+ public void deleteFontSize() {\r
+ this._has_fontSize = false;\r
+ }\r
+ //-- void deleteFontSize()\r
\r
/**\r
* Method deleteFontStyle\r
*\r
*/\r
- public void deleteFontStyle()\r
- {\r
- this._has_fontStyle= false;\r
- } //-- void deleteFontStyle()\r
+ public void deleteFontStyle() {\r
+ this._has_fontStyle = false;\r
+ }\r
+ //-- void deleteFontStyle()\r
\r
/**\r
* Method deleteHeight\r
*\r
*/\r
- public void deleteHeight()\r
- {\r
- this._has_height= false;\r
- } //-- void deleteHeight()\r
+ public void deleteHeight() {\r
+ this._has_height = false;\r
+ }\r
+ //-- void deleteHeight()\r
\r
/**\r
* Method deletePidSelected\r
*\r
*/\r
- public void deletePidSelected()\r
- {\r
- this._has_pidSelected= false;\r
- } //-- void deletePidSelected()\r
+ public void deletePidSelected() {\r
+ this._has_pidSelected = false;\r
+ }\r
+ //-- void deletePidSelected()\r
\r
/**\r
* Method deletePidThreshold\r
*\r
*/\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold()\r
+ public void deletePidThreshold() {\r
+ this._has_pidThreshold = false;\r
+ }\r
+ //-- void deletePidThreshold()\r
\r
/**\r
* Method deleteRenderGaps\r
*\r
*/\r
- public void deleteRenderGaps()\r
- {\r
- this._has_renderGaps= false;\r
- } //-- void deleteRenderGaps()\r
+ public void deleteRenderGaps() {\r
+ this._has_renderGaps = false;\r
+ }\r
+ //-- void deleteRenderGaps()\r
\r
/**\r
* Method deleteShowAnnotation\r
*\r
*/\r
- public void deleteShowAnnotation()\r
- {\r
- this._has_showAnnotation= false;\r
- } //-- void deleteShowAnnotation()\r
+ public void deleteShowAnnotation() {\r
+ this._has_showAnnotation = false;\r
+ }\r
+ //-- void deleteShowAnnotation()\r
\r
/**\r
* Method deleteShowBoxes\r
*\r
*/\r
- public void deleteShowBoxes()\r
- {\r
- this._has_showBoxes= false;\r
- } //-- void deleteShowBoxes()\r
+ public void deleteShowBoxes() {\r
+ this._has_showBoxes = false;\r
+ }\r
+ //-- void deleteShowBoxes()\r
\r
/**\r
* Method deleteShowColourText\r
*\r
*/\r
- public void deleteShowColourText()\r
- {\r
- this._has_showColourText= false;\r
- } //-- void deleteShowColourText()\r
+ public void deleteShowColourText() {\r
+ this._has_showColourText = false;\r
+ }\r
+ //-- void deleteShowColourText()\r
\r
/**\r
* Method deleteShowConservation\r
*\r
*/\r
- public void deleteShowConservation()\r
- {\r
- this._has_showConservation= false;\r
- } //-- void deleteShowConservation()\r
+ public void deleteShowConservation() {\r
+ this._has_showConservation = false;\r
+ }\r
+ //-- void deleteShowConservation()\r
\r
/**\r
* Method deleteShowFullId\r
*\r
*/\r
- public void deleteShowFullId()\r
- {\r
- this._has_showFullId= false;\r
- } //-- void deleteShowFullId()\r
+ public void deleteShowFullId() {\r
+ this._has_showFullId = false;\r
+ }\r
+ //-- void deleteShowFullId()\r
\r
/**\r
* Method deleteShowIdentity\r
*\r
*/\r
- public void deleteShowIdentity()\r
- {\r
- this._has_showIdentity= false;\r
- } //-- void deleteShowIdentity()\r
+ public void deleteShowIdentity() {\r
+ this._has_showIdentity = false;\r
+ }\r
+ //-- void deleteShowIdentity()\r
\r
/**\r
* Method deleteShowQuality\r
*\r
*/\r
- public void deleteShowQuality()\r
- {\r
- this._has_showQuality= false;\r
- } //-- void deleteShowQuality()\r
+ public void deleteShowQuality() {\r
+ this._has_showQuality = false;\r
+ }\r
+ //-- void deleteShowQuality()\r
\r
/**\r
* Method deleteShowSequenceFeatures\r
*\r
*/\r
- public void deleteShowSequenceFeatures()\r
- {\r
- this._has_showSequenceFeatures= false;\r
- } //-- void deleteShowSequenceFeatures()\r
+ public void deleteShowSequenceFeatures() {\r
+ this._has_showSequenceFeatures = false;\r
+ }\r
+ //-- void deleteShowSequenceFeatures()\r
\r
/**\r
* Method deleteShowText\r
*\r
*/\r
- public void deleteShowText()\r
- {\r
- this._has_showText= false;\r
- } //-- void deleteShowText()\r
+ public void deleteShowText() {\r
+ this._has_showText = false;\r
+ }\r
+ //-- void deleteShowText()\r
\r
/**\r
* Method deleteStartRes\r
*\r
*/\r
- public void deleteStartRes()\r
- {\r
- this._has_startRes= false;\r
- } //-- void deleteStartRes()\r
+ public void deleteStartRes() {\r
+ this._has_startRes = false;\r
+ }\r
+ //-- void deleteStartRes()\r
\r
/**\r
* Method deleteStartSeq\r
*\r
*/\r
- public void deleteStartSeq()\r
- {\r
- this._has_startSeq= false;\r
- } //-- void deleteStartSeq()\r
+ public void deleteStartSeq() {\r
+ this._has_startSeq = false;\r
+ }\r
+ //-- void deleteStartSeq()\r
\r
/**\r
* Method deleteWidth\r
*\r
*/\r
- public void deleteWidth()\r
- {\r
- this._has_width= false;\r
- } //-- void deleteWidth()\r
+ public void deleteWidth() {\r
+ this._has_width = false;\r
+ }\r
+ //-- void deleteWidth()\r
\r
/**\r
* Method deleteWrapAlignment\r
*\r
*/\r
- public void deleteWrapAlignment()\r
- {\r
- this._has_wrapAlignment= false;\r
- } //-- void deleteWrapAlignment()\r
+ public void deleteWrapAlignment() {\r
+ this._has_wrapAlignment = false;\r
+ }\r
+ //-- void deleteWrapAlignment()\r
\r
/**\r
* Method deleteXpos\r
*\r
*/\r
- public void deleteXpos()\r
- {\r
- this._has_xpos= false;\r
- } //-- void deleteXpos()\r
+ public void deleteXpos() {\r
+ this._has_xpos = false;\r
+ }\r
+ //-- void deleteXpos()\r
\r
/**\r
* Method deleteYpos\r
*\r
*/\r
- public void deleteYpos()\r
- {\r
- this._has_ypos= false;\r
- } //-- void deleteYpos()\r
+ public void deleteYpos() {\r
+ this._has_ypos = false;\r
+ }\r
+ //-- void deleteYpos()\r
\r
/**\r
* Returns the value of field 'bgColour'.\r
* @return String\r
* @return the value of field 'bgColour'.\r
*/\r
- public java.lang.String getBgColour()\r
- {\r
+ public java.lang.String getBgColour() {\r
return this._bgColour;\r
- } //-- java.lang.String getBgColour()\r
+ }\r
+ //-- java.lang.String getBgColour()\r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
* @return int\r
* @return the value of field 'consThreshold'.\r
*/\r
- public int getConsThreshold()\r
- {\r
+ public int getConsThreshold() {\r
return this._consThreshold;\r
- } //-- int getConsThreshold()\r
+ }\r
+ //-- int getConsThreshold()\r
\r
/**\r
* Returns the value of field 'conservationSelected'.\r
* @return boolean\r
* @return the value of field 'conservationSelected'.\r
*/\r
- public boolean getConservationSelected()\r
- {\r
+ public boolean getConservationSelected() {\r
return this._conservationSelected;\r
- } //-- boolean getConservationSelected()\r
+ }\r
+ //-- boolean getConservationSelected()\r
\r
/**\r
* Returns the value of field 'fontName'.\r
* @return String\r
* @return the value of field 'fontName'.\r
*/\r
- public java.lang.String getFontName()\r
- {\r
+ public java.lang.String getFontName() {\r
return this._fontName;\r
- } //-- java.lang.String getFontName()\r
+ }\r
+ //-- java.lang.String getFontName()\r
\r
/**\r
* Returns the value of field 'fontSize'.\r
* @return int\r
* @return the value of field 'fontSize'.\r
*/\r
- public int getFontSize()\r
- {\r
+ public int getFontSize() {\r
return this._fontSize;\r
- } //-- int getFontSize()\r
+ }\r
+ //-- int getFontSize()\r
\r
/**\r
* Returns the value of field 'fontStyle'.\r
* @return int\r
* @return the value of field 'fontStyle'.\r
*/\r
- public int getFontStyle()\r
- {\r
+ public int getFontStyle() {\r
return this._fontStyle;\r
- } //-- int getFontStyle()\r
+ }\r
+ //-- int getFontStyle()\r
\r
/**\r
* Returns the value of field 'height'.\r
* @return int\r
* @return the value of field 'height'.\r
*/\r
- public int getHeight()\r
- {\r
+ public int getHeight() {\r
return this._height;\r
- } //-- int getHeight()\r
+ }\r
+ //-- int getHeight()\r
\r
/**\r
* Returns the value of field 'pidSelected'.\r
* @return boolean\r
* @return the value of field 'pidSelected'.\r
*/\r
- public boolean getPidSelected()\r
- {\r
+ public boolean getPidSelected() {\r
return this._pidSelected;\r
- } //-- boolean getPidSelected()\r
+ }\r
+ //-- boolean getPidSelected()\r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
* @return int\r
* @return the value of field 'pidThreshold'.\r
*/\r
- public int getPidThreshold()\r
- {\r
+ public int getPidThreshold() {\r
return this._pidThreshold;\r
- } //-- int getPidThreshold()\r
+ }\r
+ //-- int getPidThreshold()\r
\r
/**\r
* Returns the value of field 'renderGaps'.\r
* @return boolean\r
* @return the value of field 'renderGaps'.\r
*/\r
- public boolean getRenderGaps()\r
- {\r
+ public boolean getRenderGaps() {\r
return this._renderGaps;\r
- } //-- boolean getRenderGaps()\r
+ }\r
+ //-- boolean getRenderGaps()\r
\r
/**\r
* Returns the value of field 'showAnnotation'.\r
* @return boolean\r
* @return the value of field 'showAnnotation'.\r
*/\r
- public boolean getShowAnnotation()\r
- {\r
+ public boolean getShowAnnotation() {\r
return this._showAnnotation;\r
- } //-- boolean getShowAnnotation()\r
+ }\r
+ //-- boolean getShowAnnotation()\r
\r
/**\r
* Returns the value of field 'showBoxes'.\r
* @return boolean\r
* @return the value of field 'showBoxes'.\r
*/\r
- public boolean getShowBoxes()\r
- {\r
+ public boolean getShowBoxes() {\r
return this._showBoxes;\r
- } //-- boolean getShowBoxes()\r
+ }\r
+ //-- boolean getShowBoxes()\r
\r
/**\r
* Returns the value of field 'showColourText'.\r
* @return boolean\r
* @return the value of field 'showColourText'.\r
*/\r
- public boolean getShowColourText()\r
- {\r
+ public boolean getShowColourText() {\r
return this._showColourText;\r
- } //-- boolean getShowColourText()\r
+ }\r
+ //-- boolean getShowColourText()\r
\r
/**\r
* Returns the value of field 'showConservation'.\r
* @return boolean\r
* @return the value of field 'showConservation'.\r
*/\r
- public boolean getShowConservation()\r
- {\r
+ public boolean getShowConservation() {\r
return this._showConservation;\r
- } //-- boolean getShowConservation()\r
+ }\r
+ //-- boolean getShowConservation()\r
\r
/**\r
* Returns the value of field 'showFullId'.\r
* @return boolean\r
* @return the value of field 'showFullId'.\r
*/\r
- public boolean getShowFullId()\r
- {\r
+ public boolean getShowFullId() {\r
return this._showFullId;\r
- } //-- boolean getShowFullId()\r
+ }\r
+ //-- boolean getShowFullId()\r
\r
/**\r
* Returns the value of field 'showIdentity'.\r
* @return boolean\r
* @return the value of field 'showIdentity'.\r
*/\r
- public boolean getShowIdentity()\r
- {\r
+ public boolean getShowIdentity() {\r
return this._showIdentity;\r
- } //-- boolean getShowIdentity()\r
+ }\r
+ //-- boolean getShowIdentity()\r
\r
/**\r
* Returns the value of field 'showQuality'.\r
* @return boolean\r
* @return the value of field 'showQuality'.\r
*/\r
- public boolean getShowQuality()\r
- {\r
+ public boolean getShowQuality() {\r
return this._showQuality;\r
- } //-- boolean getShowQuality()\r
+ }\r
+ //-- boolean getShowQuality()\r
\r
/**\r
* Returns the value of field 'showSequenceFeatures'.\r
* @return boolean\r
* @return the value of field 'showSequenceFeatures'.\r
*/\r
- public boolean getShowSequenceFeatures()\r
- {\r
+ public boolean getShowSequenceFeatures() {\r
return this._showSequenceFeatures;\r
- } //-- boolean getShowSequenceFeatures()\r
+ }\r
+ //-- boolean getShowSequenceFeatures()\r
\r
/**\r
* Returns the value of field 'showText'.\r
* @return boolean\r
* @return the value of field 'showText'.\r
*/\r
- public boolean getShowText()\r
- {\r
+ public boolean getShowText() {\r
return this._showText;\r
- } //-- boolean getShowText()\r
+ }\r
+ //-- boolean getShowText()\r
\r
/**\r
* Returns the value of field 'startRes'.\r
* @return int\r
* @return the value of field 'startRes'.\r
*/\r
- public int getStartRes()\r
- {\r
+ public int getStartRes() {\r
return this._startRes;\r
- } //-- int getStartRes()\r
+ }\r
+ //-- int getStartRes()\r
\r
/**\r
* Returns the value of field 'startSeq'.\r
* @return int\r
* @return the value of field 'startSeq'.\r
*/\r
- public int getStartSeq()\r
- {\r
+ public int getStartSeq() {\r
return this._startSeq;\r
- } //-- int getStartSeq()\r
+ }\r
+ //-- int getStartSeq()\r
\r
/**\r
* Returns the value of field 'title'.\r
* @return String\r
* @return the value of field 'title'.\r
*/\r
- public java.lang.String getTitle()\r
- {\r
+ public java.lang.String getTitle() {\r
return this._title;\r
- } //-- java.lang.String getTitle()\r
+ }\r
+ //-- java.lang.String getTitle()\r
\r
/**\r
* Returns the value of field 'width'.\r
* @return int\r
* @return the value of field 'width'.\r
*/\r
- public int getWidth()\r
- {\r
+ public int getWidth() {\r
return this._width;\r
- } //-- int getWidth()\r
+ }\r
+ //-- int getWidth()\r
\r
/**\r
* Returns the value of field 'wrapAlignment'.\r
* @return boolean\r
* @return the value of field 'wrapAlignment'.\r
*/\r
- public boolean getWrapAlignment()\r
- {\r
+ public boolean getWrapAlignment() {\r
return this._wrapAlignment;\r
- } //-- boolean getWrapAlignment()\r
+ }\r
+ //-- boolean getWrapAlignment()\r
\r
/**\r
* Returns the value of field 'xpos'.\r
* @return int\r
* @return the value of field 'xpos'.\r
*/\r
- public int getXpos()\r
- {\r
+ public int getXpos() {\r
return this._xpos;\r
- } //-- int getXpos()\r
+ }\r
+ //-- int getXpos()\r
\r
/**\r
* Returns the value of field 'ypos'.\r
* @return int\r
* @return the value of field 'ypos'.\r
*/\r
- public int getYpos()\r
- {\r
+ public int getYpos() {\r
return this._ypos;\r
- } //-- int getYpos()\r
+ }\r
+ //-- int getYpos()\r
\r
/**\r
* Method hasConsThreshold\r
*\r
* @return boolean\r
*/\r
- public boolean hasConsThreshold()\r
- {\r
+ public boolean hasConsThreshold() {\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold()\r
+ }\r
+ //-- boolean hasConsThreshold()\r
\r
/**\r
* Method hasConservationSelected\r
*\r
* @return boolean\r
*/\r
- public boolean hasConservationSelected()\r
- {\r
+ public boolean hasConservationSelected() {\r
return this._has_conservationSelected;\r
- } //-- boolean hasConservationSelected()\r
+ }\r
+ //-- boolean hasConservationSelected()\r
\r
/**\r
* Method hasFontSize\r
*\r
* @return boolean\r
*/\r
- public boolean hasFontSize()\r
- {\r
+ public boolean hasFontSize() {\r
return this._has_fontSize;\r
- } //-- boolean hasFontSize()\r
+ }\r
+ //-- boolean hasFontSize()\r
\r
/**\r
* Method hasFontStyle\r
*\r
* @return boolean\r
*/\r
- public boolean hasFontStyle()\r
- {\r
+ public boolean hasFontStyle() {\r
return this._has_fontStyle;\r
- } //-- boolean hasFontStyle()\r
+ }\r
+ //-- boolean hasFontStyle()\r
\r
/**\r
* Method hasHeight\r
*\r
* @return boolean\r
*/\r
- public boolean hasHeight()\r
- {\r
+ public boolean hasHeight() {\r
return this._has_height;\r
- } //-- boolean hasHeight()\r
+ }\r
+ //-- boolean hasHeight()\r
\r
/**\r
* Method hasPidSelected\r
*\r
* @return boolean\r
*/\r
- public boolean hasPidSelected()\r
- {\r
+ public boolean hasPidSelected() {\r
return this._has_pidSelected;\r
- } //-- boolean hasPidSelected()\r
+ }\r
+ //-- boolean hasPidSelected()\r
\r
/**\r
* Method hasPidThreshold\r
*\r
* @return boolean\r
*/\r
- public boolean hasPidThreshold()\r
- {\r
+ public boolean hasPidThreshold() {\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold()\r
+ }\r
+ //-- boolean hasPidThreshold()\r
\r
/**\r
* Method hasRenderGaps\r
*\r
* @return boolean\r
*/\r
- public boolean hasRenderGaps()\r
- {\r
+ public boolean hasRenderGaps() {\r
return this._has_renderGaps;\r
- } //-- boolean hasRenderGaps()\r
+ }\r
+ //-- boolean hasRenderGaps()\r
\r
/**\r
* Method hasShowAnnotation\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowAnnotation()\r
- {\r
+ public boolean hasShowAnnotation() {\r
return this._has_showAnnotation;\r
- } //-- boolean hasShowAnnotation()\r
+ }\r
+ //-- boolean hasShowAnnotation()\r
\r
/**\r
* Method hasShowBoxes\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowBoxes()\r
- {\r
+ public boolean hasShowBoxes() {\r
return this._has_showBoxes;\r
- } //-- boolean hasShowBoxes()\r
+ }\r
+ //-- boolean hasShowBoxes()\r
\r
/**\r
* Method hasShowColourText\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowColourText()\r
- {\r
+ public boolean hasShowColourText() {\r
return this._has_showColourText;\r
- } //-- boolean hasShowColourText()\r
+ }\r
+ //-- boolean hasShowColourText()\r
\r
/**\r
* Method hasShowConservation\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowConservation()\r
- {\r
+ public boolean hasShowConservation() {\r
return this._has_showConservation;\r
- } //-- boolean hasShowConservation()\r
+ }\r
+ //-- boolean hasShowConservation()\r
\r
/**\r
* Method hasShowFullId\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowFullId()\r
- {\r
+ public boolean hasShowFullId() {\r
return this._has_showFullId;\r
- } //-- boolean hasShowFullId()\r
+ }\r
+ //-- boolean hasShowFullId()\r
\r
/**\r
* Method hasShowIdentity\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowIdentity()\r
- {\r
+ public boolean hasShowIdentity() {\r
return this._has_showIdentity;\r
- } //-- boolean hasShowIdentity()\r
+ }\r
+ //-- boolean hasShowIdentity()\r
\r
/**\r
* Method hasShowQuality\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowQuality()\r
- {\r
+ public boolean hasShowQuality() {\r
return this._has_showQuality;\r
- } //-- boolean hasShowQuality()\r
+ }\r
+ //-- boolean hasShowQuality()\r
\r
/**\r
* Method hasShowSequenceFeatures\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowSequenceFeatures()\r
- {\r
+ public boolean hasShowSequenceFeatures() {\r
return this._has_showSequenceFeatures;\r
- } //-- boolean hasShowSequenceFeatures()\r
+ }\r
+ //-- boolean hasShowSequenceFeatures()\r
\r
/**\r
* Method hasShowText\r
*\r
* @return boolean\r
*/\r
- public boolean hasShowText()\r
- {\r
+ public boolean hasShowText() {\r
return this._has_showText;\r
- } //-- boolean hasShowText()\r
+ }\r
+ //-- boolean hasShowText()\r
\r
/**\r
* Method hasStartRes\r
*\r
* @return boolean\r
*/\r
- public boolean hasStartRes()\r
- {\r
+ public boolean hasStartRes() {\r
return this._has_startRes;\r
- } //-- boolean hasStartRes()\r
+ }\r
+ //-- boolean hasStartRes()\r
\r
/**\r
* Method hasStartSeq\r
*\r
* @return boolean\r
*/\r
- public boolean hasStartSeq()\r
- {\r
+ public boolean hasStartSeq() {\r
return this._has_startSeq;\r
- } //-- boolean hasStartSeq()\r
+ }\r
+ //-- boolean hasStartSeq()\r
\r
/**\r
* Method hasWidth\r
*\r
* @return boolean\r
*/\r
- public boolean hasWidth()\r
- {\r
+ public boolean hasWidth() {\r
return this._has_width;\r
- } //-- boolean hasWidth()\r
+ }\r
+ //-- boolean hasWidth()\r
\r
/**\r
* Method hasWrapAlignment\r
*\r
* @return boolean\r
*/\r
- public boolean hasWrapAlignment()\r
- {\r
+ public boolean hasWrapAlignment() {\r
return this._has_wrapAlignment;\r
- } //-- boolean hasWrapAlignment()\r
+ }\r
+ //-- boolean hasWrapAlignment()\r
\r
/**\r
* Method hasXpos\r
*\r
* @return boolean\r
*/\r
- public boolean hasXpos()\r
- {\r
+ public boolean hasXpos() {\r
return this._has_xpos;\r
- } //-- boolean hasXpos()\r
+ }\r
+ //-- boolean hasXpos()\r
\r
/**\r
* Method hasYpos\r
*\r
* @return boolean\r
*/\r
- public boolean hasYpos()\r
- {\r
+ public boolean hasYpos() {\r
return this._has_ypos;\r
- } //-- boolean hasYpos()\r
+ }\r
+ //-- boolean hasYpos()\r
\r
/**\r
* Method isValid\r
*\r
* @return boolean\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid() {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
+\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
+ //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
+ //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
-\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
+ //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'bgColour'.\r
*\r
* @param bgColour the value of field 'bgColour'.\r
*/\r
- public void setBgColour(java.lang.String bgColour)\r
- {\r
+ public void setBgColour(java.lang.String bgColour) {\r
this._bgColour = bgColour;\r
- } //-- void setBgColour(java.lang.String)\r
+ }\r
+ //-- void setBgColour(java.lang.String)\r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
*\r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
- public void setConsThreshold(int consThreshold)\r
- {\r
+ public void setConsThreshold(int consThreshold) {\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int)\r
+ }\r
+ //-- void setConsThreshold(int)\r
\r
/**\r
* Sets the value of field 'conservationSelected'.\r
* @param conservationSelected the value of field\r
* 'conservationSelected'.\r
*/\r
- public void setConservationSelected(boolean conservationSelected)\r
- {\r
+ public void setConservationSelected(boolean conservationSelected) {\r
this._conservationSelected = conservationSelected;\r
this._has_conservationSelected = true;\r
- } //-- void setConservationSelected(boolean)\r
+ }\r
+ //-- void setConservationSelected(boolean)\r
\r
/**\r
* Sets the value of field 'fontName'.\r
*\r
* @param fontName the value of field 'fontName'.\r
*/\r
- public void setFontName(java.lang.String fontName)\r
- {\r
+ public void setFontName(java.lang.String fontName) {\r
this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String)\r
+ }\r
+ //-- void setFontName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'fontSize'.\r
*\r
* @param fontSize the value of field 'fontSize'.\r
*/\r
- public void setFontSize(int fontSize)\r
- {\r
+ public void setFontSize(int fontSize) {\r
this._fontSize = fontSize;\r
this._has_fontSize = true;\r
- } //-- void setFontSize(int)\r
+ }\r
+ //-- void setFontSize(int)\r
\r
/**\r
* Sets the value of field 'fontStyle'.\r
*\r
* @param fontStyle the value of field 'fontStyle'.\r
*/\r
- public void setFontStyle(int fontStyle)\r
- {\r
+ public void setFontStyle(int fontStyle) {\r
this._fontStyle = fontStyle;\r
this._has_fontStyle = true;\r
- } //-- void setFontStyle(int)\r
+ }\r
+ //-- void setFontStyle(int)\r
\r
/**\r
* Sets the value of field 'height'.\r
*\r
* @param height the value of field 'height'.\r
*/\r
- public void setHeight(int height)\r
- {\r
+ public void setHeight(int height) {\r
this._height = height;\r
this._has_height = true;\r
- } //-- void setHeight(int)\r
+ }\r
+ //-- void setHeight(int)\r
\r
/**\r
* Sets the value of field 'pidSelected'.\r
*\r
* @param pidSelected the value of field 'pidSelected'.\r
*/\r
- public void setPidSelected(boolean pidSelected)\r
- {\r
+ public void setPidSelected(boolean pidSelected) {\r
this._pidSelected = pidSelected;\r
this._has_pidSelected = true;\r
- } //-- void setPidSelected(boolean)\r
+ }\r
+ //-- void setPidSelected(boolean)\r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
*\r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
+ public void setPidThreshold(int pidThreshold) {\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int)\r
+ }\r
+ //-- void setPidThreshold(int)\r
\r
/**\r
* Sets the value of field 'renderGaps'.\r
*\r
* @param renderGaps the value of field 'renderGaps'.\r
*/\r
- public void setRenderGaps(boolean renderGaps)\r
- {\r
+ public void setRenderGaps(boolean renderGaps) {\r
this._renderGaps = renderGaps;\r
this._has_renderGaps = true;\r
- } //-- void setRenderGaps(boolean)\r
+ }\r
+ //-- void setRenderGaps(boolean)\r
\r
/**\r
* Sets the value of field 'showAnnotation'.\r
*\r
* @param showAnnotation the value of field 'showAnnotation'.\r
*/\r
- public void setShowAnnotation(boolean showAnnotation)\r
- {\r
+ public void setShowAnnotation(boolean showAnnotation) {\r
this._showAnnotation = showAnnotation;\r
this._has_showAnnotation = true;\r
- } //-- void setShowAnnotation(boolean)\r
+ }\r
+ //-- void setShowAnnotation(boolean)\r
\r
/**\r
* Sets the value of field 'showBoxes'.\r
*\r
* @param showBoxes the value of field 'showBoxes'.\r
*/\r
- public void setShowBoxes(boolean showBoxes)\r
- {\r
+ public void setShowBoxes(boolean showBoxes) {\r
this._showBoxes = showBoxes;\r
this._has_showBoxes = true;\r
- } //-- void setShowBoxes(boolean)\r
+ }\r
+ //-- void setShowBoxes(boolean)\r
\r
/**\r
* Sets the value of field 'showColourText'.\r
*\r
* @param showColourText the value of field 'showColourText'.\r
*/\r
- public void setShowColourText(boolean showColourText)\r
- {\r
+ public void setShowColourText(boolean showColourText) {\r
this._showColourText = showColourText;\r
this._has_showColourText = true;\r
- } //-- void setShowColourText(boolean)\r
+ }\r
+ //-- void setShowColourText(boolean)\r
\r
/**\r
* Sets the value of field 'showConservation'.\r
*\r
* @param showConservation the value of field 'showConservation'\r
*/\r
- public void setShowConservation(boolean showConservation)\r
- {\r
+ public void setShowConservation(boolean showConservation) {\r
this._showConservation = showConservation;\r
this._has_showConservation = true;\r
- } //-- void setShowConservation(boolean)\r
+ }\r
+ //-- void setShowConservation(boolean)\r
\r
/**\r
* Sets the value of field 'showFullId'.\r
*\r
* @param showFullId the value of field 'showFullId'.\r
*/\r
- public void setShowFullId(boolean showFullId)\r
- {\r
+ public void setShowFullId(boolean showFullId) {\r
this._showFullId = showFullId;\r
this._has_showFullId = true;\r
- } //-- void setShowFullId(boolean)\r
+ }\r
+ //-- void setShowFullId(boolean)\r
\r
/**\r
* Sets the value of field 'showIdentity'.\r
*\r
* @param showIdentity the value of field 'showIdentity'.\r
*/\r
- public void setShowIdentity(boolean showIdentity)\r
- {\r
+ public void setShowIdentity(boolean showIdentity) {\r
this._showIdentity = showIdentity;\r
this._has_showIdentity = true;\r
- } //-- void setShowIdentity(boolean)\r
+ }\r
+ //-- void setShowIdentity(boolean)\r
\r
/**\r
* Sets the value of field 'showQuality'.\r
*\r
* @param showQuality the value of field 'showQuality'.\r
*/\r
- public void setShowQuality(boolean showQuality)\r
- {\r
+ public void setShowQuality(boolean showQuality) {\r
this._showQuality = showQuality;\r
this._has_showQuality = true;\r
- } //-- void setShowQuality(boolean)\r
+ }\r
+ //-- void setShowQuality(boolean)\r
\r
/**\r
* Sets the value of field 'showSequenceFeatures'.\r
* @param showSequenceFeatures the value of field\r
* 'showSequenceFeatures'.\r
*/\r
- public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
- {\r
+ public void setShowSequenceFeatures(boolean showSequenceFeatures) {\r
this._showSequenceFeatures = showSequenceFeatures;\r
this._has_showSequenceFeatures = true;\r
- } //-- void setShowSequenceFeatures(boolean)\r
+ }\r
+ //-- void setShowSequenceFeatures(boolean)\r
\r
/**\r
* Sets the value of field 'showText'.\r
*\r
* @param showText the value of field 'showText'.\r
*/\r
- public void setShowText(boolean showText)\r
- {\r
+ public void setShowText(boolean showText) {\r
this._showText = showText;\r
this._has_showText = true;\r
- } //-- void setShowText(boolean)\r
+ }\r
+ //-- void setShowText(boolean)\r
\r
/**\r
* Sets the value of field 'startRes'.\r
*\r
* @param startRes the value of field 'startRes'.\r
*/\r
- public void setStartRes(int startRes)\r
- {\r
+ public void setStartRes(int startRes) {\r
this._startRes = startRes;\r
this._has_startRes = true;\r
- } //-- void setStartRes(int)\r
+ }\r
+ //-- void setStartRes(int)\r
\r
/**\r
* Sets the value of field 'startSeq'.\r
*\r
* @param startSeq the value of field 'startSeq'.\r
*/\r
- public void setStartSeq(int startSeq)\r
- {\r
+ public void setStartSeq(int startSeq) {\r
this._startSeq = startSeq;\r
this._has_startSeq = true;\r
- } //-- void setStartSeq(int)\r
+ }\r
+ //-- void setStartSeq(int)\r
\r
/**\r
* Sets the value of field 'title'.\r
*\r
* @param title the value of field 'title'.\r
*/\r
- public void setTitle(java.lang.String title)\r
- {\r
+ public void setTitle(java.lang.String title) {\r
this._title = title;\r
- } //-- void setTitle(java.lang.String)\r
+ }\r
+ //-- void setTitle(java.lang.String)\r
\r
/**\r
* Sets the value of field 'width'.\r
*\r
* @param width the value of field 'width'.\r
*/\r
- public void setWidth(int width)\r
- {\r
+ public void setWidth(int width) {\r
this._width = width;\r
this._has_width = true;\r
- } //-- void setWidth(int)\r
+ }\r
+ //-- void setWidth(int)\r
\r
/**\r
* Sets the value of field 'wrapAlignment'.\r
*\r
* @param wrapAlignment the value of field 'wrapAlignment'.\r
*/\r
- public void setWrapAlignment(boolean wrapAlignment)\r
- {\r
+ public void setWrapAlignment(boolean wrapAlignment) {\r
this._wrapAlignment = wrapAlignment;\r
this._has_wrapAlignment = true;\r
- } //-- void setWrapAlignment(boolean)\r
+ }\r
+ //-- void setWrapAlignment(boolean)\r
\r
/**\r
* Sets the value of field 'xpos'.\r
*\r
* @param xpos the value of field 'xpos'.\r
*/\r
- public void setXpos(int xpos)\r
- {\r
+ public void setXpos(int xpos) {\r
this._xpos = xpos;\r
this._has_xpos = true;\r
- } //-- void setXpos(int)\r
+ }\r
+ //-- void setXpos(int)\r
\r
/**\r
* Sets the value of field 'ypos'.\r
*\r
* @param ypos the value of field 'ypos'.\r
*/\r
- public void setYpos(int ypos)\r
- {\r
+ public void setYpos(int ypos) {\r
this._ypos = ypos;\r
this._has_ypos = true;\r
- } //-- void setYpos(int)\r
+ }\r
+ //-- void setYpos(int)\r
\r
/**\r
* Method unmarshal\r
* @return Object\r
*/\r
public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, \r
+ org.exolab.castor.xml.ValidationException {\r
+ return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class,\r
+ reader);\r
+ }\r
+ //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
*\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
-\r
+ }\r
+ //-- void validate()\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
import jalview.analysis.*;\r
+\r
import jalview.util.*;\r
+\r
import java.util.*;\r
\r
+\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
*/\r
-public class Alignment implements AlignmentI\r
-{\r
+public class Alignment implements AlignmentI {\r
+ protected Vector sequences;\r
+ protected Vector groups = new Vector();\r
+ protected Vector superGroup = new Vector();\r
+ protected char gapCharacter = '-';\r
+ public AlignmentAnnotation[] annotations;\r
+ public boolean featuresAdded = false;\r
+\r
+ /** Make an alignment from an array of Sequences.\r
+ *\r
+ * @param sequences\r
+ */\r
+ public Alignment(SequenceI[] seqs) {\r
+ sequences = new Vector();\r
\r
- protected Vector sequences;\r
- protected Vector groups = new Vector();\r
- protected Vector superGroup = new Vector();\r
- protected char gapCharacter = '-';\r
- public AlignmentAnnotation [] annotations;\r
+ for (int i = 0; i < seqs.length; i++)\r
+ sequences.addElement(seqs[i]);\r
\r
- public boolean featuresAdded = false;\r
+ getWidth();\r
+ }\r
\r
- /** Make an alignment from an array of Sequences.\r
- *\r
- * @param sequences\r
- */\r
- public Alignment(SequenceI[] seqs) {\r
- sequences = new Vector();\r
+ public Vector getSequences() {\r
+ return sequences;\r
+ }\r
\r
- for (int i=0; i < seqs.length; i++)\r
- sequences.addElement(seqs[i]);\r
+ public SequenceI getSequenceAt(int i) {\r
+ if (i < sequences.size()) {\r
+ return (SequenceI) sequences.elementAt(i);\r
+ }\r
\r
- getWidth();\r
- }\r
+ return null;\r
+ }\r
\r
- public Vector getSequences() {\r
- return sequences;\r
- }\r
+ /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
+ *\r
+ * @param snew\r
+ */\r
+ public void addSequence(SequenceI snew) {\r
+ sequences.addElement(snew);\r
+ }\r
\r
- public SequenceI getSequenceAt(int i) {\r
- if (i < sequences.size()) {\r
- return (SequenceI)sequences.elementAt(i);\r
+ public void addSequence(SequenceI[] seq) {\r
+ for (int i = 0; i < seq.length; i++) {\r
+ addSequence(seq[i]);\r
+ }\r
}\r
\r
- return null;\r
- }\r
+ /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
+ *\r
+ * @param snew\r
+ */\r
+ public void setSequenceAt(int i, SequenceI snew) {\r
+ SequenceI oldseq = getSequenceAt(i);\r
+ deleteSequence(oldseq);\r
\r
- /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
- *\r
- * @param snew\r
- */\r
- public void addSequence(SequenceI snew) {\r
- sequences.addElement(snew);\r
- }\r
+ sequences.setElementAt(snew, i);\r
+ }\r
\r
- public void addSequence(SequenceI[] seq) {\r
- for (int i=0; i < seq.length; i++) {\r
- addSequence(seq[i]);\r
+ public Vector getGroups() {\r
+ return groups;\r
}\r
- }\r
\r
- /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
- *\r
- * @param snew\r
- */\r
- public void setSequenceAt(int i,SequenceI snew) {\r
- SequenceI oldseq = getSequenceAt(i);\r
- deleteSequence(oldseq);\r
+ /** Sorts the sequences by sequence group size - largest to smallest.\r
+ * Uses QuickSort.\r
+ */\r
+ public void sortGroups() {\r
+ float[] arr = new float[groups.size()];\r
+ Object[] s = new Object[groups.size()];\r
\r
- sequences.setElementAt(snew,i);\r
- }\r
+ for (int i = 0; i < groups.size(); i++) {\r
+ arr[i] = ((SequenceGroup) groups.elementAt(i)).sequences.size();\r
+ s[i] = groups.elementAt(i);\r
+ }\r
\r
- public Vector getGroups() {\r
- return groups;\r
- }\r
-\r
- /** Sorts the sequences by sequence group size - largest to smallest.\r
- * Uses QuickSort.\r
- */\r
- public void sortGroups() {\r
- float[] arr = new float [groups.size()];\r
- Object[] s = new Object[groups.size()];\r
-\r
- for (int i=0; i < groups.size(); i++) {\r
- arr[i] = ((SequenceGroup)groups.elementAt(i)).sequences.size();\r
- s[i] = groups.elementAt(i);\r
- }\r
+ QuickSort.sort(arr, s);\r
\r
- QuickSort.sort(arr,s);\r
+ Vector newg = new Vector(groups.size());\r
\r
- Vector newg = new Vector(groups.size());\r
+ for (int i = groups.size() - 1; i >= 0; i--) {\r
+ newg.addElement(s[i]);\r
+ }\r
\r
- for (int i=groups.size()-1; i >= 0; i--) {\r
- newg.addElement(s[i]);\r
+ groups = newg;\r
}\r
\r
- groups = newg;\r
- }\r
+ /** Takes out columns consisting entirely of gaps (-,.," ")\r
+ */\r
+ public void removeGaps() {\r
+ SequenceI current;\r
+ int iSize = getWidth();\r
+\r
+ for (int i = 0; i < iSize; i++) {\r
+ boolean delete = true;\r
+\r
+ for (int j = 0; j < getHeight(); j++) {\r
+ current = getSequenceAt(j);\r
+\r
+ if (current.getLength() > i) {\r
+ /* MC Should move this to a method somewhere */\r
+ if (!jalview.util.Comparison.isGap(current.getCharAt(i))) {\r
+ delete = false;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (delete) {\r
+ deleteColumns(i, i);\r
+ iSize--;\r
+ i--;\r
+ }\r
+ }\r
+ }\r
\r
- /** Takes out columns consisting entirely of gaps (-,.," ")\r
- */\r
- public void removeGaps()\r
- {\r
+ /** Returns an array of Sequences containing columns\r
+ * start to end (inclusive) only.\r
+ *\r
+ * @param start start column to fetch\r
+ * @param end end column to fetch\r
+ * @return Array of Sequences, ready to put into a new Alignment\r
+ */\r
+ public SequenceI[] getColumns(int start, int end) {\r
+ return getColumns(0, getHeight() - 1, start, end);\r
+ }\r
\r
- SequenceI current;\r
- int iSize = getWidth();\r
- for (int i=0; i < iSize; i++)\r
- {\r
- boolean delete = true;\r
- for (int j=0; j < getHeight(); j++)\r
- {\r
- current = getSequenceAt(j);\r
- if (current.getLength() > i)\r
- {\r
- /* MC Should move this to a method somewhere */\r
- if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))\r
- delete = false;\r
+ /** Removes a range of columns (start to end inclusive).\r
+ *\r
+ * @param start Start column in the alignment\r
+ * @param end End column in the alignment\r
+ */\r
+ public void deleteColumns(int start, int end) {\r
+ deleteColumns(0, getHeight() - 1, start, end);\r
+ }\r
\r
+ public void deleteColumns(int seq1, int seq2, int start, int end) {\r
+ for (int i = 0; i <= (end - start); i++) {\r
+ for (int j = seq1; j <= seq2; j++) {\r
+ getSequenceAt(j).deleteCharAt(start);\r
+ }\r
}\r
- }\r
+ }\r
\r
- if ( delete )\r
- {\r
- deleteColumns(i,i);\r
- iSize--;\r
- i--;\r
- }\r
+ public void insertColumns(SequenceI[] seqs, int pos) {\r
+ if (seqs.length == getHeight()) {\r
+ for (int i = 0; i < getHeight(); i++) {\r
+ String tmp = new String(getSequenceAt(i).getSequence());\r
+ getSequenceAt(i).setSequence(tmp.substring(0, pos) +\r
+ seqs[i].getSequence() + tmp.substring(pos));\r
+ }\r
+ }\r
}\r
\r
+ public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {\r
+ SequenceI[] seqs = new Sequence[(seq2 - seq1) + 1];\r
\r
- }\r
+ for (int i = seq1; i <= seq2; i++) {\r
+ seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
+ getSequenceAt(i).getSequence().substring(start, end),\r
+ getSequenceAt(i).findPosition(start),\r
+ getSequenceAt(i).findPosition(end));\r
+ }\r
\r
- /** Returns an array of Sequences containing columns\r
- * start to end (inclusive) only.\r
- *\r
- * @param start start column to fetch\r
- * @param end end column to fetch\r
- * @return Array of Sequences, ready to put into a new Alignment\r
- */\r
- public SequenceI[] getColumns(int start, int end) {\r
- return getColumns(0,getHeight()-1,start,end);\r
- }\r
-\r
- /** Removes a range of columns (start to end inclusive).\r
- *\r
- * @param start Start column in the alignment\r
- * @param end End column in the alignment\r
- */\r
- public void deleteColumns(int start, int end) {\r
- deleteColumns(0,getHeight()-1,start,end);\r
- }\r
+ return seqs;\r
+ }\r
\r
- public void deleteColumns(int seq1, int seq2, int start, int end) {\r
+ public void trimLeft(int i) {\r
+ for (int j = 0; j < getHeight(); j++) {\r
+ SequenceI s = getSequenceAt(j);\r
+ int newstart = s.findPosition(i);\r
\r
- for (int i=0; i <= (end-start); i++) {\r
- for (int j=seq1; j <= seq2; j++) {\r
- getSequenceAt(j).deleteCharAt(start);\r
- }\r
+ s.setStart(newstart);\r
+ s.setSequence(s.getSequence().substring(i));\r
+ }\r
}\r
- }\r
\r
- public void insertColumns(SequenceI[] seqs, int pos) {\r
- if (seqs.length == getHeight()) {\r
- for (int i=0; i < getHeight();i++) {\r
- String tmp = new String(getSequenceAt(i).getSequence());\r
- getSequenceAt(i).setSequence(tmp.substring(0,pos) + seqs[i].getSequence() + tmp.substring(pos));\r
- }\r
+ public void trimRight(int i) {\r
+ for (int j = 0; j < getHeight(); j++) {\r
+ SequenceI s = getSequenceAt(j);\r
+ int newend = s.findPosition(i);\r
\r
+ s.setEnd(newend);\r
+ s.setSequence(s.getSequence().substring(0, i + 1));\r
+ }\r
}\r
- }\r
\r
- public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {\r
- SequenceI[] seqs = new Sequence[(seq2-seq1)+1];\r
- for (int i=seq1; i<= seq2; i++ ) {\r
- seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
- getSequenceAt(i).getSequence().substring(start,end),\r
- getSequenceAt(i).findPosition(start),\r
- getSequenceAt(i).findPosition(end));\r
+ public void deleteSequence(SequenceI s) {\r
+ for (int i = 0; i < getHeight(); i++)\r
+ if (getSequenceAt(i) == s) {\r
+ deleteSequence(i);\r
+ }\r
}\r
- return seqs;\r
- }\r
\r
- public void trimLeft(int i) {\r
- for (int j = 0;j< getHeight();j++) {\r
+ public void deleteSequence(int i) {\r
+ sequences.removeElementAt(i);\r
+ }\r
\r
- SequenceI s = getSequenceAt(j);\r
- int newstart = s.findPosition(i);\r
+ public Vector removeRedundancy(float threshold, Vector sel) {\r
+ Vector del = new Vector();\r
+\r
+ for (int i = 1; i < sel.size(); i++) {\r
+ for (int j = 0; j < i; j++) {\r
+ // Only do the comparison if either have not been deleted\r
+ if (!del.contains((SequenceI) sel.elementAt(i)) ||\r
+ !del.contains((SequenceI) sel.elementAt(j))) {\r
+ // use PID instead of Comparison (which is really not pleasant)\r
+ float pid = Comparison.PID((SequenceI) sel.elementAt(j),\r
+ (SequenceI) sel.elementAt(i));\r
+\r
+ if (pid >= threshold) {\r
+ // Delete the shortest one\r
+ if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel\r
+ .elementAt(\r
+ i)).getSequence().length()) {\r
+ del.addElement(sel.elementAt(i));\r
+ } else {\r
+ del.addElement(sel.elementAt(i));\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- s.setStart(newstart);\r
- s.setSequence(s.getSequence().substring(i));\r
+ // Now delete the sequences\r
+ for (int i = 0; i < del.size(); i++)\r
+ deleteSequence((SequenceI) del.elementAt(i));\r
\r
+ return del;\r
}\r
- }\r
\r
- public void trimRight(int i) {\r
- for (int j = 0;j< getHeight();j++) {\r
- SequenceI s = getSequenceAt(j);\r
- int newend = s.findPosition(i);\r
+ public void sortByPID(SequenceI s) {\r
+ float[] scores = new float[getHeight()];\r
+ SequenceI[] seqs = new SequenceI[getHeight()];\r
+\r
+ for (int i = 0; i < getHeight(); i++) {\r
+ scores[i] = Comparison.compare(getSequenceAt(i), s);\r
+ seqs[i] = getSequenceAt(i);\r
+ }\r
+\r
+ QuickSort.sort(scores, 0, scores.length - 1, seqs);\r
+\r
+ int len = 0;\r
+\r
+ if ((getHeight() % 2) == 0) {\r
+ len = getHeight() / 2;\r
+ } else {\r
+ len = (getHeight() + 1) / 2;\r
+ }\r
\r
- s.setEnd(newend);\r
- s.setSequence(s.getSequence().substring(0,i+1));\r
+ for (int i = 0; i < len; i++) {\r
+ SequenceI tmp = seqs[i];\r
+ sequences.setElementAt(seqs[getHeight() - i - 1], i);\r
+ sequences.setElementAt(tmp, getHeight() - i - 1);\r
+ }\r
}\r
- }\r
\r
- public void deleteSequence(SequenceI s)\r
- {\r
- for (int i=0; i < getHeight(); i++)\r
- if (getSequenceAt(i) == s)\r
- deleteSequence(i);\r
- }\r
+ public void sortByID() {\r
+ String[] ids = new String[getHeight()];\r
+ SequenceI[] seqs = new SequenceI[getHeight()];\r
\r
- public void deleteSequence(int i)\r
- {\r
- sequences.removeElementAt(i);\r
- }\r
+ for (int i = 0; i < getHeight(); i++) {\r
+ ids[i] = getSequenceAt(i).getName();\r
+ seqs[i] = getSequenceAt(i);\r
+ }\r
\r
+ QuickSort.sort(ids, seqs);\r
\r
- public Vector removeRedundancy(float threshold, Vector sel) {\r
- Vector del = new Vector();\r
+ int len = 0;\r
\r
- for (int i = 1; i < sel.size(); i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- // Only do the comparison if either have not been deleted\r
- if (!del.contains( (SequenceI) sel.elementAt(i)) ||\r
- !del.contains( (SequenceI) sel.elementAt(j)))\r
- {\r
- // use PID instead of Comparison (which is really not pleasant)\r
- float pid = Comparison.PID( (SequenceI) sel.elementAt(j),\r
- (SequenceI) sel.elementAt(i));\r
+ if ((getHeight() % 2) == 0) {\r
+ len = getHeight() / 2;\r
+ } else {\r
+ len = (getHeight() + 1) / 2;\r
+ System.out.println("DEBUG:Sort len is odd = " + len); // log.\r
+ }\r
\r
- if (pid >= threshold)\r
- {\r
- // Delete the shortest one\r
- if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >\r
- ( (SequenceI) sel.elementAt(i)).getSequence().length())\r
- del.addElement(sel.elementAt(i));\r
- else\r
- del.addElement(sel.elementAt(i));\r
- }\r
+ for (int i = 0; i < len; i++) {\r
+ System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " +\r
+ seqs[getHeight() - i - 1].getName()); // log.\r
+\r
+ SequenceI tmp = seqs[i];\r
+ sequences.setElementAt(seqs[getHeight() - i - 1], i);\r
+ sequences.setElementAt(tmp, getHeight() - i - 1);\r
}\r
- }\r
}\r
\r
- // Now delete the sequences\r
- for (int i=0; i < del.size(); i++)\r
- deleteSequence((SequenceI)del.elementAt(i));\r
-\r
- return del;\r
- }\r
+ /** */\r
+ public SequenceGroup findGroup(int i) {\r
+ return findGroup(getSequenceAt(i));\r
+ }\r
\r
- public void sortByPID(SequenceI s) {\r
+ /** */\r
+ public SequenceGroup findGroup(SequenceI s) {\r
+ for (int i = 0; i < this.groups.size(); i++) {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
- float scores[] = new float[getHeight()];\r
- SequenceI seqs[] = new SequenceI[getHeight()];\r
+ if (sg.sequences.contains(s)) {\r
+ return sg;\r
+ }\r
+ }\r
\r
- for (int i = 0; i < getHeight(); i++) {\r
- scores[i] = Comparison.compare(getSequenceAt(i),s);\r
- seqs[i] = getSequenceAt(i);\r
+ return null;\r
}\r
\r
- QuickSort.sort(scores,0,scores.length-1,seqs);\r
+ public SequenceGroup[] findAllGroups(SequenceI s) {\r
+ Vector temp = new Vector();\r
+\r
+ for (int i = 0; i < this.groups.size(); i++) {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ if (sg.sequences.contains(s)) {\r
+ temp.addElement(sg);\r
+ }\r
+ }\r
+\r
+ SequenceGroup[] ret = new SequenceGroup[temp.size()];\r
\r
- int len = 0;\r
+ for (int i = 0; i < temp.size(); i++)\r
+ ret[i] = (SequenceGroup) temp.elementAt(i);\r
\r
- if (getHeight()%2 == 0) {\r
- len = getHeight()/2;\r
- } else {\r
- len = (getHeight()+1)/2;\r
+ return ret;\r
}\r
\r
- for (int i = 0; i < len; i++) {\r
- SequenceI tmp = seqs[i];\r
- sequences.setElementAt(seqs[getHeight()-i-1],i);\r
- sequences.setElementAt(tmp,getHeight()-i-1);\r
+ /** */\r
+ public void addToGroup(SequenceGroup g, SequenceI s) {\r
+ if (!(g.sequences.contains(s))) {\r
+ g.sequences.addElement(s);\r
+ }\r
}\r
- }\r
\r
- public void sortByID() {\r
- String ids[] = new String[getHeight()];\r
- SequenceI seqs[] = new SequenceI[getHeight()];\r
+ /** */\r
+ public void removeFromGroup(SequenceGroup g, SequenceI s) {\r
+ if ((g != null) && (g.sequences != null)) {\r
+ if (g.sequences.contains(s)) {\r
+ g.sequences.removeElement(s);\r
+\r
+ if (g.sequences.size() == 0) {\r
+ groups.removeElement(g);\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- for (int i = 0; i < getHeight(); i++) {\r
- ids[i] = getSequenceAt(i).getName();\r
- seqs[i] = getSequenceAt(i);\r
+ public void addSuperGroup(SuperGroup sg) {\r
+ superGroup.addElement(sg);\r
}\r
\r
- QuickSort.sort(ids,seqs);\r
+ public void removeSuperGroup(SuperGroup sg) {\r
+ superGroup.removeElement(sg);\r
+ }\r
\r
- int len = 0;\r
+ public SuperGroup getSuperGroup(SequenceGroup sg) {\r
+ for (int i = 0; i < this.superGroup.size(); i++) {\r
+ SuperGroup temp = (SuperGroup) superGroup.elementAt(i);\r
\r
- if (getHeight()%2 == 0) {\r
- len = getHeight()/2;\r
- } else {\r
- len = (getHeight()+1)/2;\r
- System.out.println("DEBUG:Sort len is odd = " + len); // log.\r
+ if (temp.sequenceGroups.contains(sg)) {\r
+ return temp;\r
+ }\r
+ }\r
+\r
+ return null;\r
}\r
- for (int i = 0; i < len; i++) {\r
- System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName()); // log.\r
- SequenceI tmp = seqs[i];\r
- sequences.setElementAt(seqs[getHeight()-i-1],i);\r
- sequences.setElementAt(tmp,getHeight()-i-1);\r
+\r
+ /** */\r
+ public void addGroup(SequenceGroup sg) {\r
+ if (!groups.contains(sg)) {\r
+ groups.addElement(sg);\r
+ }\r
}\r
- }\r
\r
- /** */\r
- public SequenceGroup findGroup(int i) {\r
- return findGroup(getSequenceAt(i));\r
- }\r
+ public void deleteAllGroups() {\r
+ groups.removeAllElements();\r
+ superGroup.removeAllElements();\r
+\r
+ int i = 0;\r
\r
- /** */\r
- public SequenceGroup findGroup(SequenceI s) {\r
- for (int i = 0; i < this.groups.size();i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
- if (sg.sequences.contains(s))\r
- return sg;\r
+ while (i < sequences.size()) {\r
+ SequenceI s = getSequenceAt(i);\r
+ s.setColor(java.awt.Color.white);\r
+ i++;\r
+ }\r
+ }\r
\r
+ /** */\r
+ public void deleteGroup(SequenceGroup g) {\r
+ if (groups.contains(g)) {\r
+ groups.removeElement(g);\r
+ }\r
}\r
- return null;\r
- }\r
\r
- public SequenceGroup [] findAllGroups(SequenceI s)\r
- {\r
+ /** */\r
+ public SequenceI findName(String name) {\r
+ int i = 0;\r
\r
- Vector temp = new Vector();\r
+ while (i < sequences.size()) {\r
+ SequenceI s = getSequenceAt(i);\r
\r
- for (int i = 0; i < this.groups.size();i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ if (s.getName().equals(name)) {\r
+ return s;\r
+ }\r
\r
- if (sg.sequences.contains(s))\r
- temp.addElement(sg);\r
+ i++;\r
+ }\r
+\r
+ return null;\r
}\r
\r
- SequenceGroup [] ret = new SequenceGroup[temp.size()];\r
- for(int i=0; i<temp.size(); i++)\r
- ret[i] = (SequenceGroup)temp.elementAt(i);\r
+ /** */\r
+ public SequenceI findbyDisplayId(String name) {\r
+ int i = 0;\r
+\r
+ while (i < sequences.size()) {\r
+ SequenceI s = getSequenceAt(i);\r
\r
- return ret;\r
+ if (s.getDisplayId().equals(name)) {\r
+ return s;\r
+ }\r
\r
- }\r
- /** */\r
- public void addToGroup(SequenceGroup g, SequenceI s) {\r
- if (!(g.sequences.contains(s))) {\r
- g.sequences.addElement(s);\r
+ i++;\r
+ }\r
+\r
+ return null;\r
}\r
- }\r
- /** */\r
- public void removeFromGroup(SequenceGroup g,SequenceI s) {\r
- if (g != null && g.sequences != null) {\r
- if (g.sequences.contains(s)) {\r
- g.sequences.removeElement(s);\r
- if (g.sequences.size() == 0) {\r
- groups.removeElement(g);\r
+\r
+ /** */\r
+ public int findIndex(SequenceI s) {\r
+ int i = 0;\r
+\r
+ while (i < sequences.size()) {\r
+ if (s == getSequenceAt(i)) {\r
+ return i;\r
+ }\r
+\r
+ i++;\r
}\r
- }\r
+\r
+ return -1;\r
+ }\r
+\r
+ public int getHeight() {\r
+ return sequences.size();\r
}\r
- }\r
\r
- public void addSuperGroup(SuperGroup sg)\r
- {\r
- superGroup.addElement(sg);\r
- }\r
+ public int getWidth() {\r
+ int maxLength = -1;\r
\r
- public void removeSuperGroup(SuperGroup sg)\r
- {\r
- superGroup.removeElement(sg);\r
- }\r
+ for (int i = 0; i < sequences.size(); i++) {\r
+ if (getSequenceAt(i).getLength() > maxLength) {\r
+ maxLength = getSequenceAt(i).getLength();\r
+ }\r
+ }\r
\r
- public SuperGroup getSuperGroup(SequenceGroup sg)\r
- {\r
- for (int i = 0; i < this.superGroup.size(); i++)\r
- {\r
- SuperGroup temp = (SuperGroup) superGroup.elementAt(i);\r
- if (temp.sequenceGroups.contains(sg))\r
- return temp;\r
+ return maxLength;\r
}\r
- return null;\r
- }\r
\r
- /** */\r
- public void addGroup(SequenceGroup sg) {\r
- if(!groups.contains(sg))\r
- groups.addElement(sg);\r
- }\r
+ public int getMaxIdLength() {\r
+ int max = 0;\r
+ int i = 0;\r
\r
- public void deleteAllGroups()\r
- {\r
- groups.removeAllElements();\r
- superGroup.removeAllElements();\r
- int i=0;\r
- while (i < sequences.size()) {\r
- SequenceI s = getSequenceAt(i);\r
- s.setColor(java.awt.Color.white);\r
- i++;\r
- }\r
-\r
-\r
- }\r
-\r
- /** */\r
- public void deleteGroup(SequenceGroup g) {\r
- if (groups.contains(g)) {\r
- groups.removeElement(g);\r
- }\r
- }\r
-\r
- /** */\r
- public SequenceI findName(String name) {\r
- int i = 0;\r
- while (i < sequences.size()) {\r
- SequenceI s = getSequenceAt(i);\r
- if (s.getName().equals(name))\r
- return s;\r
-\r
- i++;\r
- }\r
- return null;\r
- }\r
-\r
- /** */\r
- public SequenceI findbyDisplayId(String name) {\r
- int i = 0;\r
- while (i < sequences.size()) {\r
- SequenceI s = getSequenceAt(i);\r
- if (s.getDisplayId().equals(name))\r
- return s;\r
-\r
- i++;\r
- }\r
- return null;\r
- }\r
-\r
- /** */\r
- public int findIndex(SequenceI s)\r
- {\r
- int i=0;\r
- while (i < sequences.size())\r
- {\r
- if (s == getSequenceAt(i))\r
- return i;\r
-\r
- i++;\r
- }\r
- return -1;\r
- }\r
-\r
- public int getHeight() {\r
- return sequences.size();\r
- }\r
-\r
-\r
- public int getWidth()\r
- {\r
- int maxLength = -1;\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- if (getSequenceAt(i).getLength() > maxLength)\r
- maxLength = getSequenceAt(i).getLength();\r
- }\r
-\r
- return maxLength;\r
- }\r
-\r
-\r
- public int getMaxIdLength() {\r
- int max = 0;\r
- int i = 0;\r
-\r
- while (i < sequences.size()) {\r
- SequenceI seq = getSequenceAt(i);\r
- String tmp = seq.getName() + "/" + seq.getStart() + "-" + seq.getEnd();\r
-\r
- if (tmp.length() > max) {\r
- max = tmp.length();\r
- }\r
-\r
- i++;\r
- }\r
- return max;\r
- }\r
-\r
- public void setGapCharacter(char gc)\r
- {\r
- gapCharacter = gc;\r
- for (int i=0; i < sequences.size(); i++)\r
- {\r
- Sequence seq = (Sequence)sequences.elementAt(i);\r
- seq.sequence = seq.sequence.replace('.', gc);\r
- seq.sequence = seq.sequence.replace('-', gc);\r
- }\r
- }\r
+ while (i < sequences.size()) {\r
+ SequenceI seq = getSequenceAt(i);\r
+ String tmp = seq.getName() + "/" + seq.getStart() + "-" +\r
+ seq.getEnd();\r
\r
- public char getGapCharacter() {\r
- return gapCharacter;\r
- }\r
+ if (tmp.length() > max) {\r
+ max = tmp.length();\r
+ }\r
\r
- public Vector getAAFrequency()\r
- {\r
- return AAFrequency.calculate(sequences, 0, getWidth());\r
- }\r
+ i++;\r
+ }\r
\r
- public boolean isAligned()\r
- {\r
- int width = getWidth();\r
- for (int i = 0; i < sequences.size(); i++)\r
- if (getSequenceAt(i).getLength() != width)\r
- return false;\r
-\r
- return true;\r
- }\r
+ return max;\r
+ }\r
\r
- public void deleteAnnotation(AlignmentAnnotation aa)\r
- {\r
- int aSize = 1;\r
- if(annotations!=null)\r
- aSize = annotations.length;\r
+ public void setGapCharacter(char gc) {\r
+ gapCharacter = gc;\r
\r
- AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize-1];\r
+ for (int i = 0; i < sequences.size(); i++) {\r
+ Sequence seq = (Sequence) sequences.elementAt(i);\r
+ seq.sequence = seq.sequence.replace('.', gc);\r
+ seq.sequence = seq.sequence.replace('-', gc);\r
+ }\r
+ }\r
\r
- int tIndex = 0;\r
- for (int i = 0; i < aSize; i++)\r
- {\r
- if(annotations[i]==aa)\r
- continue;\r
+ public char getGapCharacter() {\r
+ return gapCharacter;\r
+ }\r
\r
+ public Vector getAAFrequency() {\r
+ return AAFrequency.calculate(sequences, 0, getWidth());\r
+ }\r
\r
- temp[tIndex] = annotations[i];\r
- tIndex++;\r
- }\r
+ public boolean isAligned() {\r
+ int width = getWidth();\r
\r
- annotations = temp;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ if (getSequenceAt(i).getLength() != width) {\r
+ return false;\r
+ }\r
\r
- }\r
+ return true;\r
+ }\r
\r
- public void addAnnotation(AlignmentAnnotation aa)\r
- {\r
- int aSize = 1;\r
- if(annotations!=null)\r
- aSize = annotations.length+1;\r
+ public void deleteAnnotation(AlignmentAnnotation aa) {\r
+ int aSize = 1;\r
\r
- AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize];\r
- int i=0;\r
- if (aSize > 1)\r
- for (i = 0; i < aSize-1; i++)\r
- temp[i] = annotations[i];\r
+ if (annotations != null) {\r
+ aSize = annotations.length;\r
+ }\r
\r
- temp[i] = aa;\r
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];\r
\r
- annotations = temp;\r
- }\r
- public AlignmentAnnotation[] getAlignmentAnnotation()\r
- {\r
- return annotations;\r
- }\r
+ int tIndex = 0;\r
\r
-}\r
+ for (int i = 0; i < aSize; i++) {\r
+ if (annotations[i] == aa) {\r
+ continue;\r
+ }\r
\r
+ temp[tIndex] = annotations[i];\r
+ tIndex++;\r
+ }\r
+\r
+ annotations = temp;\r
+ }\r
\r
+ public void addAnnotation(AlignmentAnnotation aa) {\r
+ int aSize = 1;\r
\r
+ if (annotations != null) {\r
+ aSize = annotations.length + 1;\r
+ }\r
\r
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
+ int i = 0;\r
\r
+ if (aSize > 1) {\r
+ for (i = 0; i < (aSize - 1); i++)\r
+ temp[i] = annotations[i];\r
+ }\r
\r
+ temp[i] = aa;\r
\r
+ annotations = temp;\r
+ }\r
\r
+ public AlignmentAnnotation[] getAlignmentAnnotation() {\r
+ return annotations;\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
-public class AlignmentAnnotation\r
-{\r
- public String label;\r
- public String description;\r
- public Annotation [] annotations;\r
- public boolean isGraph = false;\r
- public float graphMin, graphMax;\r
- public int windowLength;\r
-\r
- // Graphical hints and tips\r
- public boolean editable = false;\r
- public boolean hasIcons; //\r
- public boolean hasText;\r
- public boolean visible = true;\r
- public int height=0;\r
-\r
- public AlignmentAnnotation(String label, String description, Annotation [] annotations)\r
- {\r
- // always editable?\r
- editable = true;\r
- this.label = label;\r
- this.description = description;\r
- this.annotations = annotations;\r
- for(int i=0; i<annotations.length; i++)\r
- {\r
- if (annotations[i]!=null &&(\r
- annotations[i].secondaryStructure == 'H' ||\r
- annotations[i].secondaryStructure == 'E'))\r
- hasIcons = true;\r
-\r
- if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)\r
- hasText = true;\r
- }\r
- }\r
-\r
- public AlignmentAnnotation(String label, String description, Annotation [] annotations, float min, float max, int winLength)\r
- {\r
- // graphs are not editable\r
- this.label = label;\r
- this.description = description;\r
- this.annotations = annotations;\r
- isGraph = true;\r
- if(min==max)\r
- {\r
- for(int i=0; i<annotations.length; i++)\r
- {\r
- if(annotations[i]==null)\r
- continue;\r
- if(annotations[i].value>max)\r
- max = annotations[i].value;\r
- if(annotations[i].value<min)\r
- min = annotations[i].value;\r
- }\r
+public class AlignmentAnnotation {\r
+ public String label;\r
+ public String description;\r
+ public Annotation[] annotations;\r
+ public boolean isGraph = false;\r
+ public float graphMin;\r
+ public float graphMax;\r
+ public int windowLength;\r
+\r
+ // Graphical hints and tips\r
+ public boolean editable = false;\r
+ public boolean hasIcons; //\r
+ public boolean hasText;\r
+ public boolean visible = true;\r
+ public int height = 0;\r
+\r
+ public AlignmentAnnotation(String label, String description,\r
+ Annotation[] annotations) {\r
+ // always editable?\r
+ editable = true;\r
+ this.label = label;\r
+ this.description = description;\r
+ this.annotations = annotations;\r
+\r
+ for (int i = 0; i < annotations.length; i++) {\r
+ if ((annotations[i] != null) &&\r
+ ((annotations[i].secondaryStructure == 'H') ||\r
+ (annotations[i].secondaryStructure == 'E'))) {\r
+ hasIcons = true;\r
+ }\r
+\r
+ if ((annotations[i] != null) &&\r
+ (annotations[i].displayCharacter.length() > 0)) {\r
+ hasText = true;\r
+ }\r
+ }\r
}\r
\r
- graphMin = min;\r
- graphMax = max;\r
- windowLength = winLength;\r
- for(int i=0; i<annotations.length; i++)\r
- {\r
- if (annotations[i]!=null &&(\r
- annotations[i].secondaryStructure == 'H' ||\r
- annotations[i].secondaryStructure == 'E'))\r
- hasIcons = true;\r
-\r
- if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)\r
- hasText = true;\r
+ public AlignmentAnnotation(String label, String description,\r
+ Annotation[] annotations, float min, float max, int winLength) {\r
+ // graphs are not editable\r
+ this.label = label;\r
+ this.description = description;\r
+ this.annotations = annotations;\r
+ isGraph = true;\r
+\r
+ if (min == max) {\r
+ for (int i = 0; i < annotations.length; i++) {\r
+ if (annotations[i] == null) {\r
+ continue;\r
+ }\r
+\r
+ if (annotations[i].value > max) {\r
+ max = annotations[i].value;\r
+ }\r
+\r
+ if (annotations[i].value < min) {\r
+ min = annotations[i].value;\r
+ }\r
+ }\r
+ }\r
+\r
+ graphMin = min;\r
+ graphMax = max;\r
+ windowLength = winLength;\r
+\r
+ for (int i = 0; i < annotations.length; i++) {\r
+ if ((annotations[i] != null) &&\r
+ ((annotations[i].secondaryStructure == 'H') ||\r
+ (annotations[i].secondaryStructure == 'E'))) {\r
+ hasIcons = true;\r
+ }\r
+\r
+ if ((annotations[i] != null) &&\r
+ (annotations[i].displayCharacter.length() > 0)) {\r
+ hasText = true;\r
+ }\r
+ }\r
}\r
- }\r
-\r
- public String toString()\r
- {\r
- StringBuffer buffer = new StringBuffer();\r
- for(int i=0; i<annotations.length; i++)\r
- {\r
- if(annotations[i]!=null)\r
- {\r
- if(isGraph)\r
- buffer.append(annotations[i].value);\r
- else if(hasIcons)\r
- buffer.append(annotations[i].secondaryStructure);\r
- else\r
- buffer.append(annotations[i].displayCharacter);\r
-\r
- }\r
- buffer.append(", ");\r
- }\r
- if(label.equals("Consensus"))\r
- {\r
- buffer.append("\n");\r
- for (int i = 0; i < annotations.length; i++)\r
- {\r
- if (annotations[i] != null)\r
- buffer.append(annotations[i].description);\r
- buffer.append(", ");\r
- }\r
- }\r
- return buffer.toString();\r
- }\r
\r
+ public String toString() {\r
+ StringBuffer buffer = new StringBuffer();\r
+\r
+ for (int i = 0; i < annotations.length; i++) {\r
+ if (annotations[i] != null) {\r
+ if (isGraph) {\r
+ buffer.append(annotations[i].value);\r
+ } else if (hasIcons) {\r
+ buffer.append(annotations[i].secondaryStructure);\r
+ } else {\r
+ buffer.append(annotations[i].displayCharacter);\r
+ }\r
+ }\r
+\r
+ buffer.append(", ");\r
+ }\r
+\r
+ if (label.equals("Consensus")) {\r
+ buffer.append("\n");\r
+\r
+ for (int i = 0; i < annotations.length; i++) {\r
+ if (annotations[i] != null) {\r
+ buffer.append(annotations[i].description);\r
+ }\r
+\r
+ buffer.append(", ");\r
+ }\r
+ }\r
+\r
+ return buffer.toString();\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
import java.util.*;\r
\r
+\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
*/\r
public interface AlignmentI {\r
+ public int getHeight();\r
\r
- public int getHeight() ;\r
- public int getWidth() ;\r
- public int getMaxIdLength() ;\r
+ public int getWidth();\r
\r
- public boolean isAligned();\r
+ public int getMaxIdLength();\r
\r
- public Vector getSequences();\r
- public SequenceI getSequenceAt(int i);\r
+ public boolean isAligned();\r
\r
- public void addSequence(SequenceI seq) ;\r
- public void setSequenceAt(int i,SequenceI seq);\r
+ public Vector getSequences();\r
\r
- public void deleteSequence(SequenceI s) ;\r
- public void deleteSequence(int i) ;\r
+ public SequenceI getSequenceAt(int i);\r
\r
- public SequenceI[] getColumns(int start, int end) ;\r
- public SequenceI[] getColumns(int seq1, int seq2, int start, int end) ;\r
+ public void addSequence(SequenceI seq);\r
\r
- public void deleteColumns(int start, int end) ;\r
- public void deleteColumns(int seq1, int seq2, int start, int end) ;\r
+ public void setSequenceAt(int i, SequenceI seq);\r
\r
- public void insertColumns(SequenceI[] seqs, int pos) ;\r
+ public void deleteSequence(SequenceI s);\r
\r
- public SequenceI findName(String name) ;\r
- public SequenceI findbyDisplayId(String name);\r
+ public void deleteSequence(int i);\r
\r
- public int findIndex(SequenceI s) ;\r
+ public SequenceI[] getColumns(int start, int end);\r
\r
- // Modifying\r
- public void trimLeft(int i) ;\r
- public void trimRight(int i) ;\r
+ public SequenceI[] getColumns(int seq1, int seq2, int start, int end);\r
\r
- public void removeGaps() ;\r
- public Vector removeRedundancy(float threshold, Vector sel) ;\r
+ public void deleteColumns(int start, int end);\r
\r
+ public void deleteColumns(int seq1, int seq2, int start, int end);\r
\r
- // Grouping methods\r
- public SequenceGroup findGroup(int i) ;\r
- public SequenceGroup findGroup(SequenceI s) ;\r
- public SequenceGroup [] findAllGroups(SequenceI s);\r
- public void addToGroup(SequenceGroup g, SequenceI s) ;\r
- public void removeFromGroup(SequenceGroup g,SequenceI s) ;\r
- public void addGroup(SequenceGroup sg) ;\r
- public void deleteGroup(SequenceGroup g) ;\r
- public Vector getGroups();\r
- public void deleteAllGroups();\r
+ public void insertColumns(SequenceI[] seqs, int pos);\r
\r
- public void addSuperGroup(SuperGroup sg);\r
- public void removeSuperGroup(SuperGroup sg);\r
- public SuperGroup getSuperGroup(SequenceGroup sg);\r
+ public SequenceI findName(String name);\r
\r
- // Sorting\r
- public void sortGroups() ;\r
- public void sortByPID(SequenceI s) ;\r
- public void sortByID() ;\r
+ public SequenceI findbyDisplayId(String name);\r
\r
- //Annotations\r
- public void addAnnotation(AlignmentAnnotation aa);\r
- public void deleteAnnotation(AlignmentAnnotation aa);\r
- public AlignmentAnnotation [] getAlignmentAnnotation();\r
+ public int findIndex(SequenceI s);\r
\r
- public void setGapCharacter(char gc);\r
- public char getGapCharacter();\r
+ // Modifying\r
+ public void trimLeft(int i);\r
\r
- public Vector getAAFrequency();\r
-}\r
+ public void trimRight(int i);\r
+\r
+ public void removeGaps();\r
+\r
+ public Vector removeRedundancy(float threshold, Vector sel);\r
+\r
+ // Grouping methods\r
+ public SequenceGroup findGroup(int i);\r
+\r
+ public SequenceGroup findGroup(SequenceI s);\r
+\r
+ public SequenceGroup[] findAllGroups(SequenceI s);\r
+\r
+ public void addToGroup(SequenceGroup g, SequenceI s);\r
+\r
+ public void removeFromGroup(SequenceGroup g, SequenceI s);\r
+\r
+ public void addGroup(SequenceGroup sg);\r
+\r
+ public void deleteGroup(SequenceGroup g);\r
\r
+ public Vector getGroups();\r
\r
+ public void deleteAllGroups();\r
\r
+ public void addSuperGroup(SuperGroup sg);\r
+\r
+ public void removeSuperGroup(SuperGroup sg);\r
+\r
+ public SuperGroup getSuperGroup(SequenceGroup sg);\r
+\r
+ // Sorting\r
+ public void sortGroups();\r
+\r
+ public void sortByPID(SequenceI s);\r
+\r
+ public void sortByID();\r
+\r
+ //Annotations\r
+ public void addAnnotation(AlignmentAnnotation aa);\r
+\r
+ public void deleteAnnotation(AlignmentAnnotation aa);\r
+\r
+ public AlignmentAnnotation[] getAlignmentAnnotation();\r
+\r
+ public void setGapCharacter(char gc);\r
+\r
+ public char getGapCharacter();\r
+\r
+ public Vector getAAFrequency();\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.datamodel;
-
-import java.util.*;
-
+*/\r
+package jalview.datamodel;\r
+\r
+import java.util.*;\r
+\r
+\r
/**
* <p>Title: </p>
*
*
* @author not attributable
* @version 1.0
- */
-public class AlignmentOrder
-{
- public AlignmentOrder()
- {
- }
-
- public void setType(int Type)
- {
- this.Type = Type;
- }
-
- public int getType()
- {
- return Type;
- }
-
- public void setName(String Name)
- {
- this.Name = Name;
- }
-
- public String getName()
- {
- return Name;
- }
-
- public void setOrder(Vector Order)
- {
- this.Order = Order;
- }
-
- public Vector getOrder()
- {
-
- return Order;
- }
-// JBPNote : this method would return a vector containing all sequences in seqset
-// with those also contained in order at the beginning of the vector in the order
-// given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method
-// should be here for completeness.
-
-/* public Vector getOrder(AlignmentI seqset)
+ */\r
+public class AlignmentOrder {\r
+ // JBPNote : this method would return a vector containing all sequences in seqset\r
+ // with those also contained in order at the beginning of the vector in the order\r
+ // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method\r
+ // should be here for completeness.\r
+\r
+ /* public Vector getOrder(AlignmentI seqset)
{
Vector perm = new Vector(seqset.getHeight());
for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)
perm.setElement(i,...).
return Order;
}
- */
- public static final int FILE = 0;
- public static final int MSA = 1;
- public static final int USER = 2;
-
- private int Type = 0;
- private String Name;
- private Vector Order = null;
-
- /**
- * AlignmentOrder
- *
- * @param anOrder Vector
- */
- public AlignmentOrder(Vector anOrder)
- {
- Order = anOrder;
- }
-
- /**
- * AlignmentOrder
- *
- * @param orderFrom AlignmentI
- */
- public AlignmentOrder(AlignmentI orderFrom)
- {
- Order = new Vector();
-
- for (int i=0,ns=orderFrom.getHeight(); i<ns; i++)
- Order.addElement(orderFrom.getSequenceAt(i));
- }
- public AlignmentOrder(SequenceI[] orderFrom) {
- Order = new Vector();
- for (int i=0,ns=orderFrom.length; i<ns; i++)
- Order.addElement(orderFrom[i]);
- }
-
-
-
- /**
- * AlignmentOrder
- *
- * @param orderThis AlignmentI
- * @param byThat AlignmentI
- */
- /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
- {
- // Vector is an ordering of this alignment using the order of sequence objects in byThat,
- // where ids and unaligned sequences must match
-
- } */
+ */\r
+ public static final int FILE = 0;\r
+ public static final int MSA = 1;\r
+ public static final int USER = 2;\r
+ private int Type = 0;\r
+ private String Name;\r
+ private Vector Order = null;\r
+\r
+ public AlignmentOrder() {\r
+ }\r
+\r
+ /**
+ * AlignmentOrder
+ *
+ * @param anOrder Vector
+ */\r
+ public AlignmentOrder(Vector anOrder) {\r
+ Order = anOrder;\r
+ }\r
+\r
+ /**
+ * AlignmentOrder
+ *
+ * @param orderFrom AlignmentI
+ */\r
+ public AlignmentOrder(AlignmentI orderFrom) {\r
+ Order = new Vector();\r
+\r
+ for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)\r
+ Order.addElement(orderFrom.getSequenceAt(i));\r
+ }\r
+\r
+ public AlignmentOrder(SequenceI[] orderFrom) {\r
+ Order = new Vector();\r
+\r
+ for (int i = 0, ns = orderFrom.length; i < ns; i++)\r
+ Order.addElement(orderFrom[i]);\r
+ }\r
+\r
+ public void setType(int Type) {\r
+ this.Type = Type;\r
+ }\r
+\r
+ public int getType() {\r
+ return Type;\r
+ }\r
+\r
+ public void setName(String Name) {\r
+ this.Name = Name;\r
+ }\r
+\r
+ public String getName() {\r
+ return Name;\r
+ }\r
+\r
+ public void setOrder(Vector Order) {\r
+ this.Order = Order;\r
+ }\r
+\r
+ public Vector getOrder() {\r
+ return Order;\r
+ }\r
+\r
+ /**
+ * AlignmentOrder
+ *
+ * @param orderThis AlignmentI
+ * @param byThat AlignmentI
+ */\r
+\r
+ /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
+{
+ // Vector is an ordering of this alignment using the order of sequence objects in byThat,
+ // where ids and unaligned sequences must match
-}
+} */\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.datamodel;
-import java.awt.*;
-
-public class Annotation
-{
- public String displayCharacter="";
- public String description=""; // currently used as mouse over
- public char secondaryStructure=' '; // recognises H and E
- public float value;
-
- // add visual cues here
- public Color colour = Color.black;
-
- public Annotation(String displayChar, String desc, char ss, float val)
- {
- displayCharacter = displayChar;
- description = desc;
- secondaryStructure = ss;
- value = val;
- }
- public Annotation(String displayChar, String desc, char ss, float val, Color colour) {
- this(displayChar, desc, ss, val);
- this.colour = colour;
- }
-}
+*/\r
+package jalview.datamodel;\r
+\r
+import java.awt.*;\r
+\r
+\r
+public class Annotation {\r
+ public String displayCharacter = "";\r
+ public String description = ""; // currently used as mouse over\r
+ public char secondaryStructure = ' '; // recognises H and E\r
+ public float value;\r
+\r
+ // add visual cues here\r
+ public Color colour = Color.black;\r
+\r
+ public Annotation(String displayChar, String desc, char ss, float val) {\r
+ displayCharacter = displayChar;\r
+ description = desc;\r
+ secondaryStructure = ss;\r
+ value = val;\r
+ }\r
+\r
+ public Annotation(String displayChar, String desc, char ss, float val,\r
+ Color colour) {\r
+ this(displayChar, desc, ss, val);\r
+ this.colour = colour;\r
+ }\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.datamodel;
-
-public class BinaryNode
-{
-
- Object element;
- String name;
- BinaryNode left;
- BinaryNode right;
- BinaryNode parent;
- public int bootstrap;
-
- public BinaryNode()
- {
- left = right = parent = null;
- bootstrap = 0;
- }
-
- public BinaryNode(Object element, BinaryNode parent, String name)
- {
- this.element = element;
- this.parent = parent;
- this.name = name;
-
- left = right = null;
- }
-
- public Object element()
- {
- return element;
- }
-
- public Object setElement(Object v)
- {
- return element = v;
- }
-
- public BinaryNode left()
- {
- return left;
- }
-
- public BinaryNode setLeft(BinaryNode n)
- {
- return left = n;
- }
-
- public BinaryNode right()
- {
- return right;
- }
-
- public BinaryNode setRight(BinaryNode n)
- {
- return right = n;
- }
-
- public BinaryNode parent()
- {
- return parent;
- }
-
- public BinaryNode setParent(BinaryNode n)
- {
- return parent = n;
- }
-
- public boolean isLeaf()
- {
- return (left == null) && (right == null);
- }
-
- /**
- * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)
- * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to NULL - you should use
- * setChild(null), or detach() for this.
- *
- */
- public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
- {
- if (leftchild != null)
- {
- this.setLeft(leftchild);
- leftchild.detach();
- leftchild.setParent(this);
-
- }
- if (rightchild != null)
- {
- this.setRight(rightchild);
- rightchild.detach();
- rightchild.setParent(this);
- }
- }
-
- /**
- * Detaches the node from the binary tree, along with all its child nodes.
- * @return BinaryNode The detached node.
- */
- public BinaryNode detach()
- {
- if (this.parent!=null) {
- if (this.parent.left == this)
- {
- this.parent.left = null;
- }
- else
- {
- if (this.parent.right == this)
- {
- this.parent.right = null;
- }
- }
- }
- this.parent = null;
- return this;
- }
- /**
- * Traverses up through the tree until a node with a free leftchild is discovered.
- * @return BinaryNode
- */
- public BinaryNode ascendLeft() {
- BinaryNode c = this;
- do {
- c = c.parent();
- } while (c!=null && c.left()!=null && !c.left().isLeaf());
- return c;
- }
- /**
- * Traverses up through the tree until a node with a free rightchild is discovered.
- * Jalview builds trees by descent on the left, so this may be unused.
- * @return BinaryNode
- */
- public BinaryNode ascendRight() {
- BinaryNode c = this;
- do {
- c = c.parent();
- } while (c!=null && c.right()!=null && !c.right().isLeaf());
- return c;
- }
-
-
- public void setName(String name)
- {
- this.name = name;
- }
-
- public String getName()
- {
- return this.name;
- }
-
- public void setBootstrap(int boot)
- {
- this.bootstrap = boot;
- }
-
- public int getBootstrap()
- {
- return bootstrap;
- }
-}
+*/\r
+package jalview.datamodel;\r
+\r
+public class BinaryNode {\r
+ Object element;\r
+ String name;\r
+ BinaryNode left;\r
+ BinaryNode right;\r
+ BinaryNode parent;\r
+ public int bootstrap;\r
+\r
+ public BinaryNode() {\r
+ left = right = parent = null;\r
+ bootstrap = 0;\r
+ }\r
+\r
+ public BinaryNode(Object element, BinaryNode parent, String name) {\r
+ this.element = element;\r
+ this.parent = parent;\r
+ this.name = name;\r
+\r
+ left = right = null;\r
+ }\r
+\r
+ public Object element() {\r
+ return element;\r
+ }\r
+\r
+ public Object setElement(Object v) {\r
+ return element = v;\r
+ }\r
+\r
+ public BinaryNode left() {\r
+ return left;\r
+ }\r
+\r
+ public BinaryNode setLeft(BinaryNode n) {\r
+ return left = n;\r
+ }\r
+\r
+ public BinaryNode right() {\r
+ return right;\r
+ }\r
+\r
+ public BinaryNode setRight(BinaryNode n) {\r
+ return right = n;\r
+ }\r
+\r
+ public BinaryNode parent() {\r
+ return parent;\r
+ }\r
+\r
+ public BinaryNode setParent(BinaryNode n) {\r
+ return parent = n;\r
+ }\r
+\r
+ public boolean isLeaf() {\r
+ return (left == null) && (right == null);\r
+ }\r
+\r
+ /**
+ * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)
+ * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to NULL - you should use
+ * setChild(null), or detach() for this.
+ *
+ */\r
+ public void SetChildren(BinaryNode leftchild, BinaryNode rightchild) {\r
+ if (leftchild != null) {\r
+ this.setLeft(leftchild);\r
+ leftchild.detach();\r
+ leftchild.setParent(this);\r
+ }\r
+\r
+ if (rightchild != null) {\r
+ this.setRight(rightchild);\r
+ rightchild.detach();\r
+ rightchild.setParent(this);\r
+ }\r
+ }\r
+\r
+ /**
+ * Detaches the node from the binary tree, along with all its child nodes.
+ * @return BinaryNode The detached node.
+ */\r
+ public BinaryNode detach() {\r
+ if (this.parent != null) {\r
+ if (this.parent.left == this) {\r
+ this.parent.left = null;\r
+ } else {\r
+ if (this.parent.right == this) {\r
+ this.parent.right = null;\r
+ }\r
+ }\r
+ }\r
+\r
+ this.parent = null;\r
+\r
+ return this;\r
+ }\r
+\r
+ /**
+ * Traverses up through the tree until a node with a free leftchild is discovered.
+ * @return BinaryNode
+ */\r
+ public BinaryNode ascendLeft() {\r
+ BinaryNode c = this;\r
+\r
+ do {\r
+ c = c.parent();\r
+ } while ((c != null) && (c.left() != null) && !c.left().isLeaf());\r
+\r
+ return c;\r
+ }\r
+\r
+ /**
+ * Traverses up through the tree until a node with a free rightchild is discovered.
+ * Jalview builds trees by descent on the left, so this may be unused.
+ * @return BinaryNode
+ */\r
+ public BinaryNode ascendRight() {\r
+ BinaryNode c = this;\r
+\r
+ do {\r
+ c = c.parent();\r
+ } while ((c != null) && (c.right() != null) && !c.right().isLeaf());\r
+\r
+ return c;\r
+ }\r
+\r
+ public void setName(String name) {\r
+ this.name = name;\r
+ }\r
+\r
+ public String getName() {\r
+ return this.name;\r
+ }\r
+\r
+ public void setBootstrap(int boot) {\r
+ this.bootstrap = boot;\r
+ }\r
+\r
+ public int getBootstrap() {\r
+ return bootstrap;\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
-import jalview.io.*;\r
import jalview.analysis.PCA;\r
+\r
+import jalview.io.*;\r
+\r
import jalview.jbgui.*;\r
+\r
import jalview.schemes.*;\r
\r
import java.awt.*;\r
\r
+\r
public class BinarySequence extends Sequence {\r
- int[] binary;\r
- double[] dbinary;\r
-\r
- public BinarySequence(SequenceI s) {\r
- super(s.getName(),s.getSequence(),s.getStart(),s.getEnd());\r
- }\r
-\r
- public BinarySequence(String name, String sequence, int start, int end) {\r
- super(name,sequence,start,end);\r
- }\r
-\r
- public void encode() {\r
- // Set all matrix to 0\r
- dbinary = new double[getSequence().length() * 21];\r
- int nores = 21;\r
- for (int i = 0; i < dbinary.length; i++) {\r
- dbinary[i] = 0.0;\r
+ int[] binary;\r
+ double[] dbinary;\r
+\r
+ public BinarySequence(SequenceI s) {\r
+ super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());\r
+ }\r
+\r
+ public BinarySequence(String name, String sequence, int start, int end) {\r
+ super(name, sequence, start, end);\r
}\r
\r
- for (int i=0; i < getSequence().length(); i++ ) {\r
- int aanum = 20;\r
- try {\r
- aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();\r
- } catch (NullPointerException e) {\r
- aanum = 20;\r
- }\r
- if (aanum > 20) {\r
- aanum = 20;\r
- }\r
+ public void encode() {\r
+ // Set all matrix to 0\r
+ dbinary = new double[getSequence().length() * 21];\r
\r
- dbinary[i* nores + aanum] = 1.0;\r
+ int nores = 21;\r
\r
+ for (int i = 0; i < dbinary.length; i++) {\r
+ dbinary[i] = 0.0;\r
+ }\r
+\r
+ for (int i = 0; i < getSequence().length(); i++) {\r
+ int aanum = 20;\r
+\r
+ try {\r
+ aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
+ .substring(i,\r
+ i + 1))).intValue();\r
+ } catch (NullPointerException e) {\r
+ aanum = 20;\r
+ }\r
+\r
+ if (aanum > 20) {\r
+ aanum = 20;\r
+ }\r
+\r
+ dbinary[(i * nores) + aanum] = 1.0;\r
+ }\r
}\r
- }\r
-\r
- public void blosumEncode() {\r
-\r
- // Set all matrix to 0\r
- dbinary = new double[getSequence().length() * 21];\r
- int nores = 21;\r
- //for (int i = 0; i < dbinary.length; i++) {\r
- // dbinary[i] = 0.0;\r
- //}\r
-\r
- for (int i=0; i < getSequence().length(); i++ ) {\r
- int aanum = 20;\r
- try {\r
- aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();\r
- } catch (NullPointerException e) {\r
- aanum = 20;\r
- }\r
- if (aanum > 20) {\r
- aanum = 20;\r
- }\r
-\r
- // Do the blosum thing\r
- for (int j = 0;j < 20;j++) {\r
- dbinary[i * nores + j] = ResidueProperties.getBLOSUM62()[aanum][j];\r
- }\r
\r
+ public void blosumEncode() {\r
+ // Set all matrix to 0\r
+ dbinary = new double[getSequence().length() * 21];\r
+\r
+ int nores = 21;\r
+\r
+ //for (int i = 0; i < dbinary.length; i++) {\r
+ // dbinary[i] = 0.0;\r
+ //}\r
+ for (int i = 0; i < getSequence().length(); i++) {\r
+ int aanum = 20;\r
+\r
+ try {\r
+ aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
+ .substring(i,\r
+ i + 1))).intValue();\r
+ } catch (NullPointerException e) {\r
+ aanum = 20;\r
+ }\r
+\r
+ if (aanum > 20) {\r
+ aanum = 20;\r
+ }\r
+\r
+ // Do the blosum thing\r
+ for (int j = 0; j < 20; j++) {\r
+ dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];\r
+ }\r
+ }\r
}\r
- }\r
-\r
- public String toBinaryString() {\r
- String out = "";\r
- for (int i=0; i < binary.length;i++) {\r
- out += (new Integer(binary[i])).toString();\r
- if (i < binary.length-1) {\r
- out += " ";\r
- }\r
+\r
+ public String toBinaryString() {\r
+ String out = "";\r
+\r
+ for (int i = 0; i < binary.length; i++) {\r
+ out += (new Integer(binary[i])).toString();\r
+\r
+ if (i < (binary.length - 1)) {\r
+ out += " ";\r
+ }\r
+ }\r
+\r
+ return out;\r
}\r
- return out;\r
- }\r
\r
- public double[] getDBinary() {\r
- return dbinary;\r
- }\r
+ public double[] getDBinary() {\r
+ return dbinary;\r
+ }\r
\r
- public static void printMemory(Runtime rt) {\r
- System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.\r
- }\r
+ public static void printMemory(Runtime rt) {\r
+ System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
import java.util.*;\r
\r
-public class HistoryItem\r
-{\r
- public static final int EDIT = 0;\r
- public static final int SORT = 1;\r
- public static final int HIDE = 2;\r
- public static final int PASTE= 3;\r
\r
- final int type;\r
- Vector sequences;\r
- Vector alignIndex;\r
- String description;\r
- Vector hiddenSeqs;\r
+public class HistoryItem {\r
+ public static final int EDIT = 0;\r
+ public static final int SORT = 1;\r
+ public static final int HIDE = 2;\r
+ public static final int PASTE = 3;\r
+ final int type;\r
+ Vector sequences;\r
+ Vector alignIndex;\r
+ String description;\r
+ Vector hiddenSeqs;\r
\r
- public HistoryItem(String description, AlignmentI al, int type)\r
- {\r
- this.type = type;\r
- this.description = description;\r
- sequences = new Vector();\r
- alignIndex = new Vector();\r
- hiddenSeqs = new Vector();\r
+ public HistoryItem(String description, AlignmentI al, int type) {\r
+ this.type = type;\r
+ this.description = description;\r
+ sequences = new Vector();\r
+ alignIndex = new Vector();\r
+ hiddenSeqs = new Vector();\r
\r
- for (int i = 0; i < al.getHeight(); i++)\r
- {\r
- SequenceI seq = al.getSequenceAt(i);\r
- sequences.addElement(seq);\r
- alignIndex.addElement(i + "");\r
- hiddenSeqs.addElement(seq.getSequence().toString());\r
+ for (int i = 0; i < al.getHeight(); i++) {\r
+ SequenceI seq = al.getSequenceAt(i);\r
+ sequences.addElement(seq);\r
+ alignIndex.addElement(i + "");\r
+ hiddenSeqs.addElement(seq.getSequence().toString());\r
+ }\r
}\r
- }\r
-\r
- public int getType()\r
- {return type;}\r
\r
- public Vector getSequences()\r
- {return sequences;}\r
+ public int getType() {\r
+ return type;\r
+ }\r
\r
- public String getDescription()\r
- {return description; }\r
+ public Vector getSequences() {\r
+ return sequences;\r
+ }\r
\r
- public Vector getHidden()\r
- { return hiddenSeqs; }\r
+ public String getDescription() {\r
+ return description;\r
+ }\r
\r
- public int getAlignIndex(int seq)\r
- {\r
- return Integer.parseInt(alignIndex.elementAt(seq).toString());\r
- }\r
+ public Vector getHidden() {\r
+ return hiddenSeqs;\r
+ }\r
\r
+ public int getAlignIndex(int seq) {\r
+ return Integer.parseInt(alignIndex.elementAt(seq).toString());\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
+import MCview.*;\r
+\r
import jalview.analysis.*;\r
+\r
import java.awt.*;\r
+\r
import java.util.*;\r
-import MCview.*;\r
\r
\r
-public class Sequence implements SequenceI\r
-{\r
- protected String name;\r
- protected String sequence;\r
- protected String description;\r
- protected int start;\r
- protected int end;\r
- protected String displayId;\r
- protected Color color = Color.white;\r
- String pdbId;\r
-\r
- public Vector sequenceFeatures = new Vector();\r
- public void setSequenceFeatures(Vector v)\r
- {\r
- sequenceFeatures = v;\r
- }\r
-\r
- public Vector getSequenceFeatures()\r
- {return sequenceFeatures; }\r
-\r
- public void setPDBId(String id)\r
- {\r
- pdbId = id;\r
- }\r
- public String getPDBId()\r
- {\r
- return pdbId;\r
- }\r
-\r
-\r
- public Sequence(String name, String sequence, int start, int end)\r
- {\r
-\r
- this.name = name;\r
- this.sequence = sequence;\r
- this.start = start;\r
- this.end = end;\r
-\r
- setDisplayId();\r
-\r
- }\r
-\r
- public Sequence(String name,String sequence) {\r
- this(name,sequence,1,sequence.length());\r
- }\r
- public Sequence(SequenceI seq) {\r
- this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());\r
- }\r
- public String getDisplayId() {\r
- return displayId;\r
- }\r
- public void setDisplayId() {\r
- displayId = name + "/" + start + "-" + end;\r
- }\r
- public void setName(String name) {\r
- this.name = name;\r
- setDisplayId();\r
- }\r
- public String getName() {\r
- return this.name;\r
- }\r
- public void setStart(int start) {\r
- this.start = start;\r
- setDisplayId();\r
- }\r
- public int getStart() {\r
- return this.start;\r
- }\r
- public void setEnd(int end) {\r
- this.end = end;\r
- setDisplayId();\r
- }\r
- public int getEnd() {\r
- return this.end;\r
- }\r
- public int getLength() {\r
- return this.sequence.length();\r
- }\r
- public void setSequence(String seq) {\r
- this.sequence = seq;\r
- }\r
- public String getSequence() {\r
- return this.sequence;\r
- }\r
- public String getSequence(int start,int end) {\r
- // JBPNote - left to user to pad the result here (TODO:Decide on this policy)\r
- if(start>=sequence.length())\r
- return "";\r
-\r
- if(end>=sequence.length())\r
- end = sequence.length();\r
-\r
- return this.sequence.substring(start,end);\r
- }\r
-\r
- public char getCharAt(int i) {\r
- if (i < sequence.length()) {\r
- return sequence.charAt(i);\r
- } else {\r
- return ' ';\r
- }\r
- }\r
- public void setDescription(String desc) {\r
- this.description = desc;\r
- }\r
- public String getDescription() {\r
- return this.description;\r
- }\r
-\r
- public int findIndex(int pos) {\r
- // returns the alignment position for a residue\r
- int j = start;\r
- int i = 0;\r
-\r
- while (i< sequence.length() && j <= end && j <= pos) {\r
-\r
- char c = sequence.charAt(i);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
- j++;\r
-\r
- i++;\r
- }\r
- if (j == end && j < pos)\r
- return end+1;\r
- else\r
- return i;\r
-\r
- }\r
-\r
- public int findPosition(int i) {\r
- // Returns the sequence position for an alignment position\r
- int j = 0;\r
- int pos = start;\r
-\r
- while (j < i && j<sequence.length())\r
- {\r
- char c = sequence.charAt(j);\r
- if (!jalview.util.Comparison.isGap((c)))\r
- pos++;\r
-\r
- j++;\r
- }\r
- return pos;\r
- }\r
-\r
- public int[] gapMap() {\r
- // Returns an int array giving the position of each residue in the sequence in the alignment\r
- String seq = jalview.analysis.AlignSeq.extractGaps("-. ",sequence);\r
- int[] map = new int[seq.length()];\r
- int j=0;\r
- int p=0;\r
- while (j<sequence.length()) {\r
- if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {\r
- map[p++]=j;\r
- }\r
- j++;\r
- }\r
- return map;\r
- }\r
-\r
- public void deleteCharAt(int i)\r
- {\r
- if (i>=sequence.length())\r
- return;\r
- sequence = sequence.substring(0,i) + sequence.substring(i+1);\r
- }\r
-\r
- public void deleteChars(int i, int j)\r
- {\r
- if (i>=sequence.length())\r
- return;\r
- if (j>=sequence.length())\r
- sequence = sequence.substring(0,i);\r
- else\r
- sequence = sequence.substring(0,i) + sequence.substring(j);\r
- }\r
-\r
- public void insertCharAt(int i, char c)\r
- {\r
- insertCharAt(i,c,true);\r
- }\r
-\r
- public void insertCharAt(int i,char c,boolean chop) {\r
-\r
- String tmp = new String(sequence);\r
-\r
- if (i < sequence.length()) {\r
- sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);\r
- } else {\r
- // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!\r
- char[] ch = new char[1+i-sequence.length()];\r
- for (int j=0, k=ch.length; j<k; j++)\r
- ch[j] = c;\r
- sequence = tmp + String.valueOf(ch);\r
- }\r
-\r
- }\r
-\r
- public void setColor(Color c) {\r
- this.color = c;\r
- }\r
-\r
- public Color getColor() {\r
- return color;\r
- }\r
+public class Sequence implements SequenceI {\r
+ protected String name;\r
+ protected String sequence;\r
+ protected String description;\r
+ protected int start;\r
+ protected int end;\r
+ protected String displayId;\r
+ protected Color color = Color.white;\r
+ String pdbId;\r
+ public Vector sequenceFeatures = new Vector();\r
+\r
+ public Sequence(String name, String sequence, int start, int end) {\r
+ this.name = name;\r
+ this.sequence = sequence;\r
+ this.start = start;\r
+ this.end = end;\r
+\r
+ setDisplayId();\r
+ }\r
+\r
+ public Sequence(String name, String sequence) {\r
+ this(name, sequence, 1, sequence.length());\r
+ }\r
+\r
+ public Sequence(SequenceI seq) {\r
+ this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());\r
+ }\r
+\r
+ public void setSequenceFeatures(Vector v) {\r
+ sequenceFeatures = v;\r
+ }\r
+\r
+ public Vector getSequenceFeatures() {\r
+ return sequenceFeatures;\r
+ }\r
+\r
+ public void setPDBId(String id) {\r
+ pdbId = id;\r
+ }\r
+\r
+ public String getPDBId() {\r
+ return pdbId;\r
+ }\r
+\r
+ public String getDisplayId() {\r
+ return displayId;\r
+ }\r
+\r
+ public void setDisplayId() {\r
+ displayId = name + "/" + start + "-" + end;\r
+ }\r
+\r
+ public void setName(String name) {\r
+ this.name = name;\r
+ setDisplayId();\r
+ }\r
+\r
+ public String getName() {\r
+ return this.name;\r
+ }\r
+\r
+ public void setStart(int start) {\r
+ this.start = start;\r
+ setDisplayId();\r
+ }\r
+\r
+ public int getStart() {\r
+ return this.start;\r
+ }\r
+\r
+ public void setEnd(int end) {\r
+ this.end = end;\r
+ setDisplayId();\r
+ }\r
+\r
+ public int getEnd() {\r
+ return this.end;\r
+ }\r
+\r
+ public int getLength() {\r
+ return this.sequence.length();\r
+ }\r
+\r
+ public void setSequence(String seq) {\r
+ this.sequence = seq;\r
+ }\r
+\r
+ public String getSequence() {\r
+ return this.sequence;\r
+ }\r
+\r
+ public String getSequence(int start, int end) {\r
+ // JBPNote - left to user to pad the result here (TODO:Decide on this policy)\r
+ if (start >= sequence.length()) {\r
+ return "";\r
+ }\r
+\r
+ if (end >= sequence.length()) {\r
+ end = sequence.length();\r
+ }\r
+\r
+ return this.sequence.substring(start, end);\r
+ }\r
+\r
+ public char getCharAt(int i) {\r
+ if (i < sequence.length()) {\r
+ return sequence.charAt(i);\r
+ } else {\r
+ return ' ';\r
+ }\r
+ }\r
+\r
+ public void setDescription(String desc) {\r
+ this.description = desc;\r
+ }\r
+\r
+ public String getDescription() {\r
+ return this.description;\r
+ }\r
+\r
+ public int findIndex(int pos) {\r
+ // returns the alignment position for a residue\r
+ int j = start;\r
+ int i = 0;\r
+\r
+ while ((i < sequence.length()) && (j <= end) && (j <= pos)) {\r
+ char c = sequence.charAt(i);\r
+\r
+ if (!jalview.util.Comparison.isGap((c))) {\r
+ j++;\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ if ((j == end) && (j < pos)) {\r
+ return end + 1;\r
+ } else {\r
+ return i;\r
+ }\r
+ }\r
+\r
+ public int findPosition(int i) {\r
+ // Returns the sequence position for an alignment position\r
+ int j = 0;\r
+ int pos = start;\r
+\r
+ while ((j < i) && (j < sequence.length())) {\r
+ char c = sequence.charAt(j);\r
+\r
+ if (!jalview.util.Comparison.isGap((c))) {\r
+ pos++;\r
+ }\r
+\r
+ j++;\r
+ }\r
+\r
+ return pos;\r
+ }\r
+\r
+ public int[] gapMap() {\r
+ // Returns an int array giving the position of each residue in the sequence in the alignment\r
+ String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);\r
+ int[] map = new int[seq.length()];\r
+ int j = 0;\r
+ int p = 0;\r
+\r
+ while (j < sequence.length()) {\r
+ if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {\r
+ map[p++] = j;\r
+ }\r
+\r
+ j++;\r
+ }\r
+\r
+ return map;\r
+ }\r
+\r
+ public void deleteCharAt(int i) {\r
+ if (i >= sequence.length()) {\r
+ return;\r
+ }\r
+\r
+ sequence = sequence.substring(0, i) + sequence.substring(i + 1);\r
+ }\r
+\r
+ public void deleteChars(int i, int j) {\r
+ if (i >= sequence.length()) {\r
+ return;\r
+ }\r
+\r
+ if (j >= sequence.length()) {\r
+ sequence = sequence.substring(0, i);\r
+ } else {\r
+ sequence = sequence.substring(0, i) + sequence.substring(j);\r
+ }\r
+ }\r
\r
+ public void insertCharAt(int i, char c) {\r
+ insertCharAt(i, c, true);\r
+ }\r
+\r
+ public void insertCharAt(int i, char c, boolean chop) {\r
+ String tmp = new String(sequence);\r
+\r
+ if (i < sequence.length()) {\r
+ sequence = tmp.substring(0, i) + String.valueOf(c) +\r
+ tmp.substring(i);\r
+ } else {\r
+ // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!\r
+ char[] ch = new char[(1 + i) - sequence.length()];\r
+\r
+ for (int j = 0, k = ch.length; j < k; j++)\r
+ ch[j] = c;\r
+\r
+ sequence = tmp + String.valueOf(ch);\r
+ }\r
+ }\r
+\r
+ public void setColor(Color c) {\r
+ this.color = c;\r
+ }\r
+\r
+ public Color getColor() {\r
+ return color;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
import java.awt.*;\r
\r
+\r
public class SequenceFeature {\r
- int begin;\r
- int end;\r
- String type;\r
- String description;\r
- String status;\r
+ int begin;\r
+ int end;\r
+ String type;\r
+ String description;\r
+ String status;\r
\r
- public SequenceFeature()\r
- {\r
- }\r
+ public SequenceFeature() {\r
+ }\r
\r
- public SequenceFeature(String type, int start, int end, String description, String status)\r
- {\r
- this.type = type;\r
- this.begin = start;\r
- this.end = end;\r
- this.description = description;\r
- this.status = status;\r
- }\r
+ public SequenceFeature(String type, int start, int end, String description,\r
+ String status) {\r
+ this.type = type;\r
+ this.begin = start;\r
+ this.end = end;\r
+ this.description = description;\r
+ this.status = status;\r
+ }\r
\r
- public int getStart() {\r
- return begin;\r
- }\r
- public int getEnd() {\r
- return end;\r
- }\r
- public String getType() {\r
- return type;\r
- }\r
- public String getDescription() {\r
- return description;\r
- }\r
- public String getStatus()\r
- {return status;}\r
+ public int getStart() {\r
+ return begin;\r
+ }\r
\r
+ public int getEnd() {\r
+ return end;\r
+ }\r
\r
-/*\r
- <xs:enumeration value="active site" />\r
-<xs:enumeration value="binding site" />\r
-<xs:enumeration value="calcium-binding region" />\r
-<xs:enumeration value="chain" />\r
-<xs:enumeration value="cross-link" />\r
-<xs:enumeration value="disulfide bond" />\r
-<xs:enumeration value="DNA-binding region" />\r
-<xs:enumeration value="domain" />\r
-<xs:enumeration value="glycosylation site" />\r
-<xs:enumeration value="helix" />\r
-<xs:enumeration value="initiator methionine" />\r
-<xs:enumeration value="lipid moiety-binding region" />\r
-<xs:enumeration value="metal ion-binding site" />\r
-<xs:enumeration value="modified residue" />\r
-<xs:enumeration value="mutagenesis site" />\r
-<xs:enumeration value="non-consecutive residues" />\r
-<xs:enumeration value="non-terminal residue" />\r
-<xs:enumeration value="nucleotide phosphate-binding region" />\r
-<xs:enumeration value="peptide" />\r
-<xs:enumeration value="propeptide" />\r
-<xs:enumeration value="repeat" />\r
-<xs:enumeration value="selenocysteine" />\r
-<xs:enumeration value="sequence conflict" />\r
-<xs:enumeration value="sequence variant" />\r
-<xs:enumeration value="signal peptide" />\r
-<xs:enumeration value="similar" />\r
-<xs:enumeration value="site" />\r
-<xs:enumeration value="splice variant" />\r
-<xs:enumeration value="strand" />\r
-<xs:enumeration value="thioether bond" />\r
-<xs:enumeration value="thiolester bond" />\r
-<xs:enumeration value="transit peptide" />\r
-<xs:enumeration value="transmembrane region" />\r
-<xs:enumeration value="turn" />\r
-<xs:enumeration value="unsure residue" />\r
-<xs:enumeration value="zinc finger region" />\r
-*/\r
+ public String getType() {\r
+ return type;\r
+ }\r
\r
-}\r
+ public String getDescription() {\r
+ return description;\r
+ }\r
+\r
+ public String getStatus() {\r
+ return status;\r
+ }\r
\r
+ /*\r
+ <xs:enumeration value="active site" />\r
+ <xs:enumeration value="binding site" />\r
+ <xs:enumeration value="calcium-binding region" />\r
+ <xs:enumeration value="chain" />\r
+ <xs:enumeration value="cross-link" />\r
+ <xs:enumeration value="disulfide bond" />\r
+ <xs:enumeration value="DNA-binding region" />\r
+ <xs:enumeration value="domain" />\r
+ <xs:enumeration value="glycosylation site" />\r
+ <xs:enumeration value="helix" />\r
+ <xs:enumeration value="initiator methionine" />\r
+ <xs:enumeration value="lipid moiety-binding region" />\r
+ <xs:enumeration value="metal ion-binding site" />\r
+ <xs:enumeration value="modified residue" />\r
+ <xs:enumeration value="mutagenesis site" />\r
+ <xs:enumeration value="non-consecutive residues" />\r
+ <xs:enumeration value="non-terminal residue" />\r
+ <xs:enumeration value="nucleotide phosphate-binding region" />\r
+ <xs:enumeration value="peptide" />\r
+ <xs:enumeration value="propeptide" />\r
+ <xs:enumeration value="repeat" />\r
+ <xs:enumeration value="selenocysteine" />\r
+ <xs:enumeration value="sequence conflict" />\r
+ <xs:enumeration value="sequence variant" />\r
+ <xs:enumeration value="signal peptide" />\r
+ <xs:enumeration value="similar" />\r
+ <xs:enumeration value="site" />\r
+ <xs:enumeration value="splice variant" />\r
+ <xs:enumeration value="strand" />\r
+ <xs:enumeration value="thioether bond" />\r
+ <xs:enumeration value="thiolester bond" />\r
+ <xs:enumeration value="transit peptide" />\r
+ <xs:enumeration value="transmembrane region" />\r
+ <xs:enumeration value="turn" />\r
+ <xs:enumeration value="unsure residue" />\r
+ <xs:enumeration value="zinc finger region" />\r
+ */\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
-import jalview.schemes.*;\r
import jalview.analysis.*;\r
+\r
import jalview.datamodel.*;\r
-import java.util.Vector;\r
+\r
+import jalview.schemes.*;\r
+\r
import java.awt.*;\r
\r
-public class SequenceGroup\r
-{\r
- String groupName;\r
- Conservation conserve;\r
- Vector aaFrequency;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
- public Vector sequences = new Vector();\r
- int width = -1;\r
- public ColourSchemeI cs;\r
- int startRes = 0;\r
- int endRes = 0;\r
- Color outlineColour = Color.black;\r
-\r
- public SequenceGroup()\r
- {\r
- groupName = "Group";\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- cs = null;\r
- }\r
-\r
- public SequenceGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText,\r
- int start,\r
- int end)\r
- {\r
-\r
- this.groupName = groupName;\r
- this.displayBoxes = displayBoxes;\r
- this.displayText = displayText;\r
- this.colourText = colourText;\r
- this.cs = scheme;\r
- startRes = start;\r
- endRes = end;\r
- }\r
-\r
- public boolean adjustForRemoveLeft(int col)\r
- {\r
- // return value is true if the group still exists\r
- if(startRes>=col)\r
- startRes = startRes - col;\r
- if(endRes>=col)\r
- {\r
- endRes = endRes - col;\r
- if(startRes>endRes)\r
- startRes = 0;\r
+import java.util.Vector;\r
+\r
+\r
+public class SequenceGroup {\r
+ String groupName;\r
+ Conservation conserve;\r
+ Vector aaFrequency;\r
+ boolean displayBoxes;\r
+ boolean displayText;\r
+ boolean colourText;\r
+ public Vector sequences = new Vector();\r
+ int width = -1;\r
+ public ColourSchemeI cs;\r
+ int startRes = 0;\r
+ int endRes = 0;\r
+ Color outlineColour = Color.black;\r
+\r
+ public SequenceGroup() {\r
+ groupName = "Group";\r
+ this.displayBoxes = true;\r
+ this.displayText = true;\r
+ this.colourText = false;\r
+ cs = null;\r
+ }\r
+\r
+ public SequenceGroup(String groupName, ColourSchemeI scheme,\r
+ boolean displayBoxes, boolean displayText, boolean colourText,\r
+ int start, int end) {\r
+ this.groupName = groupName;\r
+ this.displayBoxes = displayBoxes;\r
+ this.displayText = displayText;\r
+ this.colourText = colourText;\r
+ this.cs = scheme;\r
+ startRes = start;\r
+ endRes = end;\r
+ }\r
+\r
+ public boolean adjustForRemoveLeft(int col) {\r
+ // return value is true if the group still exists\r
+ if (startRes >= col) {\r
+ startRes = startRes - col;\r
+ }\r
+\r
+ if (endRes >= col) {\r
+ endRes = endRes - col;\r
+\r
+ if (startRes > endRes) {\r
+ startRes = 0;\r
+ }\r
+ } else {\r
+ // must delete this group!!\r
+ return false;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ public boolean adjustForRemoveRight(int col) {\r
+ if (startRes > col) {\r
+ // delete this group\r
+ return false;\r
+ }\r
+\r
+ if (endRes >= col) {\r
+ endRes = col;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ public String getName() {\r
+ return groupName;\r
+ }\r
+\r
+ public void setName(String name) {\r
+ groupName = name;\r
+ }\r
+\r
+ public Conservation getConservation() {\r
+ return conserve;\r
+ }\r
+\r
+ public void setConservation(Conservation c) {\r
+ conserve = c;\r
+ }\r
+\r
+ public void addSequence(SequenceI s) {\r
+ if (!sequences.contains(s)) {\r
+ sequences.addElement(s);\r
+ }\r
+\r
+ if (cs != null) {\r
+ cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+ }\r
+\r
+ if (cs instanceof ConservationColourScheme) {\r
+ recalcConservation();\r
+ }\r
+ }\r
+\r
+ void recalcConservation() {\r
+ Conservation c = new Conservation(groupName,\r
+ ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
+ ccs.conserve = c;\r
}\r
- else\r
- {\r
- // must delete this group!!\r
- return false;\r
+\r
+ public void addOrRemove(SequenceI s) {\r
+ if (sequences.contains(s)) {\r
+ deleteSequence(s);\r
+ } else {\r
+ addSequence(s);\r
+ }\r
+ }\r
+\r
+ public void deleteSequence(SequenceI s) {\r
+ sequences.removeElement(s);\r
+\r
+ if (cs != null) {\r
+ cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+ }\r
+\r
+ if (cs instanceof ConservationColourScheme) {\r
+ recalcConservation();\r
+ }\r
+ }\r
+\r
+ public int getStartRes() {\r
+ return startRes;\r
+ }\r
+\r
+ public int getEndRes() {\r
+ return endRes;\r
+ }\r
+\r
+ public void setStartRes(int i) {\r
+ startRes = i;\r
}\r
\r
- return true;\r
- }\r
+ public void setEndRes(int i) {\r
+ endRes = i;\r
+ }\r
\r
- public boolean adjustForRemoveRight(int col)\r
- {\r
+ public int getSize() {\r
+ return sequences.size();\r
+ }\r
\r
- if(startRes>col)\r
- {\r
- // delete this group\r
- return false;\r
+ public SequenceI getSequenceAt(int i) {\r
+ return (SequenceI) sequences.elementAt(i);\r
}\r
\r
- if(endRes>=col)\r
- endRes = col;\r
-\r
- return true;\r
- }\r
-\r
-\r
- public String getName()\r
- {\r
- return groupName;\r
- }\r
-\r
- public void setName(String name)\r
- {\r
- groupName = name;\r
- }\r
-\r
- public Conservation getConservation()\r
- {\r
- return conserve;\r
- }\r
-\r
- public void setConservation(Conservation c)\r
- {\r
- conserve = c;\r
- }\r
-\r
- public void addSequence(SequenceI s)\r
- {\r
- if(!sequences.contains(s))\r
- sequences.addElement(s);\r
-\r
-\r
- if(cs!=null)\r
- cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );\r
-\r
- if(cs instanceof ConservationColourScheme)\r
- recalcConservation();\r
- }\r
-\r
- void recalcConservation()\r
- {\r
- Conservation c = new Conservation(groupName,\r
- ResidueProperties.propHash, 3,\r
- sequences, 0, getWidth());\r
- c.calculate();\r
- c.verdict(false, 25);\r
- ConservationColourScheme ccs = (ConservationColourScheme)cs;\r
- ccs.conserve = c;\r
- }\r
-\r
- public void addOrRemove(SequenceI s)\r
- {\r
- if(sequences.contains(s))\r
- deleteSequence(s);\r
- else\r
- addSequence(s);\r
- }\r
-\r
- public void deleteSequence(SequenceI s)\r
- {\r
- sequences.removeElement(s);\r
-\r
- if(cs!=null)\r
- cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );\r
-\r
- if(cs instanceof ConservationColourScheme)\r
- recalcConservation();\r
- }\r
-\r
-\r
- public int getStartRes()\r
- {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes()\r
- {\r
- return endRes;\r
- }\r
-\r
- public void setStartRes(int i)\r
- {\r
- startRes = i;\r
- }\r
-\r
- public void setEndRes(int i)\r
- {\r
- endRes = i;\r
- }\r
-\r
- public int getSize()\r
- {\r
- return sequences.size();\r
- }\r
-\r
- public SequenceI getSequenceAt(int i)\r
- {\r
- return (SequenceI) sequences.elementAt(i);\r
- }\r
-\r
- public void setColourText(boolean state)\r
- {\r
- colourText = state;\r
- }\r
-\r
- public boolean getColourText()\r
- {\r
- return colourText;\r
- }\r
-\r
- public void setDisplayText(boolean state)\r
- {\r
- displayText = state;\r
- }\r
-\r
- public boolean getDisplayText()\r
- {\r
- return displayText;\r
- }\r
-\r
- public void setDisplayBoxes(boolean state)\r
- {\r
- displayBoxes = state;\r
- }\r
-\r
- public boolean getDisplayBoxes()\r
- {\r
- return displayBoxes;\r
- }\r
-\r
- public int getWidth()\r
- {\r
- // MC This needs to get reset when characters are inserted and deleted\r
- if (sequences.size()>0)\r
- width = ((SequenceI) sequences.elementAt(0)).getLength();\r
- for (int i = 1; i < sequences.size(); i++)\r
- {\r
- SequenceI seq = (SequenceI) sequences.elementAt(i);\r
- if (seq.getLength() > width)\r
- width = seq.getLength();\r
+ public void setColourText(boolean state) {\r
+ colourText = state;\r
}\r
- return width;\r
- }\r
-\r
-\r
- public void setOutlineColour(Color c)\r
- {\r
- outlineColour = c;\r
- }\r
- public Color getOutlineColour()\r
- {\r
- return outlineColour;\r
- }\r
- /**\r
- *\r
- * returns the sequences in the group ordered by the ordering given by al\r
- *\r
- * @param al Alignment\r
- * @return SequenceI[]\r
- */\r
- public SequenceI[] getSequencesInOrder(Alignment al) {\r
- int sz;\r
- java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
- SequenceI[] seqs=new SequenceI[sz=sequences.size()];\r
- for(int i=0; i<sz; i++)\r
- {\r
- SequenceI seq = (SequenceI) sequences.elementAt(i);\r
- int index = al.findIndex(seq);\r
- orderedSeqs.put(index+"", seq);\r
+\r
+ public boolean getColourText() {\r
+ return colourText;\r
}\r
\r
- int index=0;\r
- for(int i=0; i<sz; i++) {\r
- SequenceI seq = null;\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
- break;\r
+ public void setDisplayText(boolean state) {\r
+ displayText = state;\r
+ }\r
+\r
+ public boolean getDisplayText() {\r
+ return displayText;\r
+ }\r
+\r
+ public void setDisplayBoxes(boolean state) {\r
+ displayBoxes = state;\r
+ }\r
+\r
+ public boolean getDisplayBoxes() {\r
+ return displayBoxes;\r
+ }\r
+\r
+ public int getWidth() {\r
+ // MC This needs to get reset when characters are inserted and deleted\r
+ if (sequences.size() > 0) {\r
+ width = ((SequenceI) sequences.elementAt(0)).getLength();\r
+ }\r
+\r
+ for (int i = 1; i < sequences.size(); i++) {\r
+ SequenceI seq = (SequenceI) sequences.elementAt(i);\r
+\r
+ if (seq.getLength() > width) {\r
+ width = seq.getLength();\r
+ }\r
}\r
- else\r
- index++;\r
- }\r
- seqs[index] = seq;\r
+\r
+ return width;\r
+ }\r
+\r
+ public void setOutlineColour(Color c) {\r
+ outlineColour = c;\r
+ }\r
+\r
+ public Color getOutlineColour() {\r
+ return outlineColour;\r
+ }\r
+\r
+ /**\r
+ *\r
+ * returns the sequences in the group ordered by the ordering given by al\r
+ *\r
+ * @param al Alignment\r
+ * @return SequenceI[]\r
+ */\r
+ public SequenceI[] getSequencesInOrder(Alignment al) {\r
+ int sz;\r
+ java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
+ SequenceI[] seqs = new SequenceI[sz = sequences.size()];\r
+\r
+ for (int i = 0; i < sz; i++) {\r
+ SequenceI seq = (SequenceI) sequences.elementAt(i);\r
+ int index = al.findIndex(seq);\r
+ orderedSeqs.put(index + "", seq);\r
+ }\r
+\r
+ int index = 0;\r
+\r
+ for (int i = 0; i < sz; i++) {\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null) {\r
+ if (orderedSeqs.containsKey(index + "")) {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ } else {\r
+ index++;\r
+ }\r
+ }\r
+\r
+ seqs[index] = seq;\r
+ }\r
+\r
+ return seqs;\r
}\r
- return seqs;\r
- }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
import jalview.jbgui.*;\r
+\r
import java.awt.*;\r
\r
import java.util.Vector;\r
\r
+\r
public interface SequenceI {\r
- public void setName(String name);\r
- public String getName();\r
+ public void setName(String name);\r
+\r
+ public String getName();\r
+\r
+ public void setStart(int start);\r
+\r
+ public int getStart();\r
+\r
+ public String getDisplayId();\r
\r
- public void setStart(int start);\r
- public int getStart();\r
+ public void setEnd(int end);\r
\r
- public String getDisplayId();\r
+ public int getEnd();\r
\r
- public void setEnd(int end);\r
- public int getEnd();\r
+ public int getLength();\r
\r
- public int getLength();\r
+ public void setSequence(String sequence);\r
\r
- public void setSequence(String sequence);\r
- public String getSequence();\r
- public String getSequence(int start,int end);\r
- public char getCharAt(int i);\r
+ public String getSequence();\r
\r
- public void setDescription(String desc);\r
- public String getDescription();\r
+ public String getSequence(int start, int end);\r
\r
- public int findIndex(int pos);\r
- public int findPosition(int i);\r
- public int[] gapMap();\r
- public void deleteChars(int i, int j);\r
- public void deleteCharAt(int i);\r
- public void insertCharAt(int i, char c);\r
- public void insertCharAt(int i,char c,boolean chop);\r
+ public char getCharAt(int i);\r
\r
- public void setColor(Color c);\r
- public Color getColor();\r
+ public void setDescription(String desc);\r
\r
- public Vector getSequenceFeatures();\r
- public void setSequenceFeatures(Vector v);\r
+ public String getDescription();\r
\r
- public void setPDBId(String id);\r
- public String getPDBId();\r
+ public int findIndex(int pos);\r
\r
- }\r
+ public int findPosition(int i);\r
\r
+ public int[] gapMap();\r
\r
+ public void deleteChars(int i, int j);\r
\r
+ public void deleteCharAt(int i);\r
\r
+ public void insertCharAt(int i, char c);\r
\r
+ public void insertCharAt(int i, char c, boolean chop);\r
\r
+ public void setColor(Color c);\r
\r
+ public Color getColor();\r
\r
+ public Vector getSequenceFeatures();\r
\r
+ public void setSequenceFeatures(Vector v);\r
\r
+ public void setPDBId(String id);\r
\r
+ public String getPDBId();\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
import java.awt.*;\r
\r
+\r
public class SequenceNode extends BinaryNode {\r
+ public float dist;\r
+ public int count;\r
+ public float height;\r
+ public float ycount;\r
+ public Color color = Color.black;\r
+ public boolean dummy = false;\r
+ private boolean placeholder = false;\r
+\r
+ public SequenceNode() {\r
+ super();\r
+ }\r
\r
- public float dist;\r
- public int count;\r
- public float height;\r
- public float ycount;\r
- public Color color = Color.black;\r
- public boolean dummy = false;\r
- private boolean placeholder = false;\r
+ public SequenceNode(Object val, SequenceNode parent, float dist, String name) {\r
+ super(val, parent, name);\r
+ this.dist = dist;\r
+ }\r
\r
- public SequenceNode() {\r
- super();\r
- }\r
+ public SequenceNode(Object val, SequenceNode parent, String name,\r
+ float dist, int bootstrap, boolean dummy) {\r
+ super(val, parent, name);\r
+ this.dist = dist;\r
+ this.bootstrap = bootstrap;\r
+ this.dummy = dummy;\r
+ }\r
\r
- public SequenceNode(Object val, SequenceNode parent, float dist,String name) {\r
- super(val,parent,name);\r
- this.dist = dist;\r
- }\r
- public SequenceNode(Object val, SequenceNode parent, String name, float dist, int bootstrap, boolean dummy) {\r
- super(val,parent,name);\r
- this.dist = dist;\r
- this.bootstrap = bootstrap;\r
- this.dummy = dummy;\r
- }\r
+ /**\r
+ * @param dummy true if node is created for the representation of polytomous trees\r
+ */\r
+ public boolean isDummy() {\r
+ return dummy;\r
+ }\r
\r
+ /* @param placeholder is true if the sequence refered to in the\r
+ * element node is not actually present in the associated alignment\r
+ */\r
+ public boolean isPlaceholder() {\r
+ return placeholder;\r
+ }\r
\r
- /**\r
- * @param dummy true if node is created for the representation of polytomous trees\r
- */\r
+ public boolean setDummy(boolean newstate) {\r
+ boolean oldstate = dummy;\r
+ dummy = newstate;\r
\r
- public boolean isDummy() {\r
- return dummy;\r
- }\r
- /* @param placeholder is true if the sequence refered to in the\r
- * element node is not actually present in the associated alignment\r
- */\r
- public boolean isPlaceholder()\r
- {\r
- return placeholder;\r
- }\r
+ return oldstate;\r
+ }\r
\r
- public boolean setDummy(boolean newstate) {\r
- boolean oldstate = dummy;\r
- dummy = newstate;\r
- return oldstate;\r
- }\r
+ public void setPlaceholder(boolean Placeholder) {\r
+ this.placeholder = Placeholder;\r
+ }\r
\r
- public void setPlaceholder(boolean Placeholder)\r
- {\r
- this.placeholder = Placeholder;\r
- }\r
+ /**\r
+ * ascends the tree but doesn't stop until a non-dummy node is discovered.\r
+ * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.\r
+ */\r
+ public SequenceNode AscendTree() {\r
+ SequenceNode c = this;\r
\r
- /**\r
- * ascends the tree but doesn't stop until a non-dummy node is discovered.\r
- * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.\r
- */\r
+ do {\r
+ c = (SequenceNode) c.parent();\r
+ } while ((c != null) && c.dummy);\r
\r
- public SequenceNode AscendTree() {\r
- SequenceNode c = this;\r
- do {\r
- c = (SequenceNode) c.parent();\r
- } while (c!=null && c.dummy);\r
- return c;\r
- }\r
+ return c;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
-import java.util.*;\r
-import java.awt.*;\r
\r
+import java.awt.*;\r
\r
-public class SequencePoint {\r
+import java.util.*;\r
\r
- // SMJS PUBLIC\r
- public SequenceI sequence;\r
- public float[] coord;\r
- // SMJS ENDPUBLIC\r
\r
- public SequencePoint(SequenceI sequence, float[] coord) {\r
- this.sequence = sequence;\r
- this.coord = coord;\r
- }\r
+public class SequencePoint {\r
+ // SMJS PUBLIC\r
+ public SequenceI sequence;\r
+ public float[] coord;\r
\r
+ // SMJS ENDPUBLIC\r
+ public SequencePoint(SequenceI sequence, float[] coord) {\r
+ this.sequence = sequence;\r
+ this.coord = coord;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.datamodel;\r
\r
-import jalview.schemes.*;\r
import jalview.analysis.*;\r
+\r
import jalview.datamodel.*;\r
+\r
+import jalview.schemes.*;\r
+\r
import java.util.*;\r
\r
-public class SuperGroup\r
-{\r
- String groupName;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
- public ColourSchemeI cs;\r
- Vector sequenceGroups = new Vector();\r
-\r
- public SuperGroup()\r
- {\r
- groupName = "Super group";\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- cs = null;\r
- }\r
-\r
-\r
- public SuperGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText)\r
- {\r
- this.groupName = groupName;\r
- this.displayBoxes = displayBoxes;\r
- this.displayText = displayText;\r
- this.colourText = colourText;\r
- this.cs = scheme;\r
- }\r
-\r
- public String getName()\r
- {\r
- return groupName;\r
- }\r
-\r
- public void setName(String name)\r
- {\r
- groupName = name;\r
- }\r
-\r
-\r
- public void addGroup(SequenceGroup sg)\r
- {\r
- if(!sequenceGroups.contains(sg))\r
- sequenceGroups.addElement(sg);\r
- }\r
-\r
- public void addOrRemove(SequenceGroup sg)\r
- {\r
- if(sequenceGroups.contains(sg))\r
- deleteGroup(sg);\r
- else\r
- addGroup(sg);\r
- }\r
-\r
- public void deleteGroup(SequenceGroup sg)\r
- {\r
- sequenceGroups.removeElement(sg);\r
- }\r
-\r
- public void setSuperGroupProperties(SequenceGroup sg)\r
- {\r
- cs = sg.cs;\r
- colourText = sg.colourText;\r
- displayText = sg.displayText;\r
- displayBoxes = sg.displayBoxes;\r
-\r
- for(int i=0; i<sequenceGroups.size(); i++)\r
- {\r
- SequenceGroup temp = (SequenceGroup)sequenceGroups.elementAt(i);\r
- temp.cs = sg.cs;\r
- temp.colourText = sg.colourText;\r
- temp.displayText = sg.displayText;\r
- temp.displayBoxes = sg.displayBoxes;\r
+\r
+public class SuperGroup {\r
+ String groupName;\r
+ boolean displayBoxes;\r
+ boolean displayText;\r
+ boolean colourText;\r
+ public ColourSchemeI cs;\r
+ Vector sequenceGroups = new Vector();\r
+\r
+ public SuperGroup() {\r
+ groupName = "Super group";\r
+ this.displayBoxes = true;\r
+ this.displayText = true;\r
+ this.colourText = false;\r
+ cs = null;\r
+ }\r
+\r
+ public SuperGroup(String groupName, ColourSchemeI scheme,\r
+ boolean displayBoxes, boolean displayText, boolean colourText) {\r
+ this.groupName = groupName;\r
+ this.displayBoxes = displayBoxes;\r
+ this.displayText = displayText;\r
+ this.colourText = colourText;\r
+ this.cs = scheme;\r
+ }\r
+\r
+ public String getName() {\r
+ return groupName;\r
}\r
- }\r
\r
+ public void setName(String name) {\r
+ groupName = name;\r
+ }\r
+\r
+ public void addGroup(SequenceGroup sg) {\r
+ if (!sequenceGroups.contains(sg)) {\r
+ sequenceGroups.addElement(sg);\r
+ }\r
+ }\r
\r
- public int getSize()\r
- {\r
- return sequenceGroups.size();\r
- }\r
+ public void addOrRemove(SequenceGroup sg) {\r
+ if (sequenceGroups.contains(sg)) {\r
+ deleteGroup(sg);\r
+ } else {\r
+ addGroup(sg);\r
+ }\r
+ }\r
+\r
+ public void deleteGroup(SequenceGroup sg) {\r
+ sequenceGroups.removeElement(sg);\r
+ }\r
\r
- public SequenceGroup getGroupeAt(int i)\r
- {\r
- return (SequenceGroup) sequenceGroups.elementAt(i);\r
- }\r
+ public void setSuperGroupProperties(SequenceGroup sg) {\r
+ cs = sg.cs;\r
+ colourText = sg.colourText;\r
+ displayText = sg.displayText;\r
+ displayBoxes = sg.displayBoxes;\r
+\r
+ for (int i = 0; i < sequenceGroups.size(); i++) {\r
+ SequenceGroup temp = (SequenceGroup) sequenceGroups.elementAt(i);\r
+ temp.cs = sg.cs;\r
+ temp.colourText = sg.colourText;\r
+ temp.displayText = sg.displayText;\r
+ temp.displayBoxes = sg.displayBoxes;\r
+ }\r
+ }\r
+\r
+ public int getSize() {\r
+ return sequenceGroups.size();\r
+ }\r
+\r
+ public SequenceGroup getGroupeAt(int i) {\r
+ return (SequenceGroup) sequenceGroups.elementAt(i);\r
+ }\r
}\r
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.ws.*;
-import java.beans.PropertyChangeEvent;
-
-public class AlignFrame extends GAlignFrame
-{
- final AlignmentPanel alignPanel;
- final AlignViewport viewport;
- public static final int NEW_WINDOW_WIDTH = 700;
- public static final int NEW_WINDOW_HEIGHT = 500;
- public String currentFileFormat = "Jalview";
-
- public AlignFrame(AlignmentI al)
- {
- viewport = new AlignViewport(al);
-
- alignPanel = new AlignmentPanel(this, viewport);
- alignPanel.annotationPanel.adjustPanelHeight();
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
- alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
-
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
-
- addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameActivated(InternalFrameEvent evt)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- { alignPanel.requestFocus(); }
- });
-
- }
- });
-
- }
-
- public void saveAlignmentMenu_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
- , new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
- currentFileFormat);
-
- chooser.setAcceptAllFileFilterUsed(false);
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText("Save");
- int value = chooser.showSaveDialog(this);
- if(value == JalviewFileChooser.APPROVE_OPTION)
- {
- currentFileFormat = chooser.getSelectedFormat();
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat);
-
- if (currentFileFormat.equals("Jalview"))
- {
- String shortName = title;
- if(shortName.indexOf(java.io.File.separatorChar)>-1)
- shortName = shortName.substring(
- shortName.lastIndexOf(java.io.File.separatorChar)+1);
-
- String choice = chooser.getSelectedFile().getPath();
- Jalview2XML.SaveState(this, choice, shortName);
- // USE Jalview2XML to save this file
- return;
- }
-
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
- try{
- java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
- out.println(output);
- out.close();
- }
- catch(Exception ex){}
- }
-
- }
-
- protected void outputText_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- Desktop.addInternalFrame(cap, "Alignment output - "+e.getActionCommand(), 600, 500);
- cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
- }
-
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
- {
- new HTMLOutput(viewport);
- }
-
- protected void createPNG_actionPerformed(ActionEvent e)
- {
- alignPanel.makePNG();
- }
-
- protected void epsFile_actionPerformed(ActionEvent e)
- {
- alignPanel.makeEPS();
- }
-
-
- public void printMenuItem_actionPerformed(ActionEvent e)
- {
- //Putting in a thread avoids Swing painting problems
- PrintThread thread = new PrintThread();
- thread.start();
- }
-
- class PrintThread extends Thread
- {
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
- printJob.setPrintable(alignPanel, pf);
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- }
- catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
- }
-
- }
-
-
-
-
- public void closeMenuItem_actionPerformed(ActionEvent e)
- {
- try{
- this.setClosed(true);
- }catch(Exception ex){}
- }
-
- Stack historyList = new Stack();
- Stack redoList = new Stack();
- private int treeCount = 0;
-
- void updateEditMenuBar()
- {
- if(historyList.size()>0)
- {
- undoMenuItem.setEnabled(true);
- HistoryItem hi = (HistoryItem)historyList.peek();
- undoMenuItem.setText("Undo "+hi.getDescription());
- }
- else
- {
- undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
- }
-
- if(redoList.size()>0)
- {
- redoMenuItem.setEnabled(true);
- HistoryItem hi = (HistoryItem)redoList.peek();
- redoMenuItem.setText("Redo "+hi.getDescription());
- }
- else
- {
- redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
- }
- }
-
- public void addHistoryItem(HistoryItem hi)
- {
- historyList.push(hi);
- updateEditMenuBar();
- }
-
- protected void undoMenuItem_actionPerformed(ActionEvent e)
- {
- HistoryItem hi = (HistoryItem)historyList.pop();
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
- restoreHistoryItem(hi);
- }
-
-
- protected void redoMenuItem_actionPerformed(ActionEvent e)
- {
- HistoryItem hi = (HistoryItem)redoList.pop();
- restoreHistoryItem(hi);
- updateEditMenuBar();
- viewport.updateConsensus();
- alignPanel.repaint();
- alignPanel.repaint();
- }
-
-
- // used by undo and redo
- void restoreHistoryItem(HistoryItem hi)
- {
- if(hi.getType()== HistoryItem.SORT)
- {
- for(int i=0; i<hi.getSequences().size(); i++)
- viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
- }
- else
- {
- for (int i = 0; i < hi.getSequences().size(); i++)
- {
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
- if(restore.getLength()==0)
- {
- restore.setSequence(hi.getHidden().elementAt(i).toString());
- viewport.alignment.getSequences().insertElementAt(
- restore,
- hi.getAlignIndex(i));
- }
- else
- restore.setSequence(hi.getHidden().elementAt(i).toString());
- }
- if(hi.getType()==HistoryItem.PASTE)
- {
- for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
- viewport.alignment.deleteSequence(i);
- }
- }
- updateEditMenuBar();
-
- viewport.updateConsensus();
- viewport.updateConservation();
- alignPanel.repaint();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- }
-
- public void moveSelectedSequences(boolean up)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
- return;
-
- if (up)
- {
- for (int i = 1; i < viewport.alignment.getHeight(); i++)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.sequences.contains(seq))
- continue;
-
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.sequences.contains(temp))
- continue;
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.sequences.contains(seq))
- continue;
-
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.sequences.contains(temp))
- continue;
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i + 1);
- }
- }
-
- alignPanel.repaint();
- }
-
-
-
- protected void copy_actionPerformed(ActionEvent e)
- {
- if(viewport.getSelectionGroup()==null)
- return;
-
- SequenceGroup sg = viewport.getSelectionGroup();
-
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- StringBuffer buffer= new StringBuffer();
-
- Hashtable orderedSeqs = new Hashtable();
- for(int i=0; i<sg.getSize(); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
- orderedSeqs.put(index+"", seq);
- }
-
- int index=0;
- for(int i=0; i<sg.getSize(); i++)
- {
- SequenceI seq = null;
- while( seq == null )
- {
- if(orderedSeqs.containsKey(index+""))
- {
- seq = (SequenceI) orderedSeqs.get(index + "");
- index++;
- break;
- }
- else
- index++;
- }
-
- buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
- +seq.findPosition( sg.getEndRes() )+ "\t"
- +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
- }
- c.setContents( new StringSelection( buffer.toString()) , null ) ;
-
- }
-
-
- protected void pasteNew_actionPerformed(ActionEvent e)
- {
- paste(true);
- }
-
- protected void pasteThis_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
- paste(false);
- }
-
- void paste(boolean newAlignment)
- {
- try{
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- Transferable contents = c.getContents(this);
- if (contents == null)
- return;
-
- String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
- StringTokenizer st = new StringTokenizer(str);
- ArrayList seqs = new ArrayList();
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- int start = Integer.parseInt(st.nextToken());
- int end = Integer.parseInt(st.nextToken());
- Sequence sequence = new Sequence(name,st.nextToken(), start, end);
-
- if(!newAlignment)
- viewport.alignment.addSequence(sequence);
- else
- seqs.add(sequence);
- }
-
- if(newAlignment)
- {
- SequenceI[] newSeqs = new SequenceI[seqs.size()];
- seqs.toArray(newSeqs);
- AlignFrame af = new AlignFrame(new Alignment(newSeqs));
- String newtitle = new String("Copied sequences");
- if( title.startsWith("Copied sequences"))
- newtitle = title;
- else
- newtitle = newtitle.concat("- from "+title);
-
- Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
- }
- else
- {
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- viewport.setEndSeq(viewport.alignment.getHeight());
- viewport.alignment.getWidth();
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
- }catch(Exception ex){}// could be anything being pasted in here
-
- }
-
-
- protected void cut_actionPerformed(ActionEvent e)
- {
- copy_actionPerformed(null);
- delete_actionPerformed(null);
- }
-
- protected void delete_actionPerformed(ActionEvent e)
- {
- boolean seqsdeleted=false;
-
- if (viewport.getSelectionGroup() == null)
- return;
-
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
-
- SequenceGroup sg = viewport.getSelectionGroup();
- for (int i=0;i < sg.sequences.size(); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.getAlignment().findIndex(seq);
- seq.deleteChars(sg.getStartRes(),sg.getEndRes()+1);
-
- if(seq.getSequence().length()<1) {
- seqsdeleted=true;
- viewport.getAlignment().deleteSequence(seq);
- } else {
- viewport.getAlignment().getSequences().setElementAt(seq, index);
- }
- }
-
- viewport.setSelectionGroup(null);
- viewport.alignment.deleteGroup(sg);
- if (seqsdeleted)
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
- if(viewport.getAlignment().getHeight()<1)
- try
- {
- this.setClosed(true);
- }catch(Exception ex){}
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
-
- protected void deleteGroups_actionPerformed(ActionEvent e)
- {
- viewport.alignment.deleteAllGroups();
- viewport.setSelectionGroup(null);
- alignPanel.repaint();
- }
-
-
-
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = new SequenceGroup();
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
- sg.addSequence( viewport.getAlignment().getSequenceAt(i));
- sg.setEndRes(viewport.alignment.getWidth());
- viewport.setSelectionGroup(sg);
- PaintRefresher.Refresh(null);
- }
-
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setSelectionGroup(null);
- viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
- PaintRefresher.Refresh(null);
- }
-
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
- sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
-
- PaintRefresher.Refresh(null);
- }
-
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
- {
- ColumnSelection colSel = viewport.getColumnSelection();
- if (colSel.size() > 0)
- {
- addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
- HistoryItem.HIDE));
- int min = colSel.getMin();
- viewport.getAlignment().trimLeft(min);
- colSel.compensateForEdit(0,min);
-
- if(viewport.getSelectionGroup()!=null)
- viewport.getSelectionGroup().adjustForRemoveLeft(min);
-
- Vector groups = viewport.alignment.getGroups();
- for(int i=0; i<groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.get(i);
- if(!sg.adjustForRemoveLeft(min))
- viewport.alignment.deleteGroup(sg);
- }
-
- alignPanel.repaint();
- }
- }
-
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)
- {
- ColumnSelection colSel = viewport.getColumnSelection();
- if (colSel.size() > 0)
- {
- addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
- HistoryItem.HIDE));
-
- int max = colSel.getMax();
- viewport.getAlignment().trimRight(max);
- if(viewport.getSelectionGroup()!=null)
- viewport.getSelectionGroup().adjustForRemoveRight(max);
-
- Vector groups = viewport.alignment.getGroups();
- for(int i=0; i<groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.get(i);
- if(!sg.adjustForRemoveRight(max))
- viewport.alignment.deleteGroup(sg);
- }
-
-
-
- alignPanel.repaint();
- }
-
- }
-
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Remove Gapped Columns",
- viewport.alignment,
- HistoryItem.HIDE));
-
- viewport.getAlignment().removeGaps();
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Remove Gaps",
- viewport.alignment,
- HistoryItem.HIDE));
- SequenceI current;
- int jSize;
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
- {
- current = viewport.getAlignment().getSequenceAt(i);
- jSize = current.getLength();
- for (int j=0; j < jSize; j++)
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))
- {
- current.deleteCharAt(j);
- j--;
- jSize--;
- }
- }
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
-
- public void padGapsMenuitem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Pad Gaps",
- viewport.alignment,
- HistoryItem.HIDE));
- SequenceI current;
- int Width = viewport.getAlignment().getWidth()-1;
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
- {
- current = viewport.getAlignment().getSequenceAt(i);
-
- if (current.getLength()<Width)
- current.insertCharAt(Width, viewport.getGapCharacter());
- }
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
-
- public void findMenuItem_actionPerformed(ActionEvent e)
- {
- JInternalFrame frame = new JInternalFrame();
- Finder finder = new Finder(viewport, alignPanel, frame);
- frame.setContentPane(finder);
- Desktop.addInternalFrame(frame, "Find", 340,110);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
-
- }
-
-
- public void font_actionPerformed(ActionEvent e)
- {
- FontChooser fc = new FontChooser( alignPanel );
- }
-
- protected void fullSeqId_actionPerformed(ActionEvent e)
- {
- viewport.setShowFullId( fullSeqId.isSelected() );
-
- alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
- alignPanel.repaint();
- }
-
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setColourText( colourTextMenuItem.isSelected() );
- alignPanel.repaint();
- }
-
- protected void wrapMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setWrapAlignment( wrapMenuItem.isSelected() );
- alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
- scaleAbove.setVisible( wrapMenuItem.isSelected() );
- scaleLeft.setVisible( wrapMenuItem.isSelected() );
- scaleRight.setVisible( wrapMenuItem.isSelected() );
- alignPanel.repaint();
- }
-
- protected void scaleAbove_actionPerformed(ActionEvent e)
- {
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- alignPanel.repaint();
- }
-
- protected void scaleLeft_actionPerformed(ActionEvent e)
- {
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());
- alignPanel.repaint();
- }
-
- protected void scaleRight_actionPerformed(ActionEvent e)
- {
- viewport.setScaleRightWrapped(scaleRight.isSelected());
- alignPanel.repaint();
- }
-
-
-
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
- alignPanel.repaint();
- }
-
- public void viewTextMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setShowText( viewTextMenuItem.isSelected() );
- alignPanel.repaint();
- }
-
-
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());
- alignPanel.repaint();
- }
-
- public void sequenceFeatures_actionPerformed(ActionEvent evt)
- {
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());
- if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
- {
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
- ((Alignment)viewport.alignment).featuresAdded = true;
- }
- alignPanel.repaint();
- }
-
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
- {
- if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
- {
- annotationPanelMenuItem.setSelected(false);
- return;
- }
- viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
- alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
- }
-
- public void overviewMenuItem_actionPerformed(ActionEvent e)
- {
- if (alignPanel.overviewPanel != null)
- return;
-
- JInternalFrame frame = new JInternalFrame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
- frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
- frame.getWidth(), frame.getHeight());
- frame.pack();
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
- {
- alignPanel.setOverviewPanel(null);
- };
- });
-
- alignPanel.setOverviewPanel( overview );
-
-
- }
-
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- changeColour( null );
- }
-
-
- public void clustalColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
- }
-
- public void zappoColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TaylorColourScheme());
- }
-
-
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- changeColour( new HydrophobicColourScheme() );
- }
-
- public void helixColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HelixColourScheme() );
- }
-
-
- public void strandColour_actionPerformed(ActionEvent e)
- {
- changeColour(new StrandColourScheme());
- }
-
-
- public void turnColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TurnColourScheme());
- }
-
-
- public void buriedColour_actionPerformed(ActionEvent e)
- {
- changeColour(new BuriedColourScheme() );
- }
-
- public void nucleotideColour_actionPerformed(ActionEvent e)
- {
- changeColour(new NucleotideColourScheme());
- }
-
-
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
- }
-
-
-
- void changeColour(ColourSchemeI cs)
- {
- int threshold = 0;
-
- if ( viewport.getAbovePIDThreshold() )
- {
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
-
- if (cs instanceof ResidueColourScheme)
- ( (ResidueColourScheme) cs).setThreshold(threshold);
- else if (cs instanceof ScoreColourScheme)
- ( (ScoreColourScheme) cs).setThreshold(threshold);
-
- viewport.setGlobalColourScheme(cs);
- }
- else if (cs instanceof ResidueColourScheme)
- ( (ResidueColourScheme) cs).setThreshold(0);
- else if (cs instanceof ScoreColourScheme)
- ( (ScoreColourScheme) cs).setThreshold(0);
-
-
-
- if (viewport.getConservationSelected())
- {
- ConservationColourScheme ccs = null;
-
- Alignment al = (Alignment) viewport.alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
-
- ccs = new ConservationColourScheme(c, cs);
-
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
- ccs.setConsensus( viewport.vconsensus );
- viewport.setGlobalColourScheme(ccs);
-
- ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
-
- }
- else
- {
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
- if (cs != null)
- cs.setConsensus(viewport.vconsensus);
- viewport.setGlobalColourScheme(cs);
- }
-
-
- if(viewport.getColourAppliesToAllGroups())
- {
- Vector groups = viewport.alignment.getGroups();
- for(int i=0; i<groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-
- if(cs==null)
- sg.cs = null;
- else if (cs instanceof ClustalxColourScheme)
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
- else if (cs instanceof UserColourScheme)
- sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
- else
- try{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- }catch(Exception ex){}
-
- if(viewport.getAbovePIDThreshold())
- {
- if (sg.cs instanceof ResidueColourScheme)
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
- else if (sg.cs instanceof ScoreColourScheme)
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-
- sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
- }
-
- if( viewport.getConservationSelected() )
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.sequences, 0, viewport.alignment.getWidth()-1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
- ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
- sg.cs = ccs;
- }
- else if(cs!=null)
- {
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
- }
-
- }
- }
-
- if(alignPanel.getOverviewPanel()!=null)
- alignPanel.getOverviewPanel().updateOverviewImage();
- alignPanel.repaint();
- }
-
- protected void modifyPID_actionPerformed(ActionEvent e)
- {
- if(viewport.getAbovePIDThreshold())
- {
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
- "Background");
- SliderPanel.showPIDSlider();
- }
- }
-
- protected void modifyConservation_actionPerformed(ActionEvent e)
- {
- if(viewport.getConservationSelected())
- {
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
- "Background");
- SliderPanel.showConservationSlider();
- }
- }
-
-
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
-
- ColourSchemeI cs = viewport.getGlobalColourScheme();
- if(cs instanceof ConservationColourScheme )
- changeColour( ((ConservationColourScheme)cs).cs );
- else
- changeColour( cs );
-
- modifyConservation_actionPerformed(null);
- }
-
- public void abovePIDThreshold_actionPerformed(ActionEvent e)
- {
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
-
- ColourSchemeI cs = viewport.getGlobalColourScheme();
-
- if(cs instanceof ConservationColourScheme )
- changeColour( ((ConservationColourScheme)cs).cs );
- else
- changeColour( cs );
-
- modifyPID_actionPerformed(null);
- }
-
-
-
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- new UserDefinedColours( alignPanel, null);
- }
-
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour( new PIDColourScheme() );
- }
-
-
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme() );
- }
-
-
-
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
- alignPanel.repaint();
- }
-
- public void sortIDMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
- AlignmentSorter.sortByID( viewport.getAlignment() );
- alignPanel.repaint();
- }
-
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
- // AlignmentSorter.sortByGroup(viewport.getAlignment());
- AlignmentSorter.sortGroups(viewport.getAlignment());
- alignPanel.repaint();
- }
-
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
- {
- RedundancyPanel sp = new RedundancyPanel(alignPanel,this);
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(sp);
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
-
- }
-
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
- {
- if((viewport.getSelectionGroup()==null) ||
- viewport.getSelectionGroup().getSize()<2)
- JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
- else
- {
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
- }
- }
-
- public void PCAMenuItem_actionPerformed(ActionEvent e)
- {
-
- if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
- || viewport.getAlignment().getHeight()<4)
- {
- JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
- +"at least 4 input sequences.",
- "Sequence selection insufficient",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- try{
- PCAPanel pcaPanel = new PCAPanel(viewport, null);
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(pcaPanel);
- Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
- }catch(java.lang.OutOfMemoryError ex)
- {
- JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
- "Out of memory", JOptionPane.WARNING_MESSAGE);
- }
-
-
- }
-
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
-
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- void NewTreePanel(String type, String pwType, String title)
- {
- String ltitle;
- final TreePanel tp;
- if (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize() > 3)
- {
- int s=0;
- SequenceGroup sg = viewport.getSelectionGroup();
-
- /* Decide if the selection is a column region */
- while (s<sg.sequences.size()) {
- if (((SequenceI) sg.sequences.elementAt(s++)).getLength()<sg.getEndRes()) {
- JOptionPane.showMessageDialog(Desktop.desktop,
- "The selected region to create a tree may\nonly contain residues or gaps.\n"
- +"Try using the Pad function in the edit menu,\n"
- +"or one of the multiple sequence alignment web services.",
- "Sequences in selection are not aligned", JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- }
- title=title+" on region";
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
- pwType,
- sg.getStartRes(), sg.getEndRes());
- }
- else
- {
-
- //are the sequences aligned?
- if(!viewport.alignment.isAligned())
- {
- JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
- +"Try using the Pad function in the edit menu,\n"
- +"or one of the multiple sequence alignment web services.",
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
- return;
- }
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
- type, pwType, 0, viewport.alignment.getWidth());
- }
-
- addTreeMenuItem(tp, title);
- viewport.setCurrentTree(tp.getTree());
-
- Desktop.addInternalFrame(tp, title+" from "+this.title, 600, 500);
- }
-
- public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
- final JMenuItem item = new JMenuItem("by "+title);
- sort.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- HistoryItem.SORT));
- // TODO: JBPNote - have to map order entries to curent SequenceI pointers
- AlignmentSorter.sortBy(viewport.getAlignment(), order);
- alignPanel.repaint();
- }
- });
- }
-
- void addTreeMenuItem(final TreePanel treePanel, String title)
- {
- final JMenuItem item = new JMenuItem(title);
-
- treeCount++;
-
- if (treeCount==1)
- sort.add(sortByTreeMenu);
-
- sortByTreeMenu.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
- HistoryItem.SORT));
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
- alignPanel.repaint();
- }
- });
-
- treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
- {
- treeCount--;
- sortByTreeMenu.remove(item);
- if (treeCount==0)
- sort.remove(sortByTreeMenu);
- };
- });
- viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() {
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (evt.getPropertyName().equals("alignment")) {
- treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
- treePanel.repaint();
- }
- }
-
- }
- );
- }
-
-
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
- {
- // TODO:resolve which menu item was actually selected
- // Now, check we have enough sequences
- SequenceI[] msa=null;
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
- {
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- SequenceGroup seqs = viewport.getSelectionGroup();
- int sz;
- msa = new SequenceI[sz=seqs.getSize()];
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
-
- }
- else
- {
- Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1) {
- msa = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
-
- }
-
- }
- if (msa!=null) {
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, false, true);
- }
- }
- public void ClustalRealign_actionPerformed(ActionEvent e)
- {
- // TODO:resolve which menu item was actually selected
- // Now, check we have enough sequences
- SequenceI[] msa=null;
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
- {
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- SequenceGroup seqs = viewport.getSelectionGroup();
- int sz;
- msa = new SequenceI[sz=seqs.getSize()];
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
-
- }
- else
- {
- Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1) {
- msa = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
-
- }
-
- }
- if (msa!=null) {
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
- }
- }
-
-
- protected void jpred_actionPerformed(ActionEvent e)
-{
- SequenceI seq=null;
- SequenceI[] msa=null;
-
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
- {
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- SequenceGroup seqs = viewport.getSelectionGroup();
- if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
- {
- seq = (SequenceI)seqs.getSequenceAt(0);
- }
- else
- {
- int sz;
- msa = new SequenceI[sz=seqs.getSize()];
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
- }
- }
- else
- {
- Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() == 1 || !viewport.alignment.isAligned())
- {
- seq = (SequenceI) seqs.elementAt(0);
- }
- else
- {
- msa = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
- }
- }
- if (msa!=null) {
- JPredClient ct = new JPredClient(title, msa);
- } else
- if (seq!=null) {
- JPredClient ct = new JPredClient(title, seq);
- } else {
- System.err.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
- }
- }
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
- {
- // TODO:resolve which menu item was actually selected
- // Now, check we have enough sequences
- SequenceI[] msa=null;
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
- {
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- SequenceGroup seqs = viewport.getSelectionGroup();
- int sz;
- msa = new SequenceI[sz=seqs.getSize()];
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
-
-
- }
- else
- {
- Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1) {
- msa = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
-
- }
-
- }
- if (msa!=null) {
- MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, false, true);
- }
- }
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select a newick-like tree file");
- chooser.setToolTipText("Load a tree file");
- int value = chooser.showOpenDialog(null);
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- try
- {
- jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
- ShowNewickTree(fin, choice);
- }
- catch (Exception ex)
- {
- JOptionPane.showMessageDialog(Desktop.desktop,
- "Problem reading tree file",
- ex.getMessage(),
- JOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
- }
- }
-
- public void ShowNewickTree(NewickFile nf, String title)
- {
- try{
- nf.parse();
- if (nf.getTree() != null)
- {
- TreePanel tp = new TreePanel(viewport,
- viewport.getAlignment().getSequences(),
- nf, "FromFile", title);
- Desktop.addInternalFrame(tp, title, 600, 500);
- addTreeMenuItem(tp, title);
- viewport.setCurrentTree(tp.getTree());
- }
- }catch(Exception ex){ex.printStackTrace();}
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.gui;\r
+\r
+import java.beans.*;\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+import java.awt.datatransfer.*;\r
+import java.awt.event.*;\r
+import java.awt.print.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
+import jalview.ws.*;\r
+\r
+public class AlignFrame\r
+ extends GAlignFrame\r
+{\r
+ public static final int NEW_WINDOW_WIDTH = 700;\r
+ public static final int NEW_WINDOW_HEIGHT = 500;\r
+ final AlignmentPanel alignPanel;\r
+ final AlignViewport viewport;\r
+ public String currentFileFormat = "Jalview";\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
+ private int treeCount = 0;\r
+\r
+ public AlignFrame(AlignmentI al)\r
+ {\r
+ viewport = new AlignViewport(al);\r
+\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+ alignPanel.annotationPanel.adjustPanelHeight();\r
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.\r
+ annotationPanel.getPreferredSize());\r
+ alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.\r
+ getPreferredSize());\r
+ alignPanel.setAnnotationVisible(viewport.getShowAnnotation());\r
+\r
+ getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
+\r
+ addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameActivated(InternalFrameEvent evt)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ alignPanel.requestFocus();\r
+ }\r
+ });\r
+ }\r
+ });\r
+ }\r
+\r
+ public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, currentFileFormat);\r
+\r
+ chooser.setAcceptAllFileFilterUsed(false);\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save Alignment to file");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ currentFileFormat = chooser.getSelectedFormat();\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
+ currentFileFormat);\r
+\r
+ if (currentFileFormat.equals("Jalview"))\r
+ {\r
+ String shortName = title;\r
+\r
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
+ {\r
+ shortName = shortName.substring(shortName.lastIndexOf(\r
+ java.io.File.separatorChar) + 1);\r
+ }\r
+\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ Jalview2XML.SaveState(this, choice, shortName);\r
+\r
+ // USE Jalview2XML to save this file\r
+ return;\r
+ }\r
+\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+\r
+ String output = FormatAdapter.formatSequences(currentFileFormat,\r
+ viewport.getAlignment().getSequences());\r
+\r
+ try\r
+ {\r
+ java.io.PrintWriter out = new java.io.PrintWriter(new java.io.\r
+ FileWriter(\r
+ choice));\r
+ out.println(output);\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ }\r
+\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
+ cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().\r
+ getSequences()));\r
+ }\r
+\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ new HTMLOutput(viewport);\r
+ }\r
+\r
+ protected void createPNG_actionPerformed(ActionEvent e)\r
+ {\r
+ alignPanel.makePNG();\r
+ }\r
+\r
+ protected void epsFile_actionPerformed(ActionEvent e)\r
+ {\r
+ alignPanel.makeEPS();\r
+ }\r
+\r
+ public void printMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ //Putting in a thread avoids Swing painting problems\r
+ PrintThread thread = new PrintThread();\r
+ thread.start();\r
+ }\r
+\r
+ public void closeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ void updateEditMenuBar()\r
+ {\r
+ if (historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) historyList.peek();\r
+ undoMenuItem.setText("Undo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setText("Undo");\r
+ }\r
+\r
+ if (redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) redoList.peek();\r
+ redoMenuItem.setText("Redo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setText("Redo");\r
+ }\r
+ }\r
+\r
+ public void addHistoryItem(HistoryItem hi)\r
+ {\r
+ historyList.push(hi);\r
+ updateEditMenuBar();\r
+ }\r
+\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) historyList.pop();\r
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
+ HistoryItem.HIDE));\r
+ restoreHistoryItem(hi);\r
+ }\r
+\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) redoList.pop();\r
+ restoreHistoryItem(hi);\r
+ updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ // used by undo and redo\r
+ void restoreHistoryItem(HistoryItem hi)\r
+ {\r
+ if (hi.getType() == HistoryItem.SORT)\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
+ {\r
+ viewport.alignment.getSequences().setElementAt(hi.getSequences()\r
+ .elementAt(i),\r
+ i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
+ {\r
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
+\r
+ if (restore.getLength() == 0)\r
+ {\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ viewport.alignment.getSequences().insertElementAt(restore,\r
+ hi.getAlignIndex(i));\r
+ }\r
+ else\r
+ {\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ }\r
+ }\r
+\r
+ if (hi.getType() == HistoryItem.PASTE)\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 1;\r
+ i > (hi.getSequences().size() - 1); i--)\r
+ {\r
+ viewport.alignment.deleteSequence(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ updateEditMenuBar();\r
+\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (up)\r
+ {\r
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+\r
+ if (!sg.sequences.contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+\r
+ if (sg.sequences.contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+\r
+ if (!sg.sequences.contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+\r
+ if (sg.sequences.contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+ }\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ StringBuffer buffer = new StringBuffer();\r
+\r
+ Hashtable orderedSeqs = new Hashtable();\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.alignment.findIndex(seq);\r
+ orderedSeqs.put(index + "", seq);\r
+ }\r
+\r
+ int index = 0;\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
+\r
+ buffer.append(seq.getName() + "\t" +\r
+ seq.findPosition(sg.getStartRes()) + "\t" +\r
+ seq.findPosition(sg.getEndRes()) + "\t" +\r
+ sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
+ }\r
+\r
+ c.setContents(new StringSelection(buffer.toString()), null);\r
+ }\r
+\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
+ HistoryItem.PASTE));\r
+ paste(false);\r
+ }\r
+\r
+ void paste(boolean newAlignment)\r
+ {\r
+ try\r
+ {\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+\r
+ if (contents == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ StringTokenizer st = new StringTokenizer(str);\r
+ ArrayList seqs = new ArrayList();\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ String name = st.nextToken();\r
+ int start = Integer.parseInt(st.nextToken());\r
+ int end = Integer.parseInt(st.nextToken());\r
+ Sequence sequence = new Sequence(name, st.nextToken(), start,\r
+ end);\r
+\r
+ if (!newAlignment)\r
+ {\r
+ viewport.alignment.addSequence(sequence);\r
+ }\r
+ else\r
+ {\r
+ seqs.add(sequence);\r
+ }\r
+ }\r
+\r
+ if (newAlignment)\r
+ {\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ seqs.toArray(newSeqs);\r
+\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
+ String newtitle = new String("Copied sequences");\r
+\r
+ if (title.startsWith("Copied sequences"))\r
+ {\r
+ newtitle = title;\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + title);\r
+ }\r
+\r
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ // could be anything being pasted in here\r
+ }\r
+\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(null);\r
+ delete_actionPerformed(null);\r
+ }\r
+\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
+ boolean seqsdeleted = false;\r
+\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.getAlignment().findIndex(seq);\r
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
+\r
+ if (seq.getSequence().length() < 1)\r
+ {\r
+ seqsdeleted = true;\r
+ viewport.getAlignment().deleteSequence(seq);\r
+ }\r
+ else\r
+ {\r
+ viewport.getAlignment().getSequences().setElementAt(seq, index);\r
+ }\r
+ }\r
+\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
+\r
+ if (seqsdeleted)\r
+ {\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
+\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.alignment.deleteAllGroups();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i));\r
+ }\r
+\r
+ sg.setEndRes(viewport.alignment.getWidth());\r
+ viewport.setSelectionGroup(sg);\r
+ PaintRefresher.Refresh(null);\r
+ }\r
+\r
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setSelectionGroup(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
+ PaintRefresher.Refresh(null);\r
+ }\r
+\r
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));\r
+ }\r
+\r
+ PaintRefresher.Refresh(null);\r
+ }\r
+\r
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ int min = colSel.getMin();\r
+ viewport.getAlignment().trimLeft(min);\r
+ colSel.compensateForEdit(0, min);\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ }\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+\r
+ if (!sg.adjustForRemoveLeft(min))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
+\r
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ int max = colSel.getMax();\r
+ viewport.getAlignment().trimRight(max);\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ }\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+\r
+ if (!sg.adjustForRemoveRight(max))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
+\r
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
+ viewport.alignment, HistoryItem.HIDE));\r
+\r
+ viewport.getAlignment().removeGaps();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ SequenceI current;\r
+ int jSize;\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+ jSize = current.getLength();\r
+\r
+ for (int j = 0; j < jSize; j++)\r
+ {\r
+ if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
+ {\r
+ current.deleteCharAt(j);\r
+ j--;\r
+ jSize--;\r
+ }\r
+ }\r
+ }\r
+\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth() - 1;\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width, viewport.getGapCharacter());\r
+ }\r
+ }\r
+\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void findMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JInternalFrame frame = new JInternalFrame();\r
+ Finder finder = new Finder(viewport, alignPanel, frame);\r
+ frame.setContentPane(finder);\r
+ Desktop.addInternalFrame(frame, "Find", 340, 110);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
+\r
+ public void font_actionPerformed(ActionEvent e)\r
+ {\r
+ FontChooser fc = new FontChooser(alignPanel);\r
+ }\r
+\r
+ protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowFullId(fullSeqId.isSelected());\r
+\r
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourText(colourTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
+ scaleAbove.setVisible(wrapMenuItem.isSelected());\r
+ scaleLeft.setVisible(wrapMenuItem.isSelected());\r
+ scaleRight.setVisible(wrapMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
+\r
+ if (viewport.showSequenceFeatures &&\r
+ ! ( (Alignment) viewport.alignment).featuresAdded)\r
+ {\r
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.\r
+ alignment,\r
+ alignPanel);\r
+ ( (Alignment) viewport.alignment).featuresAdded = true;\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (annotationPanelMenuItem.isSelected() &&\r
+ viewport.getWrapAlignment())\r
+ {\r
+ annotationPanelMenuItem.setSelected(false);\r
+\r
+ return;\r
+ }\r
+\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
+ }\r
+\r
+ public void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ JInternalFrame frame = new JInternalFrame();\r
+ OverviewPanel overview = new OverviewPanel(alignPanel);\r
+ frame.setContentPane(overview);\r
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
+ frame.getWidth(), frame.getHeight());\r
+ frame.pack();\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ alignPanel.setOverviewPanel(null);\r
+ }\r
+ ;\r
+ });\r
+\r
+ alignPanel.setOverviewPanel(overview);\r
+ }\r
+\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(null);\r
+ }\r
+\r
+ public void clustalColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ClustalxColourScheme(\r
+ viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
+ }\r
+\r
+ public void zappoColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+\r
+ public void taylorColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+\r
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+\r
+ public void helixColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+\r
+ public void strandColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+\r
+ public void turnColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+\r
+ public void buriedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+\r
+ public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
+ }\r
+\r
+ void changeColour(ColourSchemeI cs)\r
+ {\r
+ int threshold = 0;\r
+\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ {\r
+ ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ ( (ScoreColourScheme) cs).setThreshold(threshold);\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else if (cs instanceof ResidueColourScheme)\r
+ {\r
+ ( (ResidueColourScheme) cs).setThreshold(0);\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ ( (ScoreColourScheme) cs).setThreshold(0);\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ ConservationColourScheme ccs = null;\r
+\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ ccs = new ConservationColourScheme(c, cs);\r
+\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ ccs.setConsensus(viewport.vconsensus);\r
+ viewport.setGlobalColourScheme(ccs);\r
+\r
+ ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
+ "Background");\r
+ }\r
+ else\r
+ {\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ if (cs != null)\r
+ {\r
+ cs.setConsensus(viewport.vconsensus);\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+\r
+ if (viewport.getColourAppliesToAllGroups())\r
+ {\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ if (cs == null)\r
+ {\r
+ sg.cs = null;\r
+ }\r
+ else if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ }\r
+ else if (cs instanceof UserColourScheme)\r
+ {\r
+ sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ if (sg.cs instanceof ResidueColourScheme)\r
+ {\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
+ else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
+ ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ viewport.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c,\r
+ sg.cs);\r
+\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
+ sg.cs = ccs;\r
+ }\r
+ else if (cs != null)\r
+ {\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(),\r
+ "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ }\r
+\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme,\r
+ "Background");\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ }\r
+\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\r
+\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour( ( (ConservationColourScheme) cs).cs);\r
+ }\r
+ else\r
+ {\r
+ changeColour(cs);\r
+ }\r
+\r
+ modifyConservation_actionPerformed(null);\r
+ }\r
+\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
+\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
+\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour( ( (ConservationColourScheme) cs).cs);\r
+ }\r
+ else\r
+ {\r
+ changeColour(cs);\r
+ }\r
+\r
+ modifyPID_actionPerformed(null);\r
+ }\r
+\r
+ public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+\r
+ public void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+\r
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+\r
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(),\r
+ viewport.getAlignment().getSequenceAt(0));\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+\r
+ // AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+ AlignmentSorter.sortGroups(viewport.getAlignment());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(sp);\r
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
+ 100, false);\r
+ }\r
+\r
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if ( (viewport.getSelectionGroup() == null) ||\r
+ (viewport.getSelectionGroup().getSize() < 2))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "You must select at least 2 sequences.",\r
+ "Invalid Selection",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ else\r
+ {\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(new PairwiseAlignPanel(viewport));\r
+ Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
+ }\r
+ }\r
+\r
+ public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if ( ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() < 4) &&\r
+ (viewport.getSelectionGroup().getSize() > 0)) ||\r
+ (viewport.getAlignment().getHeight() < 4))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "Principal component analysis must take\n" +\r
+ "at least 4 input sequences.",\r
+ "Sequence selection insufficient",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(pcaPanel);\r
+ Desktop.addInternalFrame(frame, "Principal component analysis",\r
+ 400, 400);\r
+ }\r
+ catch (java.lang.OutOfMemoryError ex)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "Too many sequences selected\nfor Principal Component Analysis!!",\r
+ "Out of memory",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ }\r
+\r
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "PID", "Average distance tree using PID");\r
+ }\r
+\r
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
+ }\r
+\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
+ }\r
+\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+ }\r
+\r
+ void NewTreePanel(String type, String pwType, String title)\r
+ {\r
+ String ltitle;\r
+ final TreePanel tp;\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 3))\r
+ {\r
+ int s = 0;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ /* Decide if the selection is a column region */\r
+ while (s < sg.sequences.size())\r
+ {\r
+ if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <\r
+ sg.getEndRes())\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
+ "Try using the Pad function in the edit menu,\n" +\r
+ "or one of the multiple sequence alignment web services.",\r
+ "Sequences in selection are not aligned",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+ }\r
+\r
+ title = title + " on region";\r
+ tp = new TreePanel(viewport,\r
+ viewport.getSelectionGroup().sequences, type, pwType,\r
+ sg.getStartRes(), sg.getEndRes());\r
+ }\r
+ else\r
+ {\r
+ //are the sequences aligned?\r
+ if (!viewport.alignment.isAligned())\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The sequences must be aligned before creating a tree.\n" +\r
+ "Try using the Pad function in the edit menu,\n" +\r
+ "or one of the multiple sequence alignment web services.",\r
+ "Sequences not aligned",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), type, pwType,\r
+ 0,\r
+ viewport.alignment.getWidth());\r
+ }\r
+\r
+ addTreeMenuItem(tp, title);\r
+ viewport.setCurrentTree(tp.getTree());\r
+\r
+ Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
+ }\r
+\r
+ public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
+ {\r
+ final JMenuItem item = new JMenuItem("by " + title);\r
+ sort.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+\r
+ // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
+ alignPanel.repaint();\r
+ }\r
+ });\r
+ }\r
+\r
+ void addTreeMenuItem(final TreePanel treePanel, String title)\r
+ {\r
+ final JMenuItem item = new JMenuItem(title);\r
+\r
+ treeCount++;\r
+\r
+ if (treeCount == 1)\r
+ {\r
+ sort.add(sortByTreeMenu);\r
+ }\r
+\r
+ sortByTreeMenu.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Tree Sort",\r
+ viewport.alignment, HistoryItem.SORT));\r
+ AlignmentSorter.sortByTree(viewport.getAlignment(),\r
+ treePanel.getTree());\r
+ alignPanel.repaint();\r
+ }\r
+ });\r
+\r
+ treePanel.addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ treeCount--;\r
+ sortByTreeMenu.remove(item);\r
+\r
+ if (treeCount == 0)\r
+ {\r
+ sort.remove(sortByTreeMenu);\r
+ }\r
+ }\r
+ ;\r
+ });\r
+ viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());\r
+ treePanel.repaint();\r
+ }\r
+ }\r
+ });\r
+ }\r
+\r
+ public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO:resolve which menu item was actually selected\r
+ // Now, check we have enough sequences\r
+ SequenceI[] msa = null;\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 1))\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+ int sz;\r
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (msa != null)\r
+ {\r
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
+ title, msa, false, true);\r
+ }\r
+ }\r
+\r
+ public void ClustalRealign_actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO:resolve which menu item was actually selected\r
+ // Now, check we have enough sequences\r
+ SequenceI[] msa = null;\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 1))\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+ int sz;\r
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (msa != null)\r
+ {\r
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
+ title, msa, true, true);\r
+ }\r
+ }\r
+\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI seq = null;\r
+ SequenceI[] msa = null;\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 0))\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+\r
+ if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
+ {\r
+ seq = (SequenceI) seqs.getSequenceAt(0);\r
+ }\r
+ else\r
+ {\r
+ int sz;\r
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if ( (seqs.size() == 1) || !viewport.alignment.isAligned())\r
+ {\r
+ seq = (SequenceI) seqs.elementAt(0);\r
+ }\r
+ else\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (msa != null)\r
+ {\r
+ JPredClient ct = new JPredClient(title, msa);\r
+ }\r
+ else if (seq != null)\r
+ {\r
+ JPredClient ct = new JPredClient(title, seq);\r
+ }\r
+ else\r
+ {\r
+ System.err.print(\r
+ "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
+ }\r
+ }\r
+\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO:resolve which menu item was actually selected\r
+ // Now, check we have enough sequences\r
+ SequenceI[] msa = null;\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 1))\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+ int sz;\r
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (msa != null)\r
+ {\r
+ MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
+ false, true);\r
+ }\r
+ }\r
+\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // Pick the tree file\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Select a newick-like tree file");\r
+ chooser.setToolTipText("Load a tree file");\r
+\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+\r
+ try\r
+ {\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
+ "File");\r
+ ShowNewickTree(fin, choice);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "Problem reading tree file",\r
+ ex.getMessage(),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ public void ShowNewickTree(NewickFile nf, String title)\r
+ {\r
+ try\r
+ {\r
+ nf.parse();\r
+\r
+ if (nf.getTree() != null)\r
+ {\r
+ TreePanel tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), nf,\r
+ "FromFile",\r
+ title);\r
+ Desktop.addInternalFrame(tp, title, 600, 500);\r
+ addTreeMenuItem(tp, title);\r
+ viewport.setCurrentTree(tp.getTree());\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ class PrintThread\r
+ extends Thread\r
+ {\r
+ public void run()\r
+ {\r
+ PrinterJob printJob = PrinterJob.getPrinterJob();\r
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
+ printJob.setPrintable(alignPanel, pf);\r
+\r
+ if (printJob.printDialog())\r
+ {\r
+ try\r
+ {\r
+ printJob.print();\r
+ }\r
+ catch (Exception PrintException)\r
+ {\r
+ PrintException.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ }\r
+}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
+import java.util.*;\r
+\r
import java.awt.*;\r
+\r
import jalview.analysis.*;\r
-import jalview.analysis.NJTree;\r
+import jalview.bin.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import java.util.*;\r
-import jalview.bin.Cache;\r
\r
public class AlignViewport\r
{\r
int startRes;\r
int endRes;\r
-\r
int startSeq;\r
int endSeq;\r
-\r
boolean showFullId = false;\r
- boolean showText=true;\r
- boolean showColourText=false;\r
- boolean showBoxes=true;\r
- boolean wrapAlignment=false;\r
+ boolean showText = true;\r
+ boolean showColourText = false;\r
+ boolean showBoxes = true;\r
+ boolean wrapAlignment = false;\r
boolean renderGaps = true;\r
boolean showSequenceFeatures = false;\r
boolean showAnnotation = true;\r
boolean showConservation = true;\r
boolean showQuality = true;\r
boolean showIdentity = true;\r
-\r
boolean colourAppliesToAllGroups = true;\r
ColourSchemeI globalColourScheme = null;\r
boolean conservationColourSelected = false;\r
boolean abovePIDThreshold = false;\r
-\r
SequenceGroup selectionGroup = new SequenceGroup();\r
-\r
-\r
- int charHeight;\r
- int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
-\r
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
-\r
+ int charHeight;\r
+ int charWidth;\r
+ int chunkWidth;\r
+ int chunkHeight;\r
+ Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ AlignmentI alignment;\r
ColumnSelection colSel = new ColumnSelection();\r
-\r
int threshold;\r
int increment;\r
-\r
NJTree currentTree = null;\r
-\r
boolean scaleAboveWrapped = false;\r
- boolean scaleLeftWrapped = true;\r
+ boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
+ public Vector vconsensus;\r
+ AlignmentAnnotation consensus;\r
+ AlignmentAnnotation conservation;\r
+ AlignmentAnnotation quality;\r
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
\r
+ // JBPNote Prolly only need this in the applet version.\r
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.\r
+ PropertyChangeSupport(this);\r
\r
public AlignViewport(AlignmentI al)\r
{\r
setAlignment(al);\r
this.startRes = 0;\r
- this.endRes = al.getWidth()-1;\r
+ this.endRes = al.getWidth() - 1;\r
this.startSeq = 0;\r
- this.endSeq = al.getHeight()-1;\r
+ this.endSeq = al.getHeight() - 1;\r
\r
updateFromPreferences();\r
-\r
}\r
\r
public void updateFromPreferences()\r
showQuality = Preferences.showQuality;\r
showIdentity = Preferences.showIdentity;\r
showFullId = Preferences.showFullId;\r
+\r
String fontName = Preferences.fontName;\r
String fontStyle = Preferences.fontStyle;\r
String fontSize = Cache.getProperty("FONT_SIZE");\r
- if (fontName != null && fontStyle != null && fontSize != null)\r
+\r
+ if ( (fontName != null) && (fontStyle != null) && (fontSize != null))\r
{\r
int style = 0;\r
- if(fontStyle.equals("bold"))\r
+\r
+ if (fontStyle.equals("bold"))\r
+ {\r
style = 1;\r
- else if(fontStyle.equals("italic"))\r
+ }\r
+ else if (fontStyle.equals("italic"))\r
+ {\r
style = 2;\r
+ }\r
+\r
setFont(new Font(fontName, style, Integer.parseInt(fontSize)));\r
}\r
else\r
+ {\r
setFont(font);\r
+ }\r
\r
alignment.setGapCharacter(Preferences.gapSymbol);\r
\r
// as Blosum and Clustal require this to be done\r
updateConservation();\r
updateConsensus();\r
- if(Preferences.defaultColour!=null)\r
+\r
+ if (Preferences.defaultColour != null)\r
{\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);\r
- if(globalColourScheme instanceof UserColourScheme)\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
+ Preferences.defaultColour);\r
+\r
+ if (globalColourScheme instanceof UserColourScheme)\r
{\r
globalColourScheme = UserDefinedColours.loadDefaultColours();\r
}\r
- if(globalColourScheme!=null)\r
- globalColourScheme.setConsensus( vconsensus );\r
- }\r
-\r
- }\r
\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
-\r
- public Vector vconsensus;\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- AlignmentAnnotation quality;\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(vconsensus);\r
+ }\r
+ }\r
+ }\r
\r
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
+ public void showSequenceFeatures(boolean b)\r
+ {\r
+ showSequenceFeatures = b;\r
+ }\r
\r
public void updateConservation()\r
{\r
Conservation cons = new jalview.analysis.Conservation("All",\r
jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0,\r
- alignment.getWidth()-1);\r
+ alignment.getSequences(), 0, alignment.getWidth() - 1);\r
cons.calculate();\r
cons.verdict(false, ConsPercGaps);\r
cons.findQuality();\r
+\r
int alWidth = alignment.getWidth();\r
- Annotation [] annotations = new Annotation[alWidth];\r
- Annotation [] qannotations = new Annotation[alWidth];\r
+ Annotation[] annotations = new Annotation[alWidth];\r
+ Annotation[] qannotations = new Annotation[alWidth];\r
String sequence = cons.getConsSequence().getSequence();\r
- float minR,minG,minB, maxR,maxG,maxB;\r
+ float minR;\r
+ float minG;\r
+ float minB;\r
+ float maxR;\r
+ float maxG;\r
+ float maxB;\r
minR = 0.3f;\r
minG = 0.0f;\r
minB = 0f;\r
- maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality\r
+ maxR = 1.0f - minR;\r
+ maxG = 0.9f - minG;\r
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
+\r
float min = 0f;\r
float max = 11f;\r
float qmin = cons.qualityRange[0].floatValue();\r
for (int i = 0; i < alWidth; i++)\r
{\r
float value = 0;\r
+\r
try\r
+ {\r
+ value = Integer.parseInt(sequence.charAt(i) + "");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ if (sequence.charAt(i) == '*')\r
{\r
- value = Integer.parseInt(sequence.charAt(i) + "");\r
+ value = 11;\r
}\r
- catch (Exception ex)\r
+\r
+ if (sequence.charAt(i) == '+')\r
{\r
- if (sequence.charAt(i) == '*') value = 11;\r
- if (sequence.charAt(i) == '+') value = 10;\r
+ value = 10;\r
}\r
- float vprop = value-min;\r
- vprop/=max;\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+ }\r
+\r
+ float vprop = value - min;\r
+ vprop /= max;\r
+ annotations[i] = new Annotation(sequence.charAt(i) + "", "", ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+\r
// Quality calc\r
- value = ((Double) cons.quality.get(i)).floatValue();\r
+ value = ( (Double) cons.quality.get(i)).floatValue();\r
vprop = value - qmin;\r
- vprop/=qmax;\r
- qannotations[i] = new Annotation(" ",\r
- String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+ vprop /= qmax;\r
+ qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
}\r
\r
- if(conservation==null)\r
+ if (conservation == null)\r
{\r
conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than "+ConsPercGaps+"% gaps",\r
- annotations,\r
- 0f, // cons.qualityRange[0].floatValue(),\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps",\r
+ annotations, 0f, // cons.qualityRange[0].floatValue(),\r
11f, // cons.qualityRange[1].floatValue()\r
1);\r
- if(showConservation)\r
- alignment.addAnnotation(conservation);\r
+\r
+ if (showConservation)\r
+ {\r
+ alignment.addAnnotation(conservation);\r
+ }\r
+\r
quality = new AlignmentAnnotation("Quality",\r
"Alignment Quality based on Blosum62 scores",\r
qannotations,\r
cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(),\r
- 1);\r
- if(showQuality)\r
+ cons.qualityRange[1].floatValue(), 1);\r
+\r
+ if (showQuality)\r
+ {\r
alignment.addAnnotation(quality);\r
+ }\r
}\r
- else {\r
+ else\r
+ {\r
conservation.annotations = annotations;\r
quality.annotations = qannotations;\r
quality.graphMax = cons.qualityRange[1].floatValue();\r
}\r
-\r
-\r
}\r
\r
public void updateConsensus()\r
{\r
- Annotation [] annotations = new Annotation[alignment.getWidth()];\r
+ Annotation[] annotations = new Annotation[alignment.getWidth()];\r
\r
// this routine prevents vconsensus becoming a new object each time\r
// consenus is calculated. Important for speed of Blosum62\r
// and PID colouring of alignment\r
- if(vconsensus == null)\r
- vconsensus = alignment.getAAFrequency();\r
+ if (vconsensus == null)\r
+ {\r
+ vconsensus = alignment.getAAFrequency();\r
+ }\r
else\r
{\r
- Vector temp = alignment.getAAFrequency();\r
- vconsensus.clear();\r
- Enumeration e = temp.elements();\r
- while(e.hasMoreElements())\r
- {\r
- vconsensus.add(e.nextElement());\r
- }\r
+ Vector temp = alignment.getAAFrequency();\r
+ vconsensus.clear();\r
+\r
+ Enumeration e = temp.elements();\r
+\r
+ while (e.hasMoreElements())\r
+ {\r
+ vconsensus.add(e.nextElement());\r
+ }\r
}\r
+\r
Hashtable hash = null;\r
- for (int i = 0; i<alignment.getWidth(); i++)\r
+\r
+ for (int i = 0; i < alignment.getWidth(); i++)\r
{\r
- hash = (Hashtable) vconsensus.elementAt(i);\r
- float value = Float.parseFloat(hash.get("maxCount").toString());\r
- value /= Float.parseFloat(hash.get("size").toString());\r
-\r
- value *= 100;\r
- String maxRes = hash.get("maxResidue")+" ";\r
- String mouseOver = hash.get("maxResidue")+" ";\r
- if(maxRes.length()>2)\r
- {\r
- mouseOver = "["+maxRes+"] ";\r
- maxRes = "+ ";\r
- }\r
+ hash = (Hashtable) vconsensus.elementAt(i);\r
+\r
+ float value = Float.parseFloat(hash.get("maxCount").toString());\r
+ value /= Float.parseFloat(hash.get("size").toString());\r
+\r
+ value *= 100;\r
\r
- mouseOver += (int)value+"%";\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ String maxRes = hash.get("maxResidue") + " ";\r
+ String mouseOver = hash.get("maxResidue") + " ";\r
+\r
+ if (maxRes.length() > 2)\r
+ {\r
+ mouseOver = "[" + maxRes + "] ";\r
+ maxRes = "+ ";\r
+ }\r
\r
+ mouseOver += ( (int) value + "%");\r
+ annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
}\r
\r
- if(consensus==null)\r
- {\r
- consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, 1);\r
- if(showIdentity)\r
- alignment.addAnnotation(consensus);\r
- }\r
- else\r
- consensus.annotations = annotations;\r
+ if (consensus == null)\r
+ {\r
+ consensus = new AlignmentAnnotation("Consensus", "PID",\r
+ annotations, 0f, 100f, 1);\r
\r
+ if (showIdentity)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ consensus.annotations = annotations;\r
+ }\r
}\r
\r
-\r
public SequenceGroup getSelectionGroup()\r
{\r
return selectionGroup;\r
selectionGroup = sg;\r
}\r
\r
+ public boolean getConservationSelected()\r
+ {\r
+ return conservationColourSelected;\r
+ }\r
\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
+ public boolean getAbovePIDThreshold()\r
+ {\r
+ return abovePIDThreshold;\r
+ }\r
\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
+ public void setAbovePIDThreshold(boolean b)\r
+ {\r
+ abovePIDThreshold = b;\r
+ }\r
\r
- public int getStartRes() {\r
+ public int getStartRes()\r
+ {\r
return startRes;\r
}\r
\r
- public int getEndRes() {\r
+ public int getEndRes()\r
+ {\r
return endRes;\r
}\r
\r
- public int getStartSeq() {\r
+ public int getStartSeq()\r
+ {\r
return startSeq;\r
}\r
\r
public void setGlobalColourScheme(ColourSchemeI cs)\r
{\r
- globalColourScheme = cs;\r
+ globalColourScheme = cs;\r
}\r
\r
public ColourSchemeI getGlobalColourScheme()\r
return globalColourScheme;\r
}\r
\r
-\r
- public void setStartRes(int res) {\r
+ public void setStartRes(int res)\r
+ {\r
this.startRes = res;\r
}\r
- public void setStartSeq(int seq) {\r
+\r
+ public void setStartSeq(int seq)\r
+ {\r
this.startSeq = seq;\r
}\r
- public void setEndRes(int res) {\r
- if (res > alignment.getWidth()-1) {\r
+\r
+ public void setEndRes(int res)\r
+ {\r
+ if (res > (alignment.getWidth() - 1))\r
+ {\r
// log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth()-1;\r
+ res = alignment.getWidth() - 1;\r
}\r
- if (res < 0) {\r
+\r
+ if (res < 0)\r
+ {\r
res = 0;\r
}\r
+\r
this.endRes = res;\r
}\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
+\r
+ public void setEndSeq(int seq)\r
+ {\r
+ if (seq > alignment.getHeight())\r
+ {\r
seq = alignment.getHeight();\r
}\r
- if (seq < 0) {\r
+\r
+ if (seq < 0)\r
+ {\r
seq = 0;\r
}\r
+\r
this.endSeq = seq;\r
}\r
- public int getEndSeq() {\r
+\r
+ public int getEndSeq()\r
+ {\r
return endSeq;\r
}\r
\r
- public void setFont(Font f) {\r
+ public void setFont(Font f)\r
+ {\r
font = f;\r
+\r
javax.swing.JFrame temp = new javax.swing.JFrame();\r
temp.addNotify();\r
+\r
java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);\r
setCharHeight(fm.getHeight());\r
setCharWidth(fm.charWidth('M'));\r
}\r
\r
- public Font getFont() {\r
+ public Font getFont()\r
+ {\r
return font;\r
}\r
- public void setCharWidth(int w) {\r
+\r
+ public void setCharWidth(int w)\r
+ {\r
this.charWidth = w;\r
}\r
- public int getCharWidth() {\r
+\r
+ public int getCharWidth()\r
+ {\r
return charWidth;\r
}\r
- public void setCharHeight(int h) {\r
+\r
+ public void setCharHeight(int h)\r
+ {\r
this.charHeight = h;\r
}\r
- public int getCharHeight() {\r
+\r
+ public int getCharHeight()\r
+ {\r
return charHeight;\r
}\r
- public void setChunkWidth(int w) {\r
+\r
+ public void setChunkWidth(int w)\r
+ {\r
this.chunkWidth = w;\r
}\r
- public int getChunkWidth() {\r
+\r
+ public int getChunkWidth()\r
+ {\r
return chunkWidth;\r
}\r
- public void setChunkHeight(int h) {\r
+\r
+ public void setChunkHeight(int h)\r
+ {\r
this.chunkHeight = h;\r
}\r
- public int getChunkHeight() {\r
+\r
+ public int getChunkHeight()\r
+ {\r
return chunkHeight;\r
}\r
- public AlignmentI getAlignment() {\r
+\r
+ public AlignmentI getAlignment()\r
+ {\r
return alignment;\r
}\r
- public void setAlignment(AlignmentI align) {\r
+\r
+ public void setAlignment(AlignmentI align)\r
+ {\r
this.alignment = align;\r
}\r
\r
- public void setWrapAlignment(boolean state) {\r
+ public void setWrapAlignment(boolean state)\r
+ {\r
wrapAlignment = state;\r
}\r
- public void setShowText(boolean state) {\r
+\r
+ public void setShowText(boolean state)\r
+ {\r
showText = state;\r
}\r
\r
- public void setRenderGaps(boolean state){\r
+ public void setRenderGaps(boolean state)\r
+ {\r
renderGaps = state;\r
}\r
\r
-\r
public boolean getColourText()\r
{\r
return showColourText;\r
showColourText = state;\r
}\r
\r
- public void setShowBoxes(boolean state) {\r
+ public void setShowBoxes(boolean state)\r
+ {\r
showBoxes = state;\r
}\r
\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return wrapAlignment;\r
}\r
- public boolean getShowText() {\r
+\r
+ public boolean getShowText()\r
+ {\r
return showText;\r
}\r
- public boolean getShowBoxes() {\r
+\r
+ public boolean getShowBoxes()\r
+ {\r
return showBoxes;\r
}\r
\r
- public char getGapCharacter() {\r
+ public char getGapCharacter()\r
+ {\r
return getAlignment().getGapCharacter();\r
}\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
+\r
+ public void setGapCharacter(char gap)\r
+ {\r
+ if (getAlignment() != null)\r
+ {\r
getAlignment().setGapCharacter(gap);\r
}\r
}\r
- public void setThreshold(int thresh) {\r
+\r
+ public void setThreshold(int thresh)\r
+ {\r
threshold = thresh;\r
}\r
- public int getThreshold() {\r
+\r
+ public int getThreshold()\r
+ {\r
return threshold;\r
}\r
- public void setIncrement(int inc) {\r
+\r
+ public void setIncrement(int inc)\r
+ {\r
increment = inc;\r
}\r
- public int getIncrement() {\r
+\r
+ public int getIncrement()\r
+ {\r
return increment;\r
}\r
- public int getIndex(int y) {\r
- int y1 = 0;\r
+\r
+ public int getIndex(int y)\r
+ {\r
+ int y1 = 0;\r
int starty = getStartSeq();\r
- int endy = getEndSeq();\r
+ int endy = getEndSeq();\r
\r
- for (int i = starty; i <= endy; i++) {\r
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {\r
+ for (int i = starty; i <= endy; i++)\r
+ {\r
+ if ( (i < alignment.getHeight()) &&\r
+ (alignment.getSequenceAt(i) != null))\r
+ {\r
int y2 = y1 + getCharHeight();\r
\r
- if (y>=y1 && y <=y2) {\r
+ if ( (y >= y1) && (y <= y2))\r
+ {\r
return i;\r
}\r
- y1 = y2;\r
- } else {\r
+\r
+ y1 = y2;\r
+ }\r
+ else\r
+ {\r
return -1;\r
}\r
}\r
+\r
return -1;\r
}\r
\r
- public ColumnSelection getColumnSelection() {\r
+ public ColumnSelection getColumnSelection()\r
+ {\r
return colSel;\r
}\r
\r
- public void resetSeqLimits(int height) {\r
- setEndSeq(height/getCharHeight());\r
+ public void resetSeqLimits(int height)\r
+ {\r
+ setEndSeq(height / getCharHeight());\r
}\r
- public void setCurrentTree(NJTree tree) {\r
- currentTree = tree;\r
+\r
+ public void setCurrentTree(NJTree tree)\r
+ {\r
+ currentTree = tree;\r
}\r
- public NJTree getCurrentTree() {\r
+\r
+ public NJTree getCurrentTree()\r
+ {\r
return currentTree;\r
}\r
\r
public void setColourAppliesToAllGroups(boolean b)\r
- { colourAppliesToAllGroups = b; }\r
+ {\r
+ colourAppliesToAllGroups = b;\r
+ }\r
\r
public boolean getColourAppliesToAllGroups()\r
- {return colourAppliesToAllGroups; }\r
+ {\r
+ return colourAppliesToAllGroups;\r
+ }\r
\r
public boolean getShowFullId()\r
{\r
}\r
\r
public boolean getShowAnnotation()\r
- { return showAnnotation; }\r
+ {\r
+ return showAnnotation;\r
+ }\r
\r
public void setShowAnnotation(boolean b)\r
- { showAnnotation = b; }\r
+ {\r
+ showAnnotation = b;\r
+ }\r
\r
public boolean getScaleAboveWrapped()\r
- { return scaleAboveWrapped;}\r
+ {\r
+ return scaleAboveWrapped;\r
+ }\r
\r
public boolean getScaleLeftWrapped()\r
- { return scaleLeftWrapped; }\r
+ {\r
+ return scaleLeftWrapped;\r
+ }\r
\r
public boolean getScaleRightWrapped()\r
- { return scaleRightWrapped; }\r
+ {\r
+ return scaleRightWrapped;\r
+ }\r
\r
public void setScaleAboveWrapped(boolean b)\r
- { scaleAboveWrapped = b; }\r
+ {\r
+ scaleAboveWrapped = b;\r
+ }\r
\r
public void setScaleLeftWrapped(boolean b)\r
- { scaleLeftWrapped = b; }\r
+ {\r
+ scaleLeftWrapped = b;\r
+ }\r
\r
public void setScaleRightWrapped(boolean b)\r
- { scaleRightWrapped = b; }\r
- // JBPNote Prolly only need this in the applet version.\r
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);\r
- public void addPropertyChangeListener(java.beans.PropertyChangeListener listener) {\r
+ {\r
+ scaleRightWrapped = b;\r
+ }\r
+\r
+ public void addPropertyChangeListener(\r
+ java.beans.PropertyChangeListener listener)\r
+ {\r
changeSupport.addPropertyChangeListener(listener);\r
}\r
\r
- public void removePropertyChangeListener(java.beans.PropertyChangeListener listener) {\r
+ public void removePropertyChangeListener(\r
+ java.beans.PropertyChangeListener listener)\r
+ {\r
changeSupport.removePropertyChangeListener(listener);\r
}\r
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue) {\r
+\r
+ public void firePropertyChange(String prop, Object oldvalue, Object newvalue)\r
+ {\r
changeSupport.firePropertyChange(prop, oldvalue, newvalue);\r
}\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.GAlignmentPanel;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
+import java.io.*;\r
+import javax.imageio.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.awt.print.*;\r
-import java.io.*;\r
import java.awt.image.*;\r
-import org.jibble.epsgraphics.*;\r
-import javax.imageio.*;\r
+import java.awt.print.*;\r
import javax.swing.*;\r
\r
+import org.jibble.epsgraphics.*;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
\r
-\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
+public class AlignmentPanel\r
+ extends GAlignmentPanel implements AdjustmentListener, Printable\r
{\r
-\r
- AlignViewport av;\r
+ AlignViewport av;\r
OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
+ SeqPanel seqPanel;\r
+ IdPanel idPanel;\r
IdwidthAdjuster idwidthAdjuster;\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
\r
// this value is set false when selection area being dragged\r
boolean fastPaint = true;\r
+ int hextent = 0;\r
+ int vextent = 0;\r
\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
alignFrame = af;\r
- this.av = av;\r
- seqPanel = new SeqPanel (av, this);\r
- idPanel = new IdPanel (av, this);\r
+ this.av = av;\r
+ seqPanel = new SeqPanel(av, this);\r
+ idPanel = new IdPanel(av, this);\r
\r
scalePanel = new ScalePanel(av, this);\r
\r
annotationPanel = new AnnotationPanel(this);\r
alabels = new AnnotationLabels(this);\r
\r
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
+ getPreferredSize());\r
annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
annotationScroller.setViewportView(annotationPanel);\r
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
- setFocusable(true);\r
- addKeyListener(new KeyAdapter()\r
- {\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- switch(evt.getKeyCode())\r
- {\r
- case 27: // escape key\r
- av.setSelectionGroup(null);\r
- repaint();\r
- break;\r
-\r
- case KeyEvent.VK_DOWN:\r
- alignFrame.moveSelectedSequences(false);\r
- break;\r
- case KeyEvent.VK_UP:\r
- alignFrame.moveSelectedSequences(true);\r
- break;\r
- }\r
- }\r
- });\r
+ setFocusable(true);\r
+ addKeyListener(new KeyAdapter()\r
+ {\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ av.setSelectionGroup(null);\r
+ repaint();\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_DOWN:\r
+ alignFrame.moveSelectedSequences(false);\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ alignFrame.moveSelectedSequences(true);\r
+\r
+ break;\r
+ }\r
+ }\r
+ });\r
}\r
\r
public void fontChanged()\r
// to prevent drawing old image\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));\r
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));\r
+ scalePanelHolder.setPreferredSize(new Dimension(10,\r
+ av.charHeight + fm.getDescent()));\r
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10,\r
+ av.charHeight + fm.getDescent()));\r
\r
idPanel.idCanvas.gg = null;\r
annotationPanel.adjustPanelHeight();\r
+\r
Dimension d = calculateIdWidth();\r
d.setSize(d.width + 4, d.height);\r
idPanel.idCanvas.setPreferredSize(d);\r
repaint();\r
}\r
\r
-\r
Dimension calculateIdWidth()\r
{\r
Graphics g = this.getGraphics();\r
- if(g==null)\r
+\r
+ if (g == null)\r
{\r
javax.swing.JFrame f = new javax.swing.JFrame();\r
f.addNotify();\r
FontMetrics fm = g.getFontMetrics(av.font);\r
AlignmentI al = av.getAlignment();\r
\r
- int i = 0;\r
- int idWidth = 0;\r
- String id;\r
- while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
- {\r
- SequenceI s = al.getSequenceAt(i);\r
- if(av.getShowFullId())\r
- id = s.getDisplayId();\r
- else\r
- id = s.getName();\r
-\r
- if (fm.stringWidth(id) > idWidth)\r
- idWidth = fm.stringWidth(id);\r
- i++;\r
- }\r
-\r
- // Also check annotation label widths\r
- i=0;\r
- if(al.getAlignmentAnnotation()!=null)\r
- {\r
- fm = g.getFontMetrics(alabels.getFont());\r
- while (i < al.getAlignmentAnnotation().length)\r
- {\r
- String label = al.getAlignmentAnnotation()[i].label;\r
- if (fm.stringWidth(label) > idWidth)\r
- idWidth = fm.stringWidth(label);\r
- i++;\r
- }\r
- }\r
-\r
- return new Dimension(idWidth, 12);\r
- }\r
+ int i = 0;\r
+ int idWidth = 0;\r
+ String id;\r
\r
+ while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))\r
+ {\r
+ SequenceI s = al.getSequenceAt(i);\r
\r
- public void highlightSearchResults(int [] results)\r
- {\r
- seqPanel.seqCanvas.highlightSearchResults( results );\r
+ if (av.getShowFullId())\r
+ {\r
+ id = s.getDisplayId();\r
+ }\r
+ else\r
+ {\r
+ id = s.getName();\r
+ }\r
\r
- // do we need to scroll the panel?\r
- if(results!=null)\r
+ if (fm.stringWidth(id) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(id);\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ // Also check annotation label widths\r
+ i = 0;\r
+\r
+ if (al.getAlignmentAnnotation() != null)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
- int start = seq.findIndex( results[1] )-1;\r
- int end = seq.findIndex( results[2] )-1;\r
- if( av.getStartRes() > start\r
- || av.getEndRes() < end\r
- || (av.getStartSeq() > results[0]\r
- || av.getEndSeq() < results[0]))\r
- setScrollValues(start, results[0]);\r
+ fm = g.getFontMetrics(alabels.getFont());\r
+\r
+ while (i < al.getAlignmentAnnotation().length)\r
+ {\r
+ String label = al.getAlignmentAnnotation()[i].label;\r
+\r
+ if (fm.stringWidth(label) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(label);\r
+ }\r
+\r
+ i++;\r
+ }\r
}\r
\r
- }\r
+ return new Dimension(idWidth, 12);\r
+ }\r
+\r
+ public void highlightSearchResults(int[] results)\r
+ {\r
+ seqPanel.seqCanvas.highlightSearchResults(results);\r
\r
+ // do we need to scroll the panel?\r
+ if (results != null)\r
+ {\r
+ SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
+ int start = seq.findIndex(results[1]) - 1;\r
+ int end = seq.findIndex(results[2]) - 1;\r
\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
+ if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||\r
+ ( (av.getStartSeq() > results[0]) ||\r
+ (av.getEndSeq() < results[0])))\r
+ {\r
+ setScrollValues(start, results[0]);\r
+ }\r
+ }\r
+ }\r
\r
- public void setOverviewPanel(OverviewPanel op)\r
- {\r
- overviewPanel = op;\r
- }\r
+ public OverviewPanel getOverviewPanel()\r
+ {\r
+ return overviewPanel;\r
+ }\r
\r
+ public void setOverviewPanel(OverviewPanel op)\r
+ {\r
+ overviewPanel = op;\r
+ }\r
\r
public void setAnnotationVisible(boolean b)\r
{\r
annotationScroller.setVisible(b);\r
}\r
\r
-\r
public void setWrapAlignment(boolean wrap)\r
{\r
scalePanelHolder.setVisible(!wrap);\r
idSpaceFillerPanel1.setVisible(!wrap);\r
\r
repaint();\r
-\r
}\r
\r
-\r
public void setColourScheme()\r
{\r
ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
- if(av.getConservationSelected())\r
+ if (av.getConservationSelected())\r
{\r
+ Alignment al = (Alignment) av.getAlignment();\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth());\r
\r
- Alignment al = (Alignment)av.getAlignment();\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() );\r
-\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
\r
- av.setGlobalColourScheme( ccs );\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
\r
+ av.setGlobalColourScheme(ccs);\r
}\r
\r
repaint();\r
}\r
\r
-\r
- int hextent = 0;\r
- int vextent = 0;\r
-\r
// return value is true if the scroll is valid\r
public boolean scrollUp(boolean up)\r
{\r
- if(up)\r
+ if (up)\r
{\r
- if(vscroll.getValue()<1)\r
+ if (vscroll.getValue() < 1)\r
+ {\r
return false;\r
- fastPaint = false;\r
+ }\r
+\r
+ fastPaint = false;\r
vscroll.setValue(vscroll.getValue() - 1);\r
}\r
else\r
{\r
- if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())\r
- return false;\r
- fastPaint = false;\r
+ if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())\r
+ {\r
+ return false;\r
+ }\r
+\r
+ fastPaint = false;\r
vscroll.setValue(vscroll.getValue() + 1);\r
}\r
+\r
fastPaint = true;\r
+\r
return true;\r
}\r
\r
public boolean scrollRight(boolean right)\r
{\r
-\r
if (right)\r
{\r
if (hscroll.getValue() < 1)\r
+ {\r
return false;\r
+ }\r
+\r
fastPaint = false;\r
hscroll.setValue(hscroll.getValue() - 1);\r
}\r
else\r
{\r
- if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())\r
+ if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())\r
+ {\r
return false;\r
+ }\r
+\r
fastPaint = false;\r
hscroll.setValue(hscroll.getValue() + 1);\r
}\r
+\r
fastPaint = true;\r
+\r
return true;\r
}\r
\r
-\r
public void setScrollValues(int x, int y)\r
{\r
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
+ av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
+ 1);\r
\r
- hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;\r
- vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;\r
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
+ vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
\r
- if(hextent > av.alignment.getWidth())\r
+ if (hextent > av.alignment.getWidth())\r
+ {\r
hextent = av.alignment.getWidth();\r
- if(vextent > av.alignment.getHeight())\r
+ }\r
+\r
+ if (vextent > av.alignment.getHeight())\r
+ {\r
vextent = av.alignment.getHeight();\r
+ }\r
\r
- if(hextent+x > av.getAlignment().getWidth())\r
- x = av.getAlignment().getWidth()- hextent;\r
+ if ( (hextent + x) > av.getAlignment().getWidth())\r
+ {\r
+ x = av.getAlignment().getWidth() - hextent;\r
+ }\r
\r
- if(vextent+y > av.getAlignment().getHeight())\r
+ if ( (vextent + y) > av.getAlignment().getHeight())\r
+ {\r
y = av.getAlignment().getHeight() - vextent;\r
+ }\r
\r
- if(y<0)\r
+ if (y < 0)\r
+ {\r
y = 0;\r
+ }\r
\r
- if(x<0)\r
- x=0;\r
-\r
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
-\r
-\r
+ if (x < 0)\r
+ {\r
+ x = 0;\r
+ }\r
\r
+ hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
+ vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
}\r
\r
-\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
int oldX = av.getStartRes();\r
{\r
int x = hscroll.getValue();\r
av.setStartRes(x);\r
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
+ av.setEndRes( (x +\r
+ (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);\r
}\r
\r
if (evt.getSource() == vscroll)\r
{\r
int offy = vscroll.getValue();\r
+\r
if (av.getWrapAlignment())\r
{\r
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
- av.setStartRes( vscroll.getValue() * rowSize );\r
- av.setEndRes( (vscroll.getValue()+1) * rowSize );\r
+ int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+ seqCanvas.getWidth());\r
+ av.setStartRes(vscroll.getValue() * rowSize);\r
+ av.setEndRes( (vscroll.getValue() + 1) * rowSize);\r
}\r
else\r
{\r
av.setStartSeq(offy);\r
- av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());\r
+ av.setEndSeq(offy +\r
+ (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));\r
}\r
}\r
\r
- if(overviewPanel!=null)\r
+ if (overviewPanel != null)\r
+ {\r
overviewPanel.setBoxPosition();\r
+ }\r
\r
- if(av.getWrapAlignment() || !fastPaint)\r
+ if (av.getWrapAlignment() || !fastPaint)\r
+ {\r
repaint();\r
+ }\r
else\r
{\r
idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);\r
av.getStartSeq() - oldY);\r
\r
scalePanel.repaint();\r
+\r
if (av.getShowAnnotation())\r
+ {\r
annotationPanel.fastPaint(av.getStartRes() - oldX);\r
+ }\r
}\r
-\r
}\r
\r
-\r
public void paintComponent(Graphics g)\r
{\r
invalidate();\r
+\r
Dimension d = idPanel.idCanvas.getPreferredSize();\r
idPanelHolder.setPreferredSize(d);\r
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
\r
if (av.getWrapAlignment())\r
{\r
- int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ int max = av.alignment.getWidth() /\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
vscroll.setMaximum(max);\r
vscroll.setUnitIncrement(1);\r
vscroll.setVisibleAmount(1);\r
{\r
setScrollValues(av.getStartRes(), av.getStartSeq());\r
}\r
-\r
-\r
-\r
}\r
\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
+ public int print(Graphics pg, PageFormat pf, int pi)\r
+ throws PrinterException\r
{\r
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
+ pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());\r
\r
int pwidth = (int) pf.getImageableWidth();\r
int pheight = (int) pf.getImageableHeight();\r
\r
if (av.getWrapAlignment())\r
- return printWrappedAlignment(pg, pwidth,pheight, pi);\r
+ {\r
+ return printWrappedAlignment(pg, pwidth, pheight, pi);\r
+ }\r
else\r
- return printUnwrapped(pg,pwidth, pheight,pi);\r
+ {\r
+ return printUnwrapped(pg, pwidth, pheight, pi);\r
+ }\r
}\r
\r
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
+ throws PrinterException\r
{\r
+ int idWidth = calculateIdWidth().width + 4;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
\r
- int idWidth = calculateIdWidth().width + 4;\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
- int scaleHeight = av.charHeight + fm.getDescent();\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
\r
- pg.setColor(Color.white);\r
- pg.fillRect(0, 0, pwidth, pheight);\r
- pg.setFont(av.getFont());\r
+ ////////////////////////////////////\r
+ /// How many sequences and residues can we fit on a printable page?\r
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
+ int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -\r
+ 1;\r
\r
- int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1;\r
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;\r
\r
- int pagesWide = av.getAlignment().getWidth() / totalRes + 1;\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int startRes;\r
\r
- /////////////////////////////\r
- /// Only print these sequences and residues on this page\r
- int startRes, endRes, startSeq, endSeq;\r
- startRes = (pi % pagesWide) * totalRes;\r
- endRes = startRes + totalRes - 1;\r
- if (endRes > av.getAlignment().getWidth()-1)\r
- endRes = av.getAlignment().getWidth()-1;\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int endRes;\r
\r
- startSeq = (pi / pagesWide) * totalSeq;\r
- endSeq = startSeq + totalSeq;\r
- if (endSeq > av.getAlignment().getHeight())\r
- endSeq = av.getAlignment().getHeight();\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int startSeq;\r
\r
- int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int endSeq;\r
+ startRes = (pi % pagesWide) * totalRes;\r
+ endRes = (startRes + totalRes) - 1;\r
\r
- if (av.showAnnotation)\r
- pagesHigh += annotationPanel.getHeight();\r
+ if (endRes > (av.getAlignment().getWidth() - 1))\r
+ {\r
+ endRes = av.getAlignment().getWidth() - 1;\r
+ }\r
+\r
+ startSeq = (pi / pagesWide) * totalSeq;\r
+ endSeq = startSeq + totalSeq;\r
\r
- pagesHigh /= pheight;\r
+ if (endSeq > av.getAlignment().getHeight())\r
+ {\r
+ endSeq = av.getAlignment().getHeight();\r
+ }\r
\r
- if (pi >= pagesWide * pagesHigh)\r
- return Printable.NO_SUCH_PAGE;\r
+ int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
\r
- //draw Scale\r
- pg.translate(idWidth, 0);\r
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
- pg.translate( -idWidth, scaleHeight);\r
- ////////////////\r
- // Draw the ids\r
- Color currentColor = null;\r
- Color currentTextColor = null;\r
- for (int i = startSeq; i < endSeq; i++)\r
- {\r
- if (av.getSelectionGroup() != null &&\r
- av.getSelectionGroup().sequences.\r
- contains(av.getAlignment().getSequenceAt(i)))\r
- {\r
- currentColor = Color.gray;\r
- currentTextColor = Color.black;\r
- }\r
- else\r
- {\r
- currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
- }\r
+ if (av.showAnnotation)\r
+ {\r
+ pagesHigh += annotationPanel.getHeight();\r
+ }\r
\r
- pg.setColor(currentColor);\r
- pg.fillRect(0,\r
- jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
- av.getCharHeight()),\r
- idWidth,\r
- av.getCharHeight());\r
+ pagesHigh /= pheight;\r
+\r
+ if (pi >= (pagesWide * pagesHigh))\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
\r
- pg.setColor(currentTextColor);\r
+ //draw Scale\r
+ pg.translate(idWidth, 0);\r
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
+ pg.translate( -idWidth, scaleHeight);\r
\r
- String string = av.getAlignment().getSequenceAt(i).getName();\r
- if (av.getShowFullId())\r
- string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
+ ////////////////\r
+ // Draw the ids\r
+ Color currentColor = null;\r
+ Color currentTextColor = null;\r
\r
- pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight\r
- (startSeq, i, av.getCharHeight()) + av.getCharHeight() -\r
- (av.getCharHeight() / 5));\r
+ for (int i = startSeq; i < endSeq; i++)\r
+ {\r
+ if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().sequences.contains(\r
+ av.getAlignment().getSequenceAt(i)))\r
+ {\r
+ currentColor = Color.gray;\r
+ currentTextColor = Color.black;\r
+ }\r
+ else\r
+ {\r
+ currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
+ currentTextColor = Color.black;\r
}\r
\r
- // draw main sequence panel\r
- pg.translate(idWidth, 0);\r
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
- startRes, startSeq, 0);\r
+ pg.setColor(currentColor);\r
+ pg.fillRect(0,\r
+ jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
+ av.getCharHeight()), idWidth, av.getCharHeight());\r
\r
+ pg.setColor(currentTextColor);\r
\r
- if (av.showAnnotation && endSeq == av.alignment.getHeight())\r
+ String string = av.getAlignment().getSequenceAt(i).getName();\r
+\r
+ if (av.getShowFullId())\r
{\r
- pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);\r
- alabels.drawComponent( (Graphics2D) pg);\r
- pg.translate(idWidth, 0);\r
- annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1);\r
+ string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
}\r
\r
- return Printable.PAGE_EXISTS;\r
+ pg.drawString(string, 0,\r
+ (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
+ av.getCharHeight()) + av.getCharHeight()) -\r
+ (av.getCharHeight() / 5));\r
+ }\r
\r
- }\r
+ // draw main sequence panel\r
+ pg.translate(idWidth, 0);\r
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
+ startRes, startSeq, 0);\r
\r
+ if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
+ {\r
+ pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);\r
+ alabels.drawComponent( (Graphics2D) pg);\r
+ pg.translate(idWidth, 0);\r
+ annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
+ 1);\r
+ }\r
\r
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
+\r
+ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
+ int pi)\r
+ throws PrinterException\r
{\r
- int idWidth = calculateIdWidth().width + 4;\r
+ int idWidth = calculateIdWidth().width + 4;\r
\r
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);\r
- int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *\r
- ( (av.alignment.getWidth()\r
- / resWidth) + 1) * av.charHeight;\r
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
+ idWidth);\r
+ int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *\r
+ ( (av.alignment.getWidth() / resWidth) +\r
+ 1) * av.charHeight;\r
\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
\r
- pg.setColor(Color.white);\r
- pg.fillRect(0, 0, pwidth, pheight);\r
- pg.setFont(av.getFont());\r
+ ////////////////\r
+ // Draw the ids\r
+ pg.setColor(Color.black);\r
\r
- ////////////////\r
- // Draw the ids\r
- pg.setColor(Color.black);\r
+ pg.translate(0, -pi * pheight);\r
\r
- pg.translate(0, -pi * pheight);\r
+ pg.setClip(0, pi * pheight, pwidth, pheight);\r
\r
- pg.setClip(0,pi*pheight,pwidth, pheight);\r
+ int ypos = 2 * av.charHeight;\r
\r
- int ypos = 2 * av.charHeight;\r
- do\r
+ do\r
+ {\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- String string = s.getName();\r
- if (av.getShowFullId())\r
- string = s.getDisplayId();\r
-\r
- pg.drawString(string, 0,\r
- AlignmentUtil.getPixelHeight(0, i, av.charHeight) +\r
- ypos +\r
- av.charHeight - (av.charHeight / 5));\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ String string = s.getName();\r
\r
+ if (av.getShowFullId())\r
+ {\r
+ string = s.getDisplayId();\r
}\r
\r
- ypos += (av.alignment.getHeight() + 2) * av.charHeight;\r
-\r
+ pg.drawString(string, 0,\r
+ (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +\r
+ av.charHeight) - (av.charHeight / 5));\r
}\r
- while (ypos < totalHeight);\r
-\r
- pg.translate(idWidth, 0);\r
\r
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
-\r
- if (pi * pheight < totalHeight)\r
- return Printable.PAGE_EXISTS;\r
- else\r
- return Printable.NO_SUCH_PAGE;\r
+ ypos += ( (av.alignment.getHeight() + 2) * av.charHeight);\r
+ }\r
+ while (ypos < totalHeight);\r
\r
+ pg.translate(idWidth, 0);\r
\r
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
\r
+ if ( (pi * pheight) < totalHeight)\r
+ {\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
+ else\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
}\r
\r
-\r
public void makeEPS()\r
{\r
- int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;\r
+ int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
+ av.chunkHeight;\r
int width = seqPanel.getWidth() + idPanel.getWidth();\r
\r
if (!av.getWrapAlignment())\r
{\r
- height = (av.alignment.getHeight()+1) * av.charHeight + 30;\r
- width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;\r
+ height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ width = idPanel.getWidth() +\r
+ (av.alignment.getWidth() * av.charWidth);\r
+ }\r
+\r
+ if (av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.getPreferredSize().height;\r
}\r
- if(av.getShowAnnotation())\r
- {\r
- height += annotationPanel.getPreferredSize().height;\r
- }\r
\r
try\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]{"eps"},\r
- new String[]{"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"eps"},\r
+ new String[]\r
+ {"Encapsulated Postscript"},\r
+ "Encapsulated Postscript");\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
chooser.setDialogTitle("Create EPS file from alignment");\r
chooser.setToolTipText("Save");\r
\r
int value = chooser.showSaveDialog(this);\r
+\r
if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
return;\r
+ }\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
- if (av.getWrapAlignment())\r
- printWrappedAlignment(pg, width, height, 0);\r
- else\r
- printUnwrapped(pg, width, height, 0);\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+ EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,\r
+ height);\r
\r
+ if (av.getWrapAlignment())\r
+ {\r
+ printWrappedAlignment(pg, width, height, 0);\r
+ }\r
+ else\r
+ {\r
+ printUnwrapped(pg, width, height, 0);\r
+ }\r
\r
- pg.flush();\r
- pg.close();\r
+ pg.flush();\r
+ pg.close();\r
}\r
catch (Exception ex)\r
{\r
\r
public void makePNG()\r
{\r
- int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;\r
- int width = seqPanel.getWidth() + idPanel.getWidth();\r
-\r
- if (!av.getWrapAlignment())\r
- {\r
- height = (av.alignment.getHeight()+1) * av.charHeight + 30;\r
- width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;\r
- }\r
-\r
- if(av.getShowAnnotation())\r
- {\r
- height += annotationPanel.getPreferredSize().height;\r
- }\r
+ int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
+ av.chunkHeight;\r
+ int width = seqPanel.getWidth() + idPanel.getWidth();\r
\r
+ if (!av.getWrapAlignment())\r
+ {\r
+ height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ width = idPanel.getWidth() +\r
+ (av.alignment.getWidth() * av.charWidth);\r
+ }\r
\r
+ if (av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.getPreferredSize().height;\r
+ }\r
\r
try\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]{"png"},\r
- new String[]{"Portable network graphics"},\r
- "Portable network graphics");\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"png"},\r
+ new String[]\r
+ {"Portable network graphics"},\r
+ "Portable network graphics");\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
chooser.setDialogTitle("Create EPS file from alignment");\r
chooser.setToolTipText("Save");\r
\r
int value = chooser.showSaveDialog(this);\r
+\r
if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
return;\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
\r
- BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
- Graphics2D png = (Graphics2D)bi.getGraphics();\r
+ BufferedImage bi = new BufferedImage(width, height,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ Graphics2D png = (Graphics2D) bi.getGraphics();\r
\r
- png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
- if (av.getWrapAlignment())\r
- printWrappedAlignment(png, width, height, 0);\r
- else\r
- printUnwrapped(png, width, height, 0);\r
+ if (av.getWrapAlignment())\r
+ {\r
+ printWrappedAlignment(png, width, height, 0);\r
+ }\r
+ else\r
+ {\r
+ printUnwrapped(png, width, height, 0);\r
+ }\r
\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
}\r
catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
}\r
-\r
}\r
\r
-class Preview extends JFrame\r
+class Preview\r
+ extends JFrame\r
{\r
-\r
public Preview(Image image)\r
{\r
setResizable(true);\r
}\r
}\r
\r
-class PreviewPanel extends JPanel\r
+class PreviewPanel\r
+ extends JPanel\r
{\r
Image image;\r
+\r
public PreviewPanel(Image image)\r
{\r
this.image = image;\r
}\r
+\r
public void paintComponent(Graphics g)\r
{\r
- if(image!=null)\r
- g.drawImage(image,0,0,this);\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, 0, 0, this);\r
+ }\r
else\r
+ {\r
System.out.println("DEBUG:image is null");\r
+ }\r
}\r
}\r
-\r
-\r
-\r
-\r
-\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
import java.awt.image.*;\r
+import javax.swing.*;\r
+\r
import jalview.datamodel.*;\r
-import jalview.io.FormatAdapter;\r
\r
-public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener\r
+public class AnnotationLabels\r
+ extends JPanel implements MouseListener,\r
+ MouseMotionListener, ActionListener\r
{\r
- boolean active = false;\r
- Image image;\r
- AlignmentPanel ap ;\r
- boolean resizing = false;\r
- int oldY, mouseX;\r
static String ADDNEW = "Add New Row";\r
static String HIDE = "Hide This Row";\r
static String DELETE = "Delete This Row";\r
- static String SHOWALL="Show All Hidden Rows";\r
- static String OUTPUT_TEXT="Show Values In Textbox";\r
+ static String SHOWALL = "Show All Hidden Rows";\r
+ static String OUTPUT_TEXT = "Show Values In Textbox";\r
+ boolean active = false;\r
+ Image image;\r
+ AlignmentPanel ap;\r
+ boolean resizing = false;\r
+ int oldY;\r
+ int mouseX;\r
int selectedRow = 0;\r
int scrollOffset = 0;\r
\r
\r
java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
Image temp = null;\r
+\r
if (url != null)\r
+ {\r
temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+ }\r
\r
try\r
{\r
mt.addImage(temp, 0);\r
mt.waitForID(0);\r
}\r
- catch (Exception ex) {}\r
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
- BufferedImage bi = new BufferedImage(temp.getHeight(this), temp.getWidth(this),\r
+ BufferedImage bi = new BufferedImage(temp.getHeight(this),\r
+ temp.getWidth(this),\r
BufferedImage.TYPE_INT_RGB);\r
Graphics2D g = (Graphics2D) bi.getGraphics();\r
g.rotate(Math.toRadians(90));\r
{\r
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
\r
- if(evt.getActionCommand().equals(ADDNEW))\r
+ if (evt.getActionCommand().equals(ADDNEW))\r
{\r
- String label = JOptionPane.showInputDialog(this, "Label for annotation");\r
- if(label==null)\r
+ String label = JOptionPane.showInputDialog(this,\r
+ "Label for annotation");\r
+\r
+ if (label == null)\r
+ {\r
label = "";\r
- ap.av.alignment.addAnnotation(new AlignmentAnnotation\r
- (label,\r
- "New description",\r
- new Annotation[ap.av.alignment.getWidth()]));\r
+ }\r
+\r
+ ap.av.alignment.addAnnotation(new AlignmentAnnotation(label,\r
+ "New description",\r
+ new Annotation[ap.av.alignment.getWidth()]));\r
+ }\r
+ else if (evt.getActionCommand().equals(HIDE))\r
+ {\r
+ aa[selectedRow].visible = false;\r
+\r
+ if (aa[selectedRow].label.equals("Conservation"))\r
+ {\r
+ ap.av.showConservation = false;\r
+ }\r
+\r
+ if (aa[selectedRow].label.equals("Quality"))\r
+ {\r
+ ap.av.showQuality = false;\r
+ }\r
+\r
+ if (aa[selectedRow].label.equals("Consensus"))\r
+ {\r
+ ap.av.showIdentity = false;\r
+ }\r
+ }\r
+ else if (evt.getActionCommand().equals(DELETE))\r
+ {\r
+ ap.av.alignment.deleteAnnotation(aa[selectedRow]);\r
+ }\r
+ else if (evt.getActionCommand().equals(SHOWALL))\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ aa[i].visible = true;\r
+ }\r
+ }\r
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ ap.alignFrame.getTitle() + " - " +\r
+ aa[selectedRow].label, 500,\r
+ 100);\r
+ cap.setText(aa[selectedRow].toString());\r
}\r
- else if(evt.getActionCommand().equals(HIDE))\r
- {\r
- aa[selectedRow].visible = false;\r
- if(aa[selectedRow].label.equals("Conservation"))\r
- ap.av.showConservation = false;\r
- if(aa[selectedRow].label.equals("Quality"))\r
- ap.av.showQuality = false;\r
- if(aa[selectedRow].label.equals("Consensus"))\r
- ap.av.showIdentity = false;\r
- }\r
- else if(evt.getActionCommand().equals(DELETE))\r
- {\r
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);\r
- }\r
- else if(evt.getActionCommand().equals(SHOWALL))\r
- {\r
- for(int i=0; i<aa.length; i++)\r
- aa[i].visible = true;\r
- }\r
- else if(evt.getActionCommand().equals(OUTPUT_TEXT))\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap, ap.alignFrame.getTitle()+" - "+ aa[selectedRow].label, 500, 100);\r
- cap.setText( aa[selectedRow].toString() );\r
- }\r
-\r
- ap.annotationPanel.adjustPanelHeight();\r
- ap.repaint();\r
\r
+ ap.annotationPanel.adjustPanelHeight();\r
+ ap.repaint();\r
}\r
\r
public void mousePressed(MouseEvent evt)\r
{\r
int y = evt.getY() - scrollOffset;\r
\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
- if(aa==null || aa.length==0)\r
- {\r
- JPopupMenu pop = new JPopupMenu("Annotations");\r
- JMenuItem item = new JMenuItem(ADDNEW);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
- return;\r
- }\r
-\r
- int height = 0;\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
-\r
- height += aa[i].height;\r
- if(y<height)\r
- {\r
- selectedRow = i;\r
- break;\r
- }\r
- }\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
\r
+ if ( (aa == null) || (aa.length == 0))\r
+ {\r
JPopupMenu pop = new JPopupMenu("Annotations");\r
JMenuItem item = new JMenuItem(ADDNEW);\r
item.addActionListener(this);\r
pop.add(item);\r
- item = new JMenuItem(HIDE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(DELETE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(SHOWALL);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(OUTPUT_TEXT);\r
- item.addActionListener(this);\r
- pop.add(item);\r
pop.show(this, evt.getX(), evt.getY());\r
\r
+ return;\r
+ }\r
+\r
+ int height = 0;\r
+\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ height += aa[i].height;\r
+\r
+ if (y < height)\r
+ {\r
+ selectedRow = i;\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ JPopupMenu pop = new JPopupMenu("Annotations");\r
+ JMenuItem item = new JMenuItem(ADDNEW);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(HIDE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(DELETE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(SHOWALL);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(OUTPUT_TEXT);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+\r
oldY = evt.getY();\r
}\r
\r
- public void mouseReleased(MouseEvent evt){ active = false; repaint(); }\r
- public void mouseEntered(MouseEvent evt) { active = true; repaint();}\r
- public void mouseExited(MouseEvent evt) { active = false; repaint();}\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ active = false;\r
+ repaint();\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ active = true;\r
+ repaint();\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ active = false;\r
+ repaint();\r
+ }\r
+\r
public void mouseDragged(MouseEvent evt)\r
{\r
active = true;\r
+\r
Dimension d = ap.annotationScroller.getPreferredSize();\r
int dif = evt.getY() - oldY;\r
\r
dif /= ap.av.charHeight;\r
dif *= ap.av.charHeight;\r
\r
- if(d.height-dif>20)\r
+ if ( (d.height - dif) > 20)\r
{\r
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,d.height - dif));\r
+ ap.annotationScroller.setPreferredSize(new Dimension(d.width,\r
+ d.height - dif));\r
d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,d.height - dif));\r
+ ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
+ d.width, d.height - dif));\r
ap.repaint();\r
}\r
+\r
ap.addNotify();\r
}\r
\r
- public void mouseMoved(MouseEvent evt) {}\r
- public void mouseClicked(MouseEvent evt) {}\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
\r
public void paintComponent(Graphics g1)\r
{\r
- Graphics2D g = (Graphics2D)g1;\r
- g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ Graphics2D g = (Graphics2D) g1;\r
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
drawComponent(g);\r
}\r
{\r
FontMetrics fm = g.getFontMetrics(g.getFont());\r
g.setColor(Color.white);\r
- g.fillRect(0,0, getWidth(), getHeight());\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
\r
g.translate(0, scrollOffset);\r
g.setColor(Color.black);\r
\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
- int y = g.getFont().getSize();\r
- int x = 0;\r
-\r
- if(aa!=null)\r
- for(int i=0; i<aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
-\r
- x = getWidth() - fm.stringWidth(aa[i].label)-3;\r
-\r
- if(aa[i].isGraph)\r
- y+=(aa[i].height/3);\r
-\r
- g.drawString(aa[i].label, x, y);\r
-\r
- if(aa[i].isGraph)\r
- y+=(2*aa[i].height/3);\r
- else\r
- y+=aa[i].height;\r
- }\r
-\r
- if (active)\r
- {\r
- if (image != null)\r
- g.drawImage(image, 2, 0, this);\r
- }\r
-\r
- if (aa == null || aa.length<1)\r
- {\r
- g.drawString("Right click", 2, 8);\r
- g.drawString("to add annotation", 2, 18);\r
- }\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
+ int y = g.getFont().getSize();\r
+ int x = 0;\r
\r
+ if (aa != null)\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ x = getWidth() - fm.stringWidth(aa[i].label) - 3;\r
+\r
+ if (aa[i].isGraph)\r
+ {\r
+ y += (aa[i].height / 3);\r
+ }\r
+\r
+ g.drawString(aa[i].label, x, y);\r
+\r
+ if (aa[i].isGraph)\r
+ {\r
+ y += ( (2 * aa[i].height) / 3);\r
+ }\r
+ else\r
+ {\r
+ y += aa[i].height;\r
+ }\r
+ }\r
+ }\r
\r
+ if (active)\r
+ {\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, 2, 0, this);\r
+ }\r
+ }\r
\r
+ if ( (aa == null) || (aa.length < 1))\r
+ {\r
+ g.drawString("Right click", 2, 8);\r
+ g.drawString("to add annotation", 2, 18);\r
+ }\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
\r
-import javax.swing.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
import java.awt.image.*;\r
+import javax.swing.*;\r
\r
-public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- int activeRow =-1;\r
+import jalview.datamodel.*;\r
\r
- ArrayList activeRes;\r
- static String HELIX ="Helix";\r
- static String SHEET ="Sheet";\r
- static String LABEL ="Label";\r
- static String REMOVE="Remove Annotation";\r
- static String COLOUR="Colour";\r
+public class AnnotationPanel\r
+ extends JPanel implements MouseListener,\r
+ MouseMotionListener, ActionListener, AdjustmentListener\r
+{\r
+ static String HELIX = "Helix";\r
+ static String SHEET = "Sheet";\r
+ static String LABEL = "Label";\r
+ static String REMOVE = "Remove Annotation";\r
+ static String COLOUR = "Colour";\r
static Color HELIX_COLOUR = Color.red.darker();\r
static Color SHEET_COLOUR = Color.green.darker().darker();\r
\r
-\r
+ public static int GRAPH_HEIGHT = 40;\r
+ AlignViewport av;\r
+ AlignmentPanel ap;\r
+ int activeRow = -1;\r
+ ArrayList activeRes;\r
BufferedImage image;\r
Graphics2D gg;\r
FontMetrics fm;\r
- int imgWidth=0;\r
-\r
+ int imgWidth = 0;\r
boolean fastPaint = false;\r
\r
- public static int GRAPH_HEIGHT = 40;\r
-\r
-\r
-\r
public AnnotationPanel(AlignmentPanel ap)\r
{\r
this.ap = ap;\r
addMouseMotionListener(this);\r
adjustPanelHeight();\r
\r
-\r
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );\r
+ ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
}\r
\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
- ap.alabels.setScrollOffset( -evt.getValue() );\r
+ ap.alabels.setScrollOffset( -evt.getValue());\r
}\r
\r
public void adjustPanelHeight()\r
// setHeight of panels\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
int height = 0;\r
- if(aa!=null)\r
- for (int i = 0; i < aa.length; i++)\r
+\r
+ if (aa != null)\r
{\r
- if(!aa[i].visible)\r
- continue;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
\r
- aa[i].height = 0;\r
+ aa[i].height = 0;\r
\r
- if(aa[i].hasText)\r
- aa[i].height += av.charHeight;\r
- if (aa[i].hasIcons)\r
- aa[i].height += 16;\r
+ if (aa[i].hasText)\r
+ {\r
+ aa[i].height += av.charHeight;\r
+ }\r
+\r
+ if (aa[i].hasIcons)\r
+ {\r
+ aa[i].height += 16;\r
+ }\r
\r
- if (aa[i].isGraph)\r
- aa[i].height += GRAPH_HEIGHT;\r
+ if (aa[i].isGraph)\r
+ {\r
+ aa[i].height += GRAPH_HEIGHT;\r
+ }\r
\r
- if(aa[i].height==0)\r
- aa[i].height = 20;\r
- height += aa[i].height;\r
+ if (aa[i].height == 0)\r
+ {\r
+ aa[i].height = 20;\r
+ }\r
+\r
+ height += aa[i].height;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ height = 20;\r
}\r
- else height=20;\r
- this.setPreferredSize(new Dimension(1, height));\r
\r
+ this.setPreferredSize(new Dimension(1, height));\r
}\r
\r
public void addEditableColumn(int i)\r
{\r
- if(activeRow==-1)\r
+ if (activeRow == -1)\r
{\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- for(int j=0; j<aa.length; j++)\r
- if(aa[j].editable)\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ for (int j = 0; j < aa.length; j++)\r
+ {\r
+ if (aa[j].editable)\r
{\r
activeRow = j;\r
+\r
break;\r
}\r
+ }\r
}\r
\r
- if(activeRes==null)\r
+ if (activeRes == null)\r
{\r
activeRes = new ArrayList();\r
activeRes.add(String.valueOf(i));\r
+\r
return;\r
}\r
\r
activeRes.add(String.valueOf(i));\r
-\r
}\r
\r
-\r
public void actionPerformed(ActionEvent evt)\r
{\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ Annotation[] anot = aa[activeRow].annotations;\r
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- Annotation [] anot = aa[activeRow].annotations;\r
-\r
- if(evt.getActionCommand().equals(REMOVE))\r
+ if (evt.getActionCommand().equals(REMOVE))\r
{\r
- for(int i=0; i<activeRes.size(); i++)\r
+ for (int i = 0; i < activeRes.size(); i++)\r
{\r
anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
}\r
}\r
- else if(evt.getActionCommand().equals(LABEL))\r
+ else if (evt.getActionCommand().equals(LABEL))\r
{\r
- String label = JOptionPane.showInputDialog(this, "Enter Label ", "Enter label", JOptionPane.QUESTION_MESSAGE );\r
- if(label==null)\r
+ String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
+ "Enter label",\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (label == null)\r
+ {\r
label = "";\r
+ }\r
\r
- if(label.length()>0 && !aa[activeRow].hasText)\r
- aa[activeRow].hasText = true;\r
+ if ( (label.length() > 0) && !aa[activeRow].hasText)\r
+ {\r
+ aa[activeRow].hasText = true;\r
+ }\r
\r
- for(int i=0; i<activeRes.size(); i++)\r
+ for (int i = 0; i < activeRes.size(); i++)\r
{\r
int index = Integer.parseInt(activeRes.get(i).toString());\r
- if(anot[index]==null)\r
- anot[index] = new Annotation(label, "", ' ',0);\r
+\r
+ if (anot[index] == null)\r
+ {\r
+ anot[index] = new Annotation(label, "", ' ', 0);\r
+ }\r
+\r
anot[index].displayCharacter = label;\r
}\r
}\r
- else if(evt.getActionCommand().equals(COLOUR))\r
+ else if (evt.getActionCommand().equals(COLOUR))\r
{\r
- Color col = JColorChooser.showDialog(this, "Choose foreground colour", Color.black);\r
- for (int i = 0; i < activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
- if (anot[index] == null)\r
- anot[index] = new Annotation("", "", ' ', 0);\r
- anot[index].colour = col;\r
- }\r
+ Color col = JColorChooser.showDialog(this,\r
+ "Choose foreground colour",\r
+ Color.black);\r
+\r
+ for (int i = 0; i < activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\r
+\r
+ if (anot[index] == null)\r
+ {\r
+ anot[index] = new Annotation("", "", ' ', 0);\r
+ }\r
+\r
+ anot[index].colour = col;\r
+ }\r
}\r
else // HELIX OR SHEET\r
{\r
- char type = 0;\r
- String symbol = "\u03B1";\r
- if(evt.getActionCommand().equals(HELIX))\r
- type = 'H';\r
- else if(evt.getActionCommand().equals(SHEET))\r
- {\r
- type = 'E';\r
- symbol = "\u03B2";\r
- }\r
+ char type = 0;\r
+ String symbol = "\u03B1";\r
\r
- if(!aa[activeRow].hasIcons)\r
- aa[activeRow].hasIcons = true;\r
+ if (evt.getActionCommand().equals(HELIX))\r
+ {\r
+ type = 'H';\r
+ }\r
+ else if (evt.getActionCommand().equals(SHEET))\r
+ {\r
+ type = 'E';\r
+ symbol = "\u03B2";\r
+ }\r
\r
+ if (!aa[activeRow].hasIcons)\r
+ {\r
+ aa[activeRow].hasIcons = true;\r
+ }\r
\r
- String label = JOptionPane.showInputDialog("Enter a label for the structure?", symbol );\r
- if(label==null)\r
- label="";\r
+ String label = JOptionPane.showInputDialog(\r
+ "Enter a label for the structure?",\r
+ symbol);\r
\r
- if(label.length()>0 && !aa[activeRow].hasText)\r
- aa[activeRow].hasText = true;\r
+ if (label == null)\r
+ {\r
+ label = "";\r
+ }\r
\r
- for(int i=0; i<activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
- if (anot[index] == null)\r
+ if ( (label.length() > 0) && !aa[activeRow].hasText)\r
{\r
- anot[index] = new Annotation(label, "", type, 0);\r
+ aa[activeRow].hasText = true;\r
}\r
\r
- anot[ index ].secondaryStructure = type;\r
- anot[ index ].displayCharacter = label;\r
- }\r
+ for (int i = 0; i < activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\r
+\r
+ if (anot[index] == null)\r
+ {\r
+ anot[index] = new Annotation(label, "", type, 0);\r
+ }\r
+\r
+ anot[index].secondaryStructure = type;\r
+ anot[index].displayCharacter = label;\r
+ }\r
}\r
\r
adjustPanelHeight();\r
activeRes = null;\r
repaint();\r
- return;\r
-\r
\r
+ return;\r
}\r
\r
public void mousePressed(MouseEvent evt)\r
{\r
if (SwingUtilities.isRightMouseButton(evt))\r
{\r
- if(activeRes==null)\r
+ if (activeRes == null)\r
+ {\r
return;\r
+ }\r
\r
JPopupMenu pop = new JPopupMenu("Structure type");\r
JMenuItem item = new JMenuItem(HELIX);\r
item.addActionListener(this);\r
pop.add(item);\r
pop.show(this, evt.getX(), evt.getY());\r
+\r
return;\r
}\r
\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
+ if (aa == null)\r
+ {\r
return;\r
+ }\r
\r
int height = 0;\r
activeRow = -1;\r
- for(int i=0; i<aa.length; i++)\r
+\r
+ for (int i = 0; i < aa.length; i++)\r
{\r
- height+= aa[i].height;\r
+ height += aa[i].height;\r
\r
- if(evt.getY()<height)\r
+ if (evt.getY() < height)\r
{\r
- if(!aa[i].editable)\r
+ if (!aa[i].editable)\r
{\r
activeRes = null;\r
+\r
continue;\r
}\r
\r
activeRow = i;\r
+\r
break;\r
}\r
}\r
\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
-\r
- if(evt.isControlDown() || evt.isAltDown())\r
+ if (evt.isControlDown() || evt.isAltDown())\r
+ {\r
addEditableColumn(res);\r
-\r
- else if(evt.isShiftDown())\r
+ }\r
+ else if (evt.isShiftDown())\r
{\r
-\r
- if(activeRes==null)\r
- activeRes=new ArrayList();\r
+ if (activeRes == null)\r
+ {\r
+ activeRes = new ArrayList();\r
+ }\r
else\r
{\r
- int start = Integer.parseInt( activeRes.get( activeRes.size()-1 ).toString() );\r
- int end = res;\r
- if(end<start)\r
- {\r
- int temp = end;\r
- end = start;\r
- start = temp;\r
- }\r
- for(int n=start; n<=end; n++)\r
- addEditableColumn(n);\r
+ int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
+ 1).toString());\r
+ int end = res;\r
\r
+ if (end < start)\r
+ {\r
+ int temp = end;\r
+ end = start;\r
+ start = temp;\r
+ }\r
+\r
+ for (int n = start; n <= end; n++)\r
+ {\r
+ addEditableColumn(n);\r
+ }\r
}\r
}\r
else\r
{\r
- activeRes = new ArrayList();\r
- activeRes.add( String.valueOf(res) );\r
+ activeRes = new ArrayList();\r
+ activeRes.add(String.valueOf(res));\r
}\r
\r
repaint();\r
-\r
}\r
+\r
public void mouseReleased(MouseEvent evt)\r
- { }\r
+ {\r
+ }\r
+\r
public void mouseEntered(MouseEvent evt)\r
- { }\r
+ {\r
+ }\r
+\r
public void mouseExited(MouseEvent evt)\r
- { }\r
+ {\r
+ }\r
+\r
public void mouseDragged(MouseEvent evt)\r
- { }\r
+ {\r
+ }\r
+\r
public void mouseMoved(MouseEvent evt)\r
{\r
ToolTipManager.sharedInstance().registerComponent(this);\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
+\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ if (aa == null)\r
+ {\r
return;\r
+ }\r
\r
int row = -1;\r
- int height=0;\r
- for(int i=0; i<aa.length; i++)\r
- {\r
+ int height = 0;\r
\r
- if( aa[i].visible )\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (aa[i].visible)\r
+ {\r
height += aa[i].height;\r
+ }\r
\r
- if(evt.getY()<height)\r
+ if (evt.getY() < height)\r
{\r
row = i;\r
+\r
break;\r
}\r
}\r
\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+\r
+ if ( (row > -1) && (res < aa[row].annotations.length) &&\r
+ (aa[row].annotations[res] != null))\r
{\r
this.setToolTipText(aa[row].annotations[res].description);\r
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +\r
- " " +\r
+\r
+ StringBuffer text = new StringBuffer("Sequence position " +\r
+ (res + 1) + " " +\r
aa[row].annotations[res].description);\r
ap.alignFrame.statusBar.setText(text.toString());\r
}\r
-\r
-\r
}\r
- public void mouseClicked(MouseEvent evt) {}\r
\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
\r
public void paintComponent(Graphics g)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(), getHeight());\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
\r
- if(fastPaint)\r
+ if (fastPaint)\r
{\r
g.drawImage(image, 0, 0, this);\r
fastPaint = false;\r
+\r
return;\r
}\r
\r
- imgWidth = (av.endRes-av.startRes+1) *av.charWidth;\r
+ imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
\r
- image = new BufferedImage(imgWidth,\r
- ap.annotationPanel.getHeight(),\r
- BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) image.getGraphics();\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
+ image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
+ BufferedImage.TYPE_INT_RGB);\r
+ gg = (Graphics2D) image.getGraphics();\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
- gg.setFont(av.getFont());\r
- fm = gg.getFontMetrics();\r
-\r
- drawComponent( gg, av.startRes, av.endRes+1);\r
- g.drawImage( image, 0, 0, this);\r
+ gg.setFont(av.getFont());\r
+ fm = gg.getFontMetrics();\r
\r
+ drawComponent(gg, av.startRes, av.endRes + 1);\r
+ g.drawImage(image, 0, 0, this);\r
}\r
\r
public void fastPaint(int horizontal)\r
-{\r
- if( horizontal == 0\r
- || av.alignment.getAlignmentAnnotation()==null\r
- || av.alignment.getAlignmentAnnotation().length<1\r
- )\r
{\r
- repaint();\r
- return;\r
- }\r
+ if ( (horizontal == 0) ||\r
+ (av.alignment.getAlignmentAnnotation() == null) ||\r
+ (av.alignment.getAlignmentAnnotation().length < 1))\r
+ {\r
+ repaint();\r
\r
- gg.copyArea( 0,0, imgWidth, getHeight(), -horizontal*av.charWidth, 0 );\r
- int sr=av.startRes, er=av.endRes+1, transX=0;\r
+ return;\r
+ }\r
\r
- if(horizontal>0) // scrollbar pulled right, image to the left\r
- {\r
- transX = (er-sr-horizontal)*av.charWidth;\r
- sr = er - horizontal ;\r
- }\r
- else if(horizontal<0)\r
- {\r
- er = sr-horizontal;\r
- }\r
+ gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
\r
+ int sr = av.startRes;\r
+ int er = av.endRes + 1;\r
+ int transX = 0;\r
\r
- gg.translate(transX, 0);\r
+ if (horizontal > 0) // scrollbar pulled right, image to the left\r
+ {\r
+ transX = (er - sr - horizontal) * av.charWidth;\r
+ sr = er - horizontal;\r
+ }\r
+ else if (horizontal < 0)\r
+ {\r
+ er = sr - horizontal;\r
+ }\r
\r
- drawComponent(gg, sr, er);\r
+ gg.translate(transX, 0);\r
\r
- gg.translate( -transX, 0 );\r
+ drawComponent(gg, sr, er);\r
\r
- fastPaint = true;\r
- repaint();\r
-}\r
+ gg.translate( -transX, 0);\r
\r
+ fastPaint = true;\r
+ repaint();\r
+ }\r
\r
public void drawComponent(Graphics2D g, int startRes, int endRes)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,(endRes-startRes) *av.charWidth, getHeight());\r
- if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
+\r
+ if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
+ (av.alignment.getAlignmentAnnotation().length < 1))\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(), getHeight());\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations",20,15);\r
+ g.drawString("Alignment has no annotations", 20, 15);\r
+\r
return;\r
}\r
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- int j, x=0, y=0;\r
- char [] lastSS = new char[aa.length];\r
- int [] lastSSX= new int[aa.length] ;\r
- int iconOffset = av.charHeight/2;\r
+ int j;\r
+ int x = 0;\r
+ int y = 0;\r
+ char[] lastSS = new char[aa.length];\r
+ int[] lastSSX = new int[aa.length];\r
+ int iconOffset = av.charHeight / 2;\r
boolean validRes = false;\r
- //\u03B2 \u03B1\r
\r
- for(int i=0; i<aa.length; i++)\r
+ //\u03B2 \u03B1\r
+ for (int i = 0; i < aa.length; i++)\r
{\r
AlignmentAnnotation row = aa[i];\r
- if(!row.visible)\r
+\r
+ if (!row.visible)\r
+ {\r
continue;\r
+ }\r
\r
- if(row.isGraph)\r
+ if (row.isGraph)\r
{\r
// this is so that we draw the characters below the graph\r
y += row.height;\r
- if(row.hasText)\r
+\r
+ if (row.hasText)\r
+ {\r
y -= av.charHeight;\r
+ }\r
+ }\r
+\r
+ if (row.hasText)\r
+ {\r
+ iconOffset = av.charHeight / 2;\r
}\r
- if(row.hasText)\r
- iconOffset = av.charHeight/2;\r
else\r
+ {\r
iconOffset = 0;\r
+ }\r
\r
- for(j=startRes; j<endRes; j++)\r
+ for (j = startRes; j < endRes; j++)\r
{\r
- if(row.annotations.length<=j || row.annotations[j]==null)\r
- validRes = false;\r
- else\r
- validRes = true;\r
-\r
- x = (j-startRes)*av.charWidth;\r
+ if ( (row.annotations.length <= j) ||\r
+ (row.annotations[j] == null))\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
\r
+ x = (j - startRes) * av.charWidth;\r
\r
- if(activeRow==i)\r
- {\r
+ if (activeRow == i)\r
+ {\r
+ g.setColor(Color.red);\r
\r
- g.setColor(Color.red);\r
+ if (activeRes != null)\r
+ {\r
+ for (int n = 0; n < activeRes.size(); n++)\r
+ {\r
+ int v = Integer.parseInt(activeRes.get(n).toString());\r
+\r
+ if (v == j)\r
+ {\r
+ g.fillRect( (j - startRes) * av.charWidth, y,\r
+ av.charWidth, row.height);\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- if(activeRes!=null)\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.get(n).toString()) ;\r
- if (v == j)\r
- g.fillRect( (j-startRes) * av.charWidth, y, av.charWidth, row.height);\r
- }\r
- }\r
+ if (validRes &&\r
+ (row.annotations[j].displayCharacter.length() > 0))\r
+ {\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[j].displayCharacter.\r
+ charAt(\r
+ 0))) / 2;\r
+ g.setColor(row.annotations[j].colour);\r
\r
+ if (j == 0)\r
+ {\r
+ if ( (row.annotations[0].secondaryStructure == 'H') ||\r
+ (row.annotations[0].secondaryStructure == 'E'))\r
+ {\r
+ g.drawString(row.annotations[j].displayCharacter,\r
+ x, y + iconOffset + 2);\r
+ }\r
+ }\r
+ else if ( ( (row.annotations[j].secondaryStructure == 'H') ||\r
+ (row.annotations[j].secondaryStructure == 'E')) &&\r
+ ( (row.annotations[j - 1] == null) ||\r
+ (row.annotations[j].secondaryStructure != row.annotations[j -\r
+ 1].secondaryStructure)))\r
+ {\r
+ g.drawString(row.annotations[j].displayCharacter, x,\r
+ y + iconOffset + 2);\r
+ }\r
\r
+ if (!row.hasIcons)\r
+ {\r
+ g.drawString(row.annotations[j].displayCharacter,\r
+ x + charOffset, y + iconOffset + 2);\r
+ }\r
+ }\r
\r
- if(validRes && row.annotations[j].displayCharacter.length()>0)\r
- {\r
- int charOffset = (av.charWidth - fm.charWidth(row.annotations[j].displayCharacter.charAt(0)))/2;\r
- g.setColor( row.annotations[j].colour);\r
- if(j==0)\r
+ if (row.hasIcons)\r
+ {\r
+ if (!validRes ||\r
+ (row.annotations[j].secondaryStructure != lastSS[i]))\r
{\r
- if (row.annotations[0].secondaryStructure == 'H'\r
- || row.annotations[0].secondaryStructure == 'E')\r
- g.drawString(row.annotations[j].displayCharacter, x,\r
- y + iconOffset + 2);\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i], 7, 8, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ {x - 4, x - 4, x},\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 8 + iconOffset\r
+ }, 3);\r
+\r
+ break;\r
+\r
+ case 'C':\r
+ break;\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
+ x - lastSSX[i], 2);\r
+\r
+ break;\r
+ }\r
+\r
+ if (validRes)\r
+ {\r
+ lastSS[i] = row.annotations[j].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS[i] = ' ';\r
+ }\r
+\r
+ lastSSX[i] = x;\r
}\r
- else if( (row.annotations[j].secondaryStructure=='H'\r
- || row.annotations[j].secondaryStructure=='E') &&\r
- (row.annotations[j-1]==null ||\r
- row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))\r
+ }\r
\r
- g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
+ if (validRes && row.isGraph)\r
+ {\r
+ g.setColor(new Color(0, 0, 180));\r
\r
- if(!row.hasIcons)\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 2);\r
- }\r
-\r
- if(row.hasIcons)\r
- if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
- g.fillPolygon(new int[] {x - 4, x- 4, x }\r
- , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
- break;\r
- case 'C':\r
- break;\r
- default :\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
- }\r
-\r
- if(validRes)\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
- else\r
- lastSS[i] = ' ';\r
- lastSSX[i] = x;\r
- }\r
-\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0,0,180));\r
- int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);\r
-\r
- if(row.windowLength>1)\r
- {\r
- int total =0;\r
- for(int i2=j- (row.windowLength/2); i2<j+(row.windowLength/2); i2++)\r
- {\r
- if(i2<0 || i2>=av.alignment.getWidth())\r
- continue;\r
-\r
- total += row.annotations[i2].value;\r
- }\r
-\r
- total/=row.windowLength;\r
- height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
-\r
- }\r
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y-height, av.charWidth, height );\r
- }\r
+ int height = (int) ( (row.annotations[j].value / row.graphMax) *\r
+ GRAPH_HEIGHT);\r
+\r
+ if (row.windowLength > 1)\r
+ {\r
+ int total = 0;\r
\r
+ for (int i2 = j - (row.windowLength / 2);\r
+ i2 < (j + (row.windowLength / 2)); i2++)\r
+ {\r
+ if ( (i2 < 0) || (i2 >= av.alignment.getWidth()))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ total += row.annotations[i2].value;\r
+ }\r
+\r
+ total /= row.windowLength;\r
+ height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);\r
+ }\r
\r
+ g.setColor(row.annotations[j].colour);\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ }\r
}\r
\r
- x+=av.charWidth;\r
+ x += av.charWidth;\r
\r
- if(row.hasIcons)\r
- switch (lastSS[i])\r
+ if (row.hasIcons)\r
{\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4+ iconOffset, x - lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4+ iconOffset, x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x}\r
- , new int[]\r
- {y + iconOffset, y + 14+ iconOffset, y + 7+ iconOffset}\r
- , 3);\r
- break;\r
- case 'C':\r
- break;\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i], 7, 8, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ {x - 4, x - 4, x},\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 7 + iconOffset\r
+ }, 3);\r
+\r
+ break;\r
+\r
+ case 'C':\r
+ break;\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
+\r
+ break;\r
+ }\r
+ }\r
\r
+ if (row.isGraph && row.hasText)\r
+ {\r
+ y += av.charHeight;\r
}\r
\r
- if(row.isGraph && row.hasText)\r
- y+=av.charHeight;\r
- if(!row.isGraph)\r
- y+=aa[i].height;\r
+ if (!row.isGraph)\r
+ {\r
+ y += aa[i].height;\r
+ }\r
}\r
}\r
\r
// used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\r
+ public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,width, y);\r
- g.setColor(new Color(0,0,180));\r
+ g.fillRect(0, 0, width, y);\r
+ g.setColor(new Color(0, 0, 180));\r
+\r
int x = 0;\r
- for(int j=0; j<aa.annotations.length; j++)\r
+\r
+ for (int j = 0; j < aa.annotations.length; j++)\r
{\r
g.setColor(new Color(0, 0, 180));\r
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );\r
+\r
+ int height = (int) ( (aa.annotations[j].value / aa.graphMax) *\r
+ GRAPH_HEIGHT);\r
g.fillRect(x, y - height, av.charWidth, height);\r
- x+=av.charWidth;\r
+ x += av.charWidth;\r
}\r
}\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
import java.util.*;\r
/**\r
* NOTE: Columns are zero based.\r
*/\r
-public class ColumnSelection{\r
+public class ColumnSelection\r
+{\r
Vector selected = new Vector();\r
\r
- public void addElement(int col) {\r
+ public void addElement(int col)\r
+ {\r
selected.addElement(new Integer(col));\r
}\r
\r
- public void clear() {\r
+ public void clear()\r
+ {\r
selected.removeAllElements();\r
}\r
\r
- public void removeElement(int col) {\r
+ public void removeElement(int col)\r
+ {\r
Integer colInt = new Integer(col);\r
- if (selected.contains(colInt)) {\r
+\r
+ if (selected.contains(colInt))\r
+ {\r
selected.removeElement(colInt);\r
- } else {\r
- System.err.println("WARNING: Tried to remove Integer NOT in ColumnSelection");\r
+ }\r
+ else\r
+ {\r
+ System.err.println(\r
+ "WARNING: Tried to remove Integer NOT in ColumnSelection");\r
}\r
}\r
\r
- public boolean contains(int col) {\r
+ public boolean contains(int col)\r
+ {\r
return selected.contains(new Integer(col));\r
}\r
\r
- public int columnAt(int i) {\r
- return ((Integer)selected.elementAt(i)).intValue();\r
+ public int columnAt(int i)\r
+ {\r
+ return ( (Integer) selected.elementAt(i)).intValue();\r
}\r
\r
- public int size() {\r
+ public int size()\r
+ {\r
return selected.size();\r
}\r
\r
- public int getMax() {\r
+ public int getMax()\r
+ {\r
int max = -1;\r
\r
- for (int i=0;i<selected.size();i++) {\r
- if (columnAt(i) > max) {\r
+ for (int i = 0; i < selected.size(); i++)\r
+ {\r
+ if (columnAt(i) > max)\r
+ {\r
max = columnAt(i);\r
}\r
}\r
+\r
return max;\r
}\r
\r
- public int getMin() {\r
+ public int getMin()\r
+ {\r
int min = 1000000000;\r
\r
- for (int i=0;i<selected.size();i++) {\r
- if (columnAt(i) < min) {\r
+ for (int i = 0; i < selected.size(); i++)\r
+ {\r
+ if (columnAt(i) < min)\r
+ {\r
min = columnAt(i);\r
}\r
}\r
+\r
return min;\r
}\r
\r
- public Vector asVector() {\r
+ public Vector asVector()\r
+ {\r
return selected;\r
}\r
\r
- public void compensateForEdit(int start, int change) {\r
- for (int i=0; i < size();i++) {\r
+ public void compensateForEdit(int start, int change)\r
+ {\r
+ for (int i = 0; i < size(); i++)\r
+ {\r
int temp = columnAt(i);\r
\r
if (temp >= start)\r
- selected.setElementAt(new Integer(temp-change),i);\r
+ {\r
+ selected.setElementAt(new Integer(temp - change), i);\r
+ }\r
}\r
}\r
}\r
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.gui;
-
-import jalview.jbgui.GCutAndPasteTransfer;
-import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.datatransfer.*;
-import jalview.datamodel.Alignment;
-import jalview.io.FormatAdapter;
-import jalview.datamodel.SequenceI;
-import javax.swing.JOptionPane;
-import jalview.io.IdentifyFile;
-
-public class CutAndPasteTransfer extends GCutAndPasteTransfer
-{
- public void setForInput()
- {
- getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
- }
-
- public String getText()
- {
- return textarea.getText();
- }
-
- public void setText(String text)
- {
- textarea.setText(text);
- }
-
- public void copyItem_actionPerformed(ActionEvent e)
- {
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- c.setContents( new StringSelection( textarea.getText()) , null ) ;
- }
-
- public void pasteMenu_actionPerformed(ActionEvent e)
- {
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- Transferable contents = c.getContents(this);
- if (contents == null)
- return;
- try{
- textarea.setText( (String) contents.getTransferData(DataFlavor.
- stringFlavor));
- }catch(Exception ex){}
- }
-
- public void ok_actionPerformed(ActionEvent e)
- {
- String format = IdentifyFile.Identify(getText(), "Paste");
- SequenceI [] sequences = null;
-
- if (FormatAdapter.formats.contains( format ))
- sequences = FormatAdapter.readFile(getText(), "Paste", format);
-
-
- if(sequences!=null)
- {
- AlignFrame af = new AlignFrame(new Alignment(sequences));
- af.currentFileFormat = format;
- Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
- AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
- try
- { af.setMaximum(Preferences.showFullscreen); }
- catch (Exception ex)
- {}
- try
- {
- this.setClosed(true);
- }
- catch (Exception ex)
- {}
-
-
- }
- else
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't read the pasted text.\n"
- + "Formats currently supported are\n"
- +
- "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",
- "Error parsing text",
- JOptionPane.WARNING_MESSAGE);
- }
-
- public void cancel_actionPerformed(ActionEvent e)
- {
- try{
- this.setClosed(true);
- }catch(Exception ex){}
- }
-
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.gui;\r
+\r
+import java.awt.*;\r
+import java.awt.datatransfer.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
+\r
+public class CutAndPasteTransfer\r
+ extends GCutAndPasteTransfer\r
+{\r
+ public void setForInput()\r
+ {\r
+ getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);\r
+ }\r
+\r
+ public String getText()\r
+ {\r
+ return textarea.getText();\r
+ }\r
+\r
+ public void setText(String text)\r
+ {\r
+ textarea.setText(text);\r
+ }\r
+\r
+ public void copyItem_actionPerformed(ActionEvent e)\r
+ {\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ c.setContents(new StringSelection(textarea.getText()), null);\r
+ }\r
+\r
+ public void pasteMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+\r
+ if (contents == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ textarea.setText( (String) contents.getTransferData(\r
+ DataFlavor.stringFlavor));\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ public void ok_actionPerformed(ActionEvent e)\r
+ {\r
+ String format = IdentifyFile.Identify(getText(), "Paste");\r
+ SequenceI[] sequences = null;\r
+\r
+ if (FormatAdapter.formats.contains(format))\r
+ {\r
+ sequences = FormatAdapter.readFile(getText(), "Paste", format);\r
+ }\r
+\r
+ if (sequences != null)\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+ af.currentFileFormat = format;\r
+ Desktop.addInternalFrame(af, "Cut & Paste input - " + format,\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.statusBar.setText("Successfully pasted alignment file");\r
+\r
+ try\r
+ {\r
+ af.setMaximum(Preferences.showFullscreen);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ else\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't read the pasted text.\n" +\r
+ "Formats currently supported are\n" +\r
+ "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",\r
+ "Error parsing text",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ }\r
+\r
+ public void cancel_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.gui.*;\r
-import jalview.io.*;\r
-import jalview.datamodel.*;\r
-import javax.swing.*;\r
import java.awt.*;\r
-import java.awt.event.*;\r
+import java.awt.datatransfer.*;\r
import java.awt.dnd.*;\r
+import java.awt.event.*;\r
import javax.swing.*;\r
-import java.awt.datatransfer.*;\r
-import jalview.bin.Cache;\r
\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
\r
-public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener\r
+public class Desktop\r
+ extends jalview.jbgui.GDesktop implements DropTargetListener\r
{\r
public static JDesktopPane desktop;\r
static int openFrameCount = 0;\r
- static final int xOffset = 30, yOffset = 30;\r
+ static final int xOffset = 30;\r
+ static final int yOffset = 30;\r
\r
public Desktop()\r
{\r
- Image image =null;\r
- try{\r
+ Image image = null;\r
+\r
+ try\r
+ {\r
java.net.URL url = getClass().getResource("/images/logo.gif");\r
- if(url!=null)\r
+\r
+ if (url != null)\r
{\r
image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+\r
MediaTracker mt = new MediaTracker(this);\r
mt.addImage(image, 0);\r
mt.waitForID(0);\r
setIconImage(image);\r
}\r
-\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
setTitle("Jalview 2005");\r
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
setContentPane(desktop);\r
desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
\r
-\r
// This line prevents Windows Look&Feel resizing all new windows to maximum\r
// if previous window was maximised\r
- desktop.setDesktopManager( new DefaultDesktopManager() );\r
-\r
+ desktop.setDesktopManager(new DefaultDesktopManager());\r
\r
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
\r
- if(x!=null && y!=null && width!=null && height!=null)\r
+ if ( (x != null) && (y != null) && (width != null) && (height != null))\r
{\r
- setBounds( Integer.parseInt(x), Integer.parseInt(y),\r
- Integer.parseInt(width), Integer.parseInt(height));\r
+ setBounds(Integer.parseInt(x), Integer.parseInt(y),\r
+ Integer.parseInt(width), Integer.parseInt(height));\r
}\r
else\r
- setBounds( (int)(screenSize.width-900)/2,\r
- (int)(screenSize.height-650)/2,\r
- 900 ,\r
- 650);\r
+ {\r
+ setBounds( (int) (screenSize.width - 900) / 2,\r
+ (int) (screenSize.height - 650) / 2, 900, 650);\r
+ }\r
\r
-this.addWindowListener(new WindowAdapter()\r
-{\r
-public void windowClosing(WindowEvent evt)\r
-{\r
- jalview.bin.Cache.setProperty("SCREEN_X",\r
- getBounds().x + "");\r
- jalview.bin.Cache.setProperty("SCREEN_Y",\r
- getBounds().y + "");\r
- jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
-}\r
-});\r
-setVisible(true);\r
+ this.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x +\r
+ "");\r
+ jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y +\r
+ "");\r
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH",\r
+ getWidth() + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT",\r
+ getHeight() + "");\r
+ }\r
+ });\r
+ setVisible(true);\r
\r
-this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
\r
-/////////Add a splashscreen on startup\r
- /////////Add a splashscreen on startup\r
+ /////////Add a splashscreen on startup\r
+ /////////Add a splashscreen on startup\r
JInternalFrame frame = new JInternalFrame();\r
\r
SplashScreen splash = new SplashScreen(frame, image);\r
frame.setContentPane(splash);\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- addInternalFrame(frame, "", 750,160, false);\r
- frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));\r
+ addInternalFrame(frame, "", 750, 160, false);\r
+ frame.setLocation( (int) ( (getWidth() - 750) / 2),\r
+ (int) ( (getHeight() - 160) / 2));\r
}\r
- public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
+\r
+ public static void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h)\r
{\r
addInternalFrame(frame, title, w, h, true);\r
}\r
\r
- public static void addInternalFrame(final JInternalFrame frame, String title,\r
- int w,\r
- int h,\r
- boolean resizable )\r
+ public static void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h,\r
+ boolean resizable)\r
{\r
- desktop.add(frame);\r
- openFrameCount++;\r
- try {\r
- frame.setSelected(true);\r
- } catch (java.beans.PropertyVetoException e) {}\r
- frame.setTitle(title);\r
- frame.setSize(w,h);\r
- frame.setClosable(true);\r
- frame.setResizable(resizable);\r
- frame.setMaximizable(resizable);\r
- frame.setIconifiable(resizable);\r
- frame.setFrameIcon(null);\r
- frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
- frame.toFront();\r
- final JMenuItem menuItem = new JMenuItem(title);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- openFrameCount--;\r
- windowMenu.remove(menuItem);\r
- };\r
- });\r
-\r
- menuItem.addActionListener(new ActionListener()\r
+ desktop.add(frame);\r
+ openFrameCount++;\r
+\r
+ try\r
+ {\r
+ frame.setSelected(true);\r
+ }\r
+ catch (java.beans.PropertyVetoException e)\r
+ {\r
+ }\r
+\r
+ frame.setTitle(title);\r
+ frame.setSize(w, h);\r
+ frame.setClosable(true);\r
+ frame.setResizable(resizable);\r
+ frame.setMaximizable(resizable);\r
+ frame.setIconifiable(resizable);\r
+ frame.setFrameIcon(null);\r
+ frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);\r
+ frame.toFront();\r
+\r
+ final JMenuItem menuItem = new JMenuItem(title);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ openFrameCount--;\r
+ windowMenu.remove(menuItem);\r
+ }\r
+ ;\r
+ });\r
+\r
+ menuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- try{ frame.setSelected(true); frame.setIcon(false); }\r
- catch(java.beans.PropertyVetoException ex){};\r
+ try\r
+ {\r
+ frame.setSelected(true);\r
+ frame.setIcon(false);\r
+ }\r
+ catch (java.beans.PropertyVetoException ex)\r
+ {\r
+ }\r
+\r
+ ;\r
}\r
});\r
\r
- frame.setVisible(true);\r
- windowMenu.add(menuItem);\r
- }\r
+ frame.setVisible(true);\r
+ windowMenu.add(menuItem);\r
+ }\r
\r
- public void dragEnter(DropTargetDragEvent evt){}\r
- public void dragExit(DropTargetEvent evt){}\r
- public void dragOver(DropTargetDragEvent evt){}\r
- public void dropActionChanged(DropTargetDragEvent evt){}\r
- public void drop(DropTargetDropEvent evt)\r
-{\r
- Transferable t = evt.getTransferable();\r
- if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
- return;\r
-\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
- try{\r
- java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
-\r
- for (int i = 0; i < files.size(); i++)\r
- {\r
- String file = files.get(i).toString();\r
- String protocol = "File";\r
- if(file.endsWith(".jar"))\r
- Jalview2XML.LoadJalviewAlign(file);\r
+ public void dragEnter(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ public void dragExit(DropTargetEvent evt)\r
+ {\r
+ }\r
+\r
+ public void dragOver(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ public void dropActionChanged(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ public void drop(DropTargetDropEvent evt)\r
+ {\r
+ Transferable t = evt.getTransferable();\r
+\r
+ if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ {\r
+ return;\r
+ }\r
+\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+\r
+ try\r
+ {\r
+ java.util.List files = (java.util.List) t.getTransferData(DataFlavor.\r
+ javaFileListFlavor);\r
+\r
+ for (int i = 0; i < files.size(); i++)\r
+ {\r
+ String file = files.get(i).toString();\r
+ String protocol = "File";\r
+\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ Jalview2XML.LoadJalviewAlign(file);\r
+ }\r
+ else\r
+ {\r
+ String format = jalview.io.IdentifyFile.Identify(file,\r
+ protocol);\r
+ LoadFile(file, protocol, format);\r
+ }\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Open local file");\r
+ chooser.setToolTipText("Open");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ if (chooser.getSelectedFormat().equals("Jalview"))\r
+ {\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");\r
+ Jalview2XML.LoadJalviewAlign(choice);\r
+ }\r
else\r
{\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
- LoadFile(file, protocol, format);\r
+ String format = IdentifyFile.Identify(choice, "File");\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
+ LoadFile(choice, "File", format);\r
}\r
- }\r
+ }\r
+ }\r
\r
- }catch(Exception ex){ex.printStackTrace();}\r
+ public void LoadFile(String file, String protocol, String format)\r
+ {\r
+ LoadingThread loader = new LoadingThread(file, protocol, format);\r
+ loader.start();\r
}\r
\r
+ public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ String url = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter url of input file", "Input alignment from URL",\r
+ JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")\r
+ .toString();\r
+\r
+ if (url == null)\r
+ {\r
+ return;\r
+ }\r
\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}\r
- ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- if(chooser.getSelectedFormat().equals("Jalview"))\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");\r
- Jalview2XML.LoadJalviewAlign(choice);\r
- }\r
- else\r
- {\r
- String format = IdentifyFile.Identify(choice, "File");\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
- LoadFile(choice, "File", format);\r
- }\r
- }\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
- loader.start();\r
- }\r
-\r
- class LoadingThread extends Thread\r
- {\r
- String file, protocol, format;\r
-\r
- public LoadingThread(String file, String protocol, String format)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- }\r
- public void run()\r
- {\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatAdapter.formats.contains(format))\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
-\r
- if (sequences != null && sequences.length>0)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.currentFileFormat = format;\r
- af.statusBar.setText("Successfully loaded file " + file);\r
- try{\r
- af.setMaximum(Preferences.showFullscreen);\r
- }catch(Exception ex){}\r
-\r
- }\r
- else\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n"\r
- + "Formats currently supported are\n"\r
- + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
- ,"Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
- }\r
-\r
-\r
- public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
- "Input alignment from URL",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, null,\r
- "http://www.").toString();\r
- if (url == null)\r
- return;\r
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
-\r
- if (format.equals("URL NOT FOUND"))\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
+ String format = IdentifyFile.Identify(url, "URL");\r
+\r
+ if (format.equals("URL NOT FOUND"))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't locate " + url,\r
+ "URL not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
\r
LoadFile(url, "URL", format);\r
- }\r
+ }\r
\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput();\r
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
- }\r
+ public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput();\r
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
+ }\r
\r
-/*\r
-* Exit the program\r
-*/\r
- public void quit_actionPerformed(ActionEvent e)\r
- {\r
- if(jalview.bin.Jalview.applet!=null)\r
- jalview.bin.Jalview.applet.destroy();\r
+ /*\r
+ * Exit the program\r
+ */\r
+ public void quit_actionPerformed(ActionEvent e)\r
+ {\r
+ if (jalview.bin.Jalview.applet != null)\r
+ {\r
+ jalview.bin.Jalview.applet.destroy();\r
+ }\r
else\r
+ {\r
System.exit(0);\r
- }\r
-\r
-\r
-\r
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE\r
- +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
- +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
- +"\nFor all issues relating to Jalview, email help@jalview.org"\r
- +"\n\nIf you use JalView, please cite:"\r
- +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""\r
- +"\nBioinformatics, 2004 12;426-7.",\r
- "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
+ }\r
+ }\r
+\r
+ public void aboutMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "JalView 2005 version " +\r
+ jalview.bin.Cache.VERSION +\r
+ "; last updated: " +\r
+ jalview.bin.Cache.BUILD_DATE +\r
+ "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +\r
+ "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +\r
+ "\nFor all issues relating to Jalview, email help@jalview.org" +\r
+ "\n\nIf you use JalView, please cite:" +\r
+ "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +\r
+ "\nBioinformatics, 2004 12;426-7.",\r
+ "About Jalview",\r
+ JOptionPane.INFORMATION_MESSAGE);\r
+ }\r
+\r
+ public void documentationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
- javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");\r
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);\r
\r
javax.help.HelpBroker hb = hs.createHelpBroker();\r
hb.setLocation(new Point(200, 50));\r
- hb.setSize(new Dimension(800,700));\r
+ hb.setSize(new Dimension(800, 700));\r
hb.setCurrentID("home");\r
hb.setDisplayed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
- Preferences pref = new Preferences();\r
- }\r
-\r
- public void saveState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty("LAST_DIRECTORY"),\r
- new String[]\r
- {"jar"}, new String[]{"Jalview Project"}, "Jalview Project");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save State");\r
- int value = chooser.showSaveDialog(this);\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- java.io.File choice = chooser.getSelectedFile();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- Jalview2XML.SaveState(choice);\r
- }\r
-\r
- }\r
-\r
-\r
- public void loadState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"jar"}, new String[]{"Jalview Project"}, "Jalview Project");\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Restore state");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getAbsolutePath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- Jalview2XML.LoadJalviewAlign(choice);\r
- }\r
- }\r
-}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ protected void preferences_actionPerformed(ActionEvent e)\r
+ {\r
+ Preferences pref = new Preferences();\r
+ }\r
+\r
+ public void saveState_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"jar"},\r
+ new String[]\r
+ {"Jalview Project"}, "Jalview Project");\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save State");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ java.io.File choice = chooser.getSelectedFile();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
+ Jalview2XML.SaveState(choice);\r
+ }\r
+ }\r
\r
+ public void loadState_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"jar"},\r
+ new String[]\r
+ {"Jalview Project"}, "Jalview Project");\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Restore state");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getAbsolutePath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+ Jalview2XML.LoadJalviewAlign(choice);\r
+ }\r
+ }\r
+\r
+ class LoadingThread\r
+ extends Thread\r
+ {\r
+ String file;\r
+ String protocol;\r
+ String format;\r
+\r
+ public LoadingThread(String file, String protocol, String format)\r
+ {\r
+ this.file = file;\r
+ this.protocol = protocol;\r
+ this.format = format;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ SequenceI[] sequences = null;\r
+\r
+ if (FormatAdapter.formats.contains(format))\r
+ {\r
+ sequences = FormatAdapter.readFile(file, protocol, format);\r
+ }\r
+\r
+ if ( (sequences != null) && (sequences.length > 0))\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+ addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.currentFileFormat = format;\r
+ af.statusBar.setText("Successfully loaded file " + file);\r
+\r
+ try\r
+ {\r
+ af.setMaximum(Preferences.showFullscreen);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ else\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't open file.\n" +\r
+ "Formats currently supported are\n" +\r
+ "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
+ , "Error loading file",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ }\r
+ }\r
+}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
import java.util.*;\r
\r
+import java.awt.*;\r
+\r
+import jalview.datamodel.*;\r
+\r
public class FeatureRenderer\r
{\r
AlignViewport av;\r
-\r
SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
+ SequenceGroup[] allGroups = null;\r
Color resBoxColour;\r
Graphics graphics;\r
\r
this.av = av;\r
}\r
\r
-\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)\r
+ public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int x1, int y1, int width,\r
+ int height)\r
{\r
Vector features = seq.getSequenceFeatures();\r
Enumeration e = features.elements();\r
- while( e.hasMoreElements() )\r
+\r
+ while (e.hasMoreElements())\r
{\r
- SequenceFeature sf = (SequenceFeature)e.nextElement();\r
- if(sf.getStart()>seq.getEnd())\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+\r
+ if (sf.getStart() > seq.getEnd())\r
+ {\r
continue;\r
+ }\r
\r
- int fstart = seq.findIndex(sf.getStart())-1;\r
- int fend = seq.findIndex(sf.getEnd())-1;\r
+ int fstart = seq.findIndex(sf.getStart()) - 1;\r
+ int fend = seq.findIndex(sf.getEnd()) - 1;\r
\r
- if( (fstart<=end && fend>=start) )\r
+ if ( ( (fstart <= end) && (fend >= start)))\r
{\r
- if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
- fstart = 0;// but the feature end is still valid!!\r
+ if (fstart < 0)\r
+ { // fix for if the feature we have starts before the sequence start,\r
+ fstart = 0; // but the feature end is still valid!!\r
+ }\r
\r
- if(fstart==fend)\r
+ if (fstart == fend)\r
{\r
g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
+ g.fillRoundRect( (fstart - start) * width, y1, width,\r
+ height, 4, 4);\r
g.setColor(Color.white);\r
\r
char s = seq.getSequence().charAt(fstart);\r
FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s))/2;\r
- int pady = height/5;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
-\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (fstart - start)),\r
+ (y1 + height) - pady);\r
}\r
else\r
{\r
for (int i = fstart; i <= fend; i++)\r
{\r
char s = seq.getSequence().charAt(i);\r
- if( jalview.util.Comparison.isGap(s) )\r
+\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
continue;\r
+ }\r
\r
g.setColor(Color.blue);\r
- g.fillRect( (i-start) * width, y1, width, height);\r
+ g.fillRect( (i - start) * width, y1, width, height);\r
\r
g.setColor(Color.white);\r
\r
int charOffset = (width - fm.charWidth(s)) / 2;\r
int pady = height / 5;\r
g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i-start),\r
- y1 + height - pady);\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - pady);\r
}\r
}\r
}\r
-\r
}\r
- }\r
-\r
+ }\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.GFinder;\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
import javax.swing.event.*;\r
-import java.util.*;\r
-import java.awt.*;\r
\r
-public class Finder extends GFinder\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+\r
+public class Finder\r
+ extends GFinder\r
{\r
AlignViewport av;\r
AlignmentPanel ap;\r
JInternalFrame frame;\r
SuperGroup searchGroup;\r
Vector searchResults;\r
-\r
int seqIndex = 0;\r
int resIndex = 0;\r
+\r
public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)\r
{\r
this.av = av;\r
SwingUtilities.invokeLater(new Runnable()\r
{\r
public void run()\r
- { textfield.requestFocus(); }\r
- });\r
- }\r
-\r
- public void internalFrameClosing(InternalFrameEvent evt)\r
- {\r
- cancel_actionPerformed(null);\r
- }\r
-});\r
+ {\r
+ textfield.requestFocus();\r
+ }\r
+ });\r
+ }\r
\r
+ public void internalFrameClosing(InternalFrameEvent evt)\r
+ {\r
+ cancel_actionPerformed(null);\r
+ }\r
+ });\r
}\r
\r
public void textfield_actionPerformed(ActionEvent e)\r
\r
public void findAll_actionPerformed(ActionEvent e)\r
{\r
- resIndex=0;\r
- seqIndex=0;\r
+ resIndex = 0;\r
+ seqIndex = 0;\r
doSearch(true);\r
}\r
\r
public void cancel_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
// if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( null );\r
- ap.idPanel.highlightSearchResults( null );\r
- // frame.setClosed(true);\r
- }catch(Exception ex){ }\r
- }\r
+ ap.highlightSearchResults(null);\r
+ ap.idPanel.highlightSearchResults(null);\r
\r
+ // frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
\r
public void createNewGroup_actionPerformed(ActionEvent e)\r
{\r
+ Color[] newColors = new Color[24];\r
\r
- Color [] newColors = new Color[24];\r
- for(int i=0; i<24; i++)\r
- newColors[i] = new Color(60,160,115);\r
-\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
- String searchString = textfield.getText();\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ newColors[i] = new Color(60, 160, 115);\r
+ }\r
\r
- searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(\r
+ newColors);\r
+ String searchString = textfield.getText();\r
\r
+ searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
\r
- for(int i=0; i<searchResults.size(); i+=3)\r
+ for (int i = 0; i < searchResults.size(); i += 3)\r
{\r
// its possible edits may have occurred since search was performed\r
// account for this here\r
-\r
- SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );\r
- int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;\r
- int endRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;\r
-\r
- SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes );\r
+ SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(\r
+ searchResults.elementAt(i).toString()));\r
+ int startRes = seq.findIndex(Integer.parseInt(\r
+ searchResults.elementAt(i + 1).toString())) - 1;\r
+ int endRes = seq.findIndex(Integer.parseInt(\r
+ searchResults.elementAt(i + 2).toString())) - 1;\r
+\r
+ SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,\r
+ false, startRes, endRes);\r
sg.addSequence(seq);\r
av.alignment.addGroup(sg);\r
- searchGroup.addGroup( sg );\r
-\r
+ searchGroup.addGroup(sg);\r
}\r
\r
ap.av.alignment.addSuperGroup(searchGroup);\r
- ap.highlightSearchResults( null );\r
+ ap.highlightSearchResults(null);\r
}\r
\r
-\r
void doSearch(boolean findAll)\r
{\r
createNewGroup.setEnabled(false);\r
\r
String searchString = textfield.getText().toUpperCase();\r
\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
+ com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
\r
searchResults = new Vector();\r
- int [] allResults = null;\r
+\r
+ int[] allResults = null;\r
\r
Sequence seq;\r
- String item=null;\r
+ String item = null;\r
boolean found = false;\r
\r
////// is the searchString a residue number?\r
- try{\r
+ try\r
+ {\r
int res = Integer.parseInt(searchString);\r
found = true;\r
\r
- if(av.getSelectionGroup().getSize()>0)\r
- seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));\r
+ if (av.getSelectionGroup().getSize() > 0)\r
+ {\r
+ seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
+ }\r
else\r
- seq = (Sequence)av.getAlignment().getSequenceAt(0);\r
+ {\r
+ seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
+ }\r
\r
- searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );\r
- searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
- searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
+ searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));\r
+ searchResults.add(Integer.toString(seq.findIndex(res) - 1));\r
+ searchResults.add(Integer.toString(seq.findIndex(res) - 1));\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ }\r
\r
- }catch(NumberFormatException ex){}\r
///////////////////////////////////////////////\r
+ Color[] newColors = new Color[24];\r
\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ newColors[i] = new Color(60, 160, 115);\r
+ }\r
\r
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(\r
+ newColors);\r
\r
- Color [] newColors = new Color[24];\r
- for(int i=0; i<24; i++)\r
- newColors[i] = new Color(60,160,115);\r
-\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
-\r
- searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+ searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
\r
int end = av.alignment.getHeight();\r
\r
SequenceGroup selection = av.getSelectionGroup();\r
- if(selection!=null)\r
- if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))\r
- selection = null;\r
\r
- while( !found && seqIndex<end)\r
+ if (selection != null)\r
{\r
- seq = (Sequence)av.alignment.getSequenceAt(seqIndex);\r
+ if ( (selection.getSize() < 1) ||\r
+ ( (selection.getEndRes() - selection.getStartRes()) < 2))\r
+ {\r
+ selection = null;\r
+ }\r
+ }\r
\r
+ while (!found && (seqIndex < end))\r
+ {\r
+ seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
\r
- if(selection!=null && !selection.sequences.contains(seq))\r
+ if ( (selection != null) && !selection.sequences.contains(seq))\r
{\r
seqIndex++;\r
- resIndex=0;\r
+ resIndex = 0;\r
+\r
continue;\r
}\r
\r
item = seq.getSequence().toUpperCase();\r
\r
- if(selection!=null && selection.getEndRes()<av.alignment.getWidth())\r
- item = item.substring(0, selection.getEndRes()+1);\r
+ if ( (selection != null) &&\r
+ (selection.getEndRes() < av.alignment.getWidth()))\r
+ {\r
+ item = item.substring(0, selection.getEndRes() + 1);\r
+ }\r
\r
///Shall we ignore gaps????\r
StringBuffer noGaps = new StringBuffer();\r
- int insertCount=0;\r
+ int insertCount = 0;\r
Vector spaces = new Vector();\r
\r
- for (int j=0; j < item.length(); j++)\r
+ for (int j = 0; j < item.length(); j++)\r
{\r
-\r
- if(!jalview.util.Comparison.isGap(item.charAt(j)))\r
- {\r
- noGaps.append(item.charAt(j));\r
- spaces.add(new Integer(insertCount));\r
- }\r
+ if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
+ {\r
+ noGaps.append(item.charAt(j));\r
+ spaces.add(new Integer(insertCount));\r
+ }\r
else\r
- insertCount++;\r
+ {\r
+ insertCount++;\r
+ }\r
}\r
\r
-\r
-\r
- for(int r = resIndex; r<noGaps.length(); r++)\r
+ for (int r = resIndex; r < noGaps.length(); r++)\r
{\r
-\r
- if( regex.searchFrom( noGaps.toString(), r ) )\r
- {\r
- resIndex = regex.matchedFrom();\r
- if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())\r
- continue;\r
-\r
- searchResults.add( Integer.toString( seqIndex) );\r
-\r
- int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );\r
- int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );\r
-\r
- searchResults.addElement( sres+"" );\r
- searchResults.addElement( eres+"" );\r
-\r
- if(!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
- break;\r
- }\r
-\r
- r=resIndex;\r
- }\r
+ if (regex.searchFrom(noGaps.toString(), r))\r
+ {\r
+ resIndex = regex.matchedFrom();\r
+\r
+ if ( (selection != null) &&\r
+ ( (resIndex +\r
+ Integer.parseInt(spaces.get(resIndex).toString())) <\r
+ selection.getStartRes()))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ searchResults.add(Integer.toString(seqIndex));\r
+\r
+ int sres = seq.findPosition(resIndex +\r
+ Integer.parseInt(spaces.elementAt(\r
+ resIndex)\r
+ .toString()));\r
+ int eres = seq.findPosition(regex.matchedTo() - 1 +\r
+ Integer.parseInt(spaces.elementAt(regex.\r
+ matchedTo() -\r
+ 1).toString()));\r
+\r
+ searchResults.addElement(sres + "");\r
+ searchResults.addElement(eres + "");\r
+\r
+ if (!findAll)\r
+ {\r
+ // thats enough, break and display the result\r
+ found = true;\r
+ resIndex++;\r
+\r
+ break;\r
+ }\r
+\r
+ r = resIndex;\r
+ }\r
}\r
- if(!found)\r
+\r
+ if (!found)\r
{\r
seqIndex++;\r
resIndex = 0;\r
}\r
}\r
\r
-\r
Vector idMatch = new Vector();\r
- for(int id = 0; id<av.alignment.getHeight(); id++)\r
+\r
+ for (int id = 0; id < av.alignment.getHeight(); id++)\r
{\r
- if( regex.search( av.alignment.getSequenceAt(id).getName() ) )\r
- idMatch.add( av.alignment.getSequenceAt(id) );\r
+ if (regex.search(av.alignment.getSequenceAt(id).getName()))\r
+ {\r
+ idMatch.add(av.alignment.getSequenceAt(id));\r
+ }\r
}\r
\r
- if(searchResults.size()==0 && idMatch.size()>0)\r
- ap.idPanel.highlightSearchResults( idMatch );\r
-\r
+ if ( (searchResults.size() == 0) && (idMatch.size() > 0))\r
+ {\r
+ ap.idPanel.highlightSearchResults(idMatch);\r
+ }\r
\r
- if(searchResults.size()>0)\r
+ if (searchResults.size() > 0)\r
{\r
allResults = new int[searchResults.size()];\r
- for(int i=0; i<searchResults.size(); i++)\r
+\r
+ for (int i = 0; i < searchResults.size(); i++)\r
+ {\r
allResults[i] = Integer.parseInt(searchResults.get(i).toString());\r
+ }\r
\r
createNewGroup.setEnabled(true);\r
}\r
else\r
{\r
- JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);\r
- resIndex=0;\r
- seqIndex=0;\r
+ JOptionPane.showInternalMessageDialog(this, "Finished searching",\r
+ null,\r
+ JOptionPane.INFORMATION_MESSAGE);\r
+ resIndex = 0;\r
+ seqIndex = 0;\r
}\r
\r
// if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( allResults );\r
+ ap.highlightSearchResults(allResults);\r
\r
if (findAll)\r
{\r
- String message = (searchResults.size()/3) + " matches found.";\r
+ String message = (searchResults.size() / 3) + " matches found.";\r
JOptionPane.showInternalMessageDialog(this, message, null,\r
JOptionPane.INFORMATION_MESSAGE);\r
}\r
-\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.GFontChooser;\r
-import jalview.gui.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
-import javax.swing.event.*;\r
-import jalview.bin.Cache;\r
\r
+import jalview.bin.*;\r
+import jalview.jbgui.*;\r
\r
-public class FontChooser extends GFontChooser\r
+public class FontChooser\r
+ extends GFontChooser\r
{\r
AlignmentPanel ap;\r
Font oldFont;\r
{\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Change Font", 480,100, false);\r
+ Desktop.addInternalFrame(frame, "Change Font", 480, 100, false);\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
\r
this.ap = ap;\r
- String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
- for(int i=0; i<fonts.length; i++)\r
+\r
+ String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
+ .getAvailableFontFamilyNames();\r
+\r
+ for (int i = 0; i < fonts.length; i++)\r
+ {\r
fontName.addItem(fonts[i]);\r
+ }\r
\r
- for(int i=1; i<31; i++)\r
- fontSize.addItem(i+"");\r
+ for (int i = 1; i < 31; i++)\r
+ {\r
+ fontSize.addItem(i + "");\r
+ }\r
\r
- fontStyle.addItem("plain");\r
- fontStyle.addItem("bold");\r
- fontStyle.addItem("italic");\r
+ fontStyle.addItem("plain");\r
+ fontStyle.addItem("bold");\r
+ fontStyle.addItem("italic");\r
\r
- oldFont = ap.av.getFont();\r
- fontName.setSelectedItem(oldFont.getName());\r
- fontSize.setSelectedItem(oldFont.getSize()+"");\r
- fontStyle.setSelectedIndex(oldFont.getStyle());\r
+ oldFont = ap.av.getFont();\r
+ fontName.setSelectedItem(oldFont.getName());\r
+ fontSize.setSelectedItem(oldFont.getSize() + "");\r
+ fontStyle.setSelectedIndex(oldFont.getStyle());\r
\r
- init = false;\r
+ init = false;\r
}\r
\r
protected void ok_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
frame.setClosed(true);\r
- }catch(Exception ex){}\r
-\r
- if(ap.getOverviewPanel()!=null)\r
- ap.getOverviewPanel().updateOverviewImage();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ if (ap.getOverviewPanel() != null)\r
+ {\r
+ ap.getOverviewPanel().updateOverviewImage();\r
+ }\r
}\r
\r
protected void cancel_actionPerformed(ActionEvent e)\r
ap.av.setFont(oldFont);\r
ap.repaint();\r
fontName.setSelectedItem(oldFont.getName());\r
- fontSize.setSelectedItem(oldFont.getSize()+"");\r
+ fontSize.setSelectedItem(oldFont.getSize() + "");\r
fontStyle.setSelectedIndex(oldFont.getStyle());\r
- try{\r
+\r
+ try\r
+ {\r
frame.setClosed(true);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
\r
void changeFont()\r
{\r
Font newFont = new Font(fontName.getSelectedItem().toString(),\r
fontStyle.getSelectedIndex(),\r
- Integer.parseInt(fontSize.getSelectedItem().toString())\r
- );\r
+ Integer.parseInt(fontSize.getSelectedItem().\r
+ toString()));\r
ap.av.setFont(newFont);\r
ap.fontChanged();\r
}\r
\r
protected void fontName_actionPerformed(ActionEvent e)\r
{\r
- if(init) return;\r
+ if (init)\r
+ {\r
+ return;\r
+ }\r
+\r
changeFont();\r
}\r
\r
protected void fontSize_actionPerformed(ActionEvent e)\r
{\r
- if(init) return;\r
+ if (init)\r
+ {\r
+ return;\r
+ }\r
+\r
changeFont();\r
}\r
\r
protected void fontStyle_actionPerformed(ActionEvent e)\r
{\r
- if(init) return;\r
+ if (init)\r
+ {\r
+ return;\r
+ }\r
+\r
changeFont();\r
}\r
\r
public void defaultButton_actionPerformed(ActionEvent e)\r
{\r
Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());\r
- Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex()+"");\r
+ Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex() + "");\r
Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());\r
}\r
-\r
-\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
import java.awt.*;\r
-import java.awt.Graphics2D.*;\r
import java.awt.image.*;\r
import javax.swing.*;\r
-import jalview.datamodel.*;\r
+\r
import jalview.analysis.*;\r
-public class IdCanvas extends JPanel\r
+import jalview.datamodel.*;\r
+\r
+public class IdCanvas\r
+ extends JPanel\r
{\r
protected AlignViewport av;\r
-\r
- protected boolean showScores = true;\r
-\r
- protected int maxIdLength = -1;\r
- protected String maxIdStr = null;\r
+ protected boolean showScores = true;\r
+ protected int maxIdLength = -1;\r
+ protected String maxIdStr = null;\r
BufferedImage image;\r
Graphics2D gg;\r
- int imgHeight=0;\r
+ int imgHeight = 0;\r
boolean fastPaint = false;\r
-\r
java.util.Vector searchResults;\r
\r
public IdCanvas(AlignViewport av)\r
{\r
setLayout(new BorderLayout());\r
- this.av = av;\r
+ this.av = av;\r
PaintRefresher.Register(this);\r
}\r
\r
- public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {\r
- int charHeight = av.getCharHeight();\r
+ public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,\r
+ int ypos)\r
+ {\r
+ int charHeight = av.getCharHeight();\r
\r
- if(searchResults!=null && searchResults.contains(s))\r
- {\r
- gg.setColor(Color.black);\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.white);\r
- }\r
- else if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {\r
- gg.setColor(Color.lightGray);\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.white);\r
- } else {\r
- gg.setColor(s.getColor());\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.black);\r
- }\r
+ if ( (searchResults != null) && searchResults.contains(s))\r
+ {\r
+ gg.setColor(Color.black);\r
+ gg.fillRect(0,\r
+ AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
+ getWidth(), charHeight);\r
+ gg.setColor(Color.white);\r
+ }\r
+ else if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().sequences.contains(s))\r
+ {\r
+ gg.setColor(Color.lightGray);\r
+ gg.fillRect(0,\r
+ AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
+ getWidth(), charHeight);\r
+ gg.setColor(Color.white);\r
+ }\r
+ else\r
+ {\r
+ gg.setColor(s.getColor());\r
+ gg.fillRect(0,\r
+ AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
+ getWidth(), charHeight);\r
+ gg.setColor(Color.black);\r
+ }\r
\r
- String string = s.getName();\r
- if(av.getShowFullId())\r
- string = s.getDisplayId();\r
+ String string = s.getName();\r
\r
- gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight- (charHeight/5));\r
+ if (av.getShowFullId())\r
+ {\r
+ string = s.getDisplayId();\r
+ }\r
\r
+ gg.drawString(string, 0,\r
+ (AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +\r
+ charHeight) - (charHeight / 5));\r
}\r
\r
public void fastPaint(int vertical)\r
{\r
- if(gg==null)\r
- { repaint(); return;}\r
+ if (gg == null)\r
+ {\r
+ repaint();\r
\r
- gg.copyArea( 0,0, getWidth(), imgHeight, 0, -vertical*av.charHeight );\r
+ return;\r
+ }\r
\r
- int ss=av.startSeq, es=av.endSeq, transY = 0;\r
- if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\r
- if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time\r
- ss = av.startSeq;\r
- else\r
- transY = imgHeight - vertical * av.charHeight;\r
- }\r
- else if (vertical < 0)\r
- {\r
- es = ss - vertical;\r
- if(es > av.endSeq)\r
- es = av.endSeq;\r
- }\r
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);\r
\r
+ int ss = av.startSeq;\r
+ int es = av.endSeq;\r
+ int transY = 0;\r
\r
+ if (vertical > 0) // scroll down\r
+ {\r
+ ss = es - vertical;\r
\r
- gg.translate(0, transY);\r
+ if (ss < av.startSeq)\r
+ { // ie scrolling too fast, more than a page at a time\r
+ ss = av.startSeq;\r
+ }\r
+ else\r
+ {\r
+ transY = imgHeight - (vertical * av.charHeight);\r
+ }\r
+ }\r
+ else if (vertical < 0)\r
+ {\r
+ es = ss - vertical;\r
+\r
+ if (es > av.endSeq)\r
+ {\r
+ es = av.endSeq;\r
+ }\r
+ }\r
\r
- drawIds(ss, es);\r
+ gg.translate(0, transY);\r
\r
- gg.translate( 0, -transY );\r
+ drawIds(ss, es);\r
\r
+ gg.translate(0, -transY);\r
\r
- fastPaint = true;\r
- repaint();\r
+ fastPaint = true;\r
+ repaint();\r
}\r
\r
public void paintComponent(Graphics g)\r
{\r
fastPaint = false;\r
g.drawImage(image, 0, 0, this);\r
+\r
return;\r
}\r
\r
imgHeight = getHeight();\r
- imgHeight -= imgHeight % av.charHeight;\r
+ imgHeight -= (imgHeight % av.charHeight);\r
\r
- if (imgHeight<1)\r
+ if (imgHeight < 1)\r
+ {\r
return;\r
+ }\r
\r
- image = new BufferedImage(getWidth(), imgHeight, BufferedImage.TYPE_INT_RGB);\r
+ image = new BufferedImage(getWidth(), imgHeight,\r
+ BufferedImage.TYPE_INT_RGB);\r
gg = (Graphics2D) image.getGraphics();\r
+\r
//Fill in the background\r
gg.setColor(Color.white);\r
gg.fillRect(0, 0, getWidth(), imgHeight);\r
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
av.getFont().getSize());\r
gg.setFont(italic);\r
\r
- drawIds( av.getStartSeq(), av.endSeq);\r
+ drawIds(av.getStartSeq(), av.endSeq);\r
\r
g.drawImage(image, 0, 0, this);\r
}\r
\r
void drawIds(int starty, int endy)\r
{\r
- Color currentColor = Color.white;\r
+ Color currentColor = Color.white;\r
Color currentTextColor = Color.black;\r
\r
if (av.getWrapAlignment())\r
{\r
+ int rowSize = av.getEndRes() - av.getStartRes();\r
\r
- int rowSize = av.getEndRes() - av.getStartRes();\r
- // Draw the rest of the panels\r
-\r
- for(int ypos=2*av.charHeight, row=av.startRes;\r
- ypos <= getHeight() && row<av.alignment.getWidth();\r
- ypos += av.chunkHeight, row+=rowSize )\r
- {\r
- for (int i = starty; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- drawIdString(gg, s, i, 0, ypos);\r
- }\r
- }\r
-\r
-\r
- } else\r
+ // Draw the rest of the panels\r
+ for (int ypos = 2 * av.charHeight, row = av.startRes;\r
+ (ypos <= getHeight()) && (row < av.alignment.getWidth());\r
+ ypos += av.chunkHeight, row += rowSize)\r
+ {\r
+ for (int i = starty; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ drawIdString(gg, s, i, 0, ypos);\r
+ }\r
+ }\r
+ }\r
+ else\r
{\r
-\r
//Now draw the id strings\r
for (int i = starty; i < endy; i++)\r
{\r
// Selected sequence colours\r
-\r
- if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ if ( (searchResults != null) &&\r
+ searchResults.contains(av.alignment.getSequenceAt(i)))\r
{\r
gg.setColor(Color.black);\r
currentColor = Color.black;\r
currentTextColor = Color.white;\r
- }\r
- else if (av.getSelectionGroup()!= null\r
- && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))\r
+ }\r
+ else if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().sequences.contains(\r
+ av.alignment.getSequenceAt(i)))\r
{\r
currentColor = Color.lightGray;\r
currentTextColor = Color.black;\r
\r
gg.fillRect(0,\r
AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- getWidth(),\r
- av.charHeight);\r
+ getWidth(), av.charHeight);\r
\r
gg.setColor(currentTextColor);\r
+\r
String string = av.alignment.getSequenceAt(i).getName();\r
- if(av.getShowFullId())\r
+\r
+ if (av.getShowFullId())\r
+ {\r
string = av.alignment.getSequenceAt(i).getDisplayId();\r
+ }\r
+\r
gg.drawString(string, 0,\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +\r
- av.charHeight - (av.charHeight / 5));\r
+ (AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +\r
+ av.charHeight) - (av.charHeight / 5));\r
}\r
\r
// add a border\r
gg.setColor(Color.white);\r
- gg.fillRect(getWidth()-4,0,4,getHeight());\r
+ gg.fillRect(getWidth() - 4, 0, 4, getHeight());\r
}\r
-\r
}\r
\r
public void setHighlighted(java.util.Vector found)\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
import javax.swing.*;\r
\r
-public class IdPanel extends JPanel implements MouseListener, MouseMotionListener {\r
+import jalview.datamodel.*;\r
\r
- protected IdCanvas idCanvas;\r
- protected AlignViewport av;\r
+public class IdPanel\r
+ extends JPanel implements MouseListener,\r
+ MouseMotionListener\r
+{\r
+ protected IdCanvas idCanvas;\r
+ protected AlignViewport av;\r
protected AlignmentPanel alignPanel;\r
ScrollThread scrollThread = null;\r
-\r
- int offy;\r
- int width;\r
+ int offy;\r
+ int width;\r
int lastid = -1;\r
boolean mouseDragging = false;\r
\r
public IdPanel(AlignViewport av, AlignmentPanel parent)\r
{\r
- this.av = av;\r
+ this.av = av;\r
alignPanel = parent;\r
idCanvas = new IdCanvas(av);\r
setLayout(new BorderLayout());\r
addMouseMotionListener(this);\r
}\r
\r
- public void mouseMoved(MouseEvent e) {}\r
-\r
+ public void mouseMoved(MouseEvent e)\r
+ {\r
+ }\r
\r
- public void mouseDragged(MouseEvent e) {\r
+ public void mouseDragged(MouseEvent e)\r
+ {\r
mouseDragging = true;\r
\r
int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y -= (2 * av.charHeight);\r
+ }\r
+\r
int seq = av.getIndex(y);\r
\r
- if(seq<0)\r
+ if (seq < 0)\r
+ {\r
return;\r
+ }\r
\r
if (seq < lastid)\r
+ {\r
selectSeqs(lastid - 1, seq);\r
+ }\r
else if (seq > lastid)\r
+ {\r
selectSeqs(lastid + 1, seq);\r
+ }\r
\r
lastid = seq;\r
alignPanel.repaint();\r
{\r
if (e.getClickCount() == 2)\r
{\r
- int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
-\r
- int seq = av.getIndex(y);\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
-\r
- try{\r
- jalview.util.BrowserLauncher.openURL(\r
- "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +\r
- "]+-vn+2");\r
- }catch(Exception ex){\r
- // TODO: JBPNote : state dependent error message for real browserLaunch problems rather than unix misconfiguration.\r
- System.err.println(\r
- ex.getMessage()+"\nUnixers: Try adding this jalview.browser property line \n"\r
- +"in your jalview.properties file (/usr/local/bin/firefox is an exanmple browser path):\n"\r
- +"jalview.browser=/usr/local/bin/firefox\n");\r
- //ex.printStackTrace();\r
- }\r
- }\r
+ int y = e.getY();\r
\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y -= (2 * av.charHeight);\r
+ }\r
+\r
+ int seq = av.getIndex(y);\r
+ String id = av.getAlignment().getSequenceAt(seq).getName();\r
+\r
+ try\r
+ {\r
+ jalview.util.BrowserLauncher.openURL(\r
+ "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" +\r
+ id + "]+-vn+2");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ // TODO: JBPNote : state dependent error message for real browserLaunch problems rather than unix misconfiguration.\r
+ System.err.println(ex.getMessage() +\r
+ "\nUnixers: Try adding this jalview.browser property line \n" +\r
+ "in your jalview.properties file (/usr/local/bin/firefox is an exanmple browser path):\n" +\r
+ "jalview.browser=/usr/local/bin/firefox\n");\r
+\r
+ //ex.printStackTrace();\r
+ }\r
+ }\r
}\r
+\r
public void mouseEntered(MouseEvent e)\r
{\r
- if(scrollThread!=null)\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
}\r
\r
- public void mouseExited (MouseEvent e)\r
+ public void mouseExited(MouseEvent e)\r
{\r
- if(av.getWrapAlignment())\r
+ if (av.getWrapAlignment())\r
+ {\r
return;\r
+ }\r
\r
- if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)\r
+ if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))\r
{\r
scrollThread = new ScrollThread(true);\r
}\r
\r
- if(mouseDragging && e.getY()>=getHeight() && av.alignment.getHeight()>av.getEndSeq())\r
+ if (mouseDragging && (e.getY() >= getHeight()) &&\r
+ (av.alignment.getHeight() > av.getEndSeq()))\r
{\r
scrollThread = new ScrollThread(false);\r
}\r
}\r
\r
-\r
- public void mousePressed(MouseEvent e) {\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
if (e.getClickCount() == 2)\r
+ {\r
return;\r
+ }\r
\r
int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y -= (2 * av.charHeight);\r
+ }\r
\r
int seq = av.getIndex(y);\r
+\r
if (seq == -1)\r
+ {\r
return;\r
+ }\r
\r
if (javax.swing.SwingUtilities.isRightMouseButton(e))\r
{\r
jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,\r
- (Sequence)av.getAlignment().getSequenceAt(seq));\r
+ (Sequence) av.getAlignment().getSequenceAt(seq));\r
pop.show(this, e.getX(), y);\r
+\r
return;\r
}\r
\r
- if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)\r
+ if (!e.isControlDown() && !e.isShiftDown() &&\r
+ (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))\r
{\r
-\r
SequenceGroup selection = new SequenceGroup();\r
- SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));\r
+ SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(\r
+ seq));\r
selection.setStartRes(0);\r
- selection.setEndRes(av.alignment.getWidth()-1);\r
- for (int i =0; i< sg.getSize(); i++)\r
+ selection.setEndRes(av.alignment.getWidth() - 1);\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
selection.addSequence(sg.getSequenceAt(i));\r
+ }\r
\r
av.setSelectionGroup(selection);\r
+\r
return;\r
}\r
\r
- if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))\r
+ if ( (av.getSelectionGroup() == null) ||\r
+ (!e.isControlDown() && (av.getSelectionGroup() != null)))\r
+ {\r
av.setSelectionGroup(new SequenceGroup());\r
+ }\r
\r
av.getSelectionGroup().setStartRes(0);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);\r
+ av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);\r
\r
- if(e.isShiftDown() && lastid!=-1)\r
+ if (e.isShiftDown() && (lastid != -1))\r
+ {\r
selectSeqs(lastid, seq);\r
+ }\r
else\r
+ {\r
selectSeq(seq);\r
+ }\r
\r
alignPanel.repaint();\r
}\r
void selectSeq(int seq)\r
{\r
lastid = seq;\r
+\r
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);\r
av.getSelectionGroup().addOrRemove(pickedSeq);\r
}\r
\r
- void selectSeqs(int start, int end) {\r
-\r
+ void selectSeqs(int start, int end)\r
+ {\r
lastid = start;\r
- if (end < start)\r
- {\r
- int tmp = start;\r
- start = end;\r
- end = tmp;\r
- lastid = end;\r
- }\r
-\r
- for (int i = start; i <= end; i++)\r
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));\r
\r
- }\r
+ if (end < start)\r
+ {\r
+ int tmp = start;\r
+ start = end;\r
+ end = tmp;\r
+ lastid = end;\r
+ }\r
\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));\r
+ }\r
+ }\r
\r
public void mouseReleased(MouseEvent e)\r
{\r
- if(scrollThread!=null)\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
\r
mouseDragging = false;\r
PaintRefresher.Refresh(this);\r
}\r
\r
- public void highlightSearchResults( java.util.Vector found )\r
+ public void highlightSearchResults(java.util.Vector found)\r
{\r
- idCanvas.setHighlighted( found );\r
+ idCanvas.setHighlighted(found);\r
\r
- if(found == null)\r
+ if (found == null)\r
+ {\r
return;\r
+ }\r
\r
- int index = av.alignment.findIndex( (SequenceI)found.get(0));\r
+ int index = av.alignment.findIndex( (SequenceI) found.get(0));\r
\r
// do we need to scroll the panel?\r
- if(av.getStartSeq()>index || av.getEndSeq()<index)\r
- alignPanel.setScrollValues( av.getStartRes(), index);\r
+ if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))\r
+ {\r
+ alignPanel.setScrollValues(av.getStartRes(), index);\r
+ }\r
}\r
\r
// this class allows scrolling off the bottom of the visible alignment\r
{\r
boolean running = false;\r
boolean up = true;\r
+\r
public ScrollThread(boolean up)\r
{\r
this.up = up;\r
public void run()\r
{\r
running = true;\r
+\r
while (running)\r
{\r
- if(alignPanel.scrollUp(up))\r
+ if (alignPanel.scrollUp(up))\r
{\r
// scroll was ok, so add new sequence to selection\r
int seq = av.getStartSeq();\r
- if(!up)\r
+\r
+ if (!up)\r
+ {\r
seq = av.getEndSeq();\r
+ }\r
\r
if (seq < lastid)\r
+ {\r
selectSeqs(lastid - 1, seq);\r
+ }\r
else if (seq > lastid)\r
+ {\r
selectSeqs(lastid + 1, seq);\r
+ }\r
\r
lastid = seq;\r
}\r
else\r
+ {\r
running = false;\r
+ }\r
\r
alignPanel.repaint();\r
+\r
try\r
{\r
Thread.sleep(100);\r
}\r
catch (Exception ex)\r
- {}\r
+ {\r
+ }\r
}\r
}\r
-}\r
-\r
+ }\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
\r
-\r
-public class IdwidthAdjuster extends JPanel implements MouseListener, MouseMotionListener\r
+public class IdwidthAdjuster\r
+ extends JPanel implements MouseListener,\r
+ MouseMotionListener\r
{\r
boolean active = false;\r
- int oldX=0;\r
+ int oldX = 0;\r
Image image;\r
- AlignmentPanel ap ;\r
+ AlignmentPanel ap;\r
\r
public IdwidthAdjuster(AlignmentPanel ap)\r
{\r
this.ap = ap;\r
+\r
java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
- if (url != null)\r
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+\r
+ if (url != null)\r
+ {\r
+ image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+ }\r
\r
addMouseListener(this);\r
addMouseMotionListener(this);\r
}\r
\r
public void mousePressed(MouseEvent evt)\r
- { oldX = evt.getX(); }\r
+ {\r
+ oldX = evt.getX();\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ active = false;\r
+ repaint();\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ active = true;\r
+ repaint();\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ active = false;\r
+ repaint();\r
+ }\r
\r
- public void mouseReleased(MouseEvent evt){ active = false; repaint(); }\r
- public void mouseEntered(MouseEvent evt) { active = true; repaint();}\r
- public void mouseExited(MouseEvent evt) { active = false; repaint();}\r
public void mouseDragged(MouseEvent evt)\r
{\r
active = true;\r
+\r
Dimension d = ap.idPanel.idCanvas.getPreferredSize();\r
int dif = evt.getX() - oldX;\r
\r
- if(d.width+dif>20 || dif>0)\r
+ if ( ( (d.width + dif) > 20) || (dif > 0))\r
{\r
- ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,d.height));\r
+ ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,\r
+ d.height));\r
ap.repaint();\r
}\r
\r
oldX = evt.getX();\r
}\r
\r
- public void mouseMoved(MouseEvent evt) {}\r
- public void mouseClicked(MouseEvent evt) {}\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
\r
public void paintComponent(Graphics g)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0, getWidth(), getHeight());\r
- if(active)\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
+\r
+ if (active)\r
{\r
- if(image!=null)\r
- g.drawImage(image, getWidth()-20, 2, this);\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, getWidth() - 20, 2, this);\r
+ }\r
}\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
import java.io.*;\r
+import java.net.*;\r
import java.util.*;\r
import java.util.jar.*;\r
\r
+import javax.swing.*;\r
+\r
import jalview.binding.*;\r
+import jalview.io.*;\r
import jalview.schemes.*;\r
-import javax.swing.JInternalFrame;\r
-import java.net.URL;\r
-import jalview.io.SequenceFeatureFetcher;\r
-\r
\r
public class Jalview2XML\r
{\r
-\r
// SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
public static void SaveState(File statefile)\r
{\r
- long creation = System.currentTimeMillis();\r
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
- if(frames==null)\r
- return;\r
-\r
- try{\r
- FileOutputStream fos = new FileOutputStream(statefile);\r
- JarOutputStream jout = new JarOutputStream(fos);\r
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
- ////////////////////////////////////////////////////\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));\r
-\r
- Vector shortNames = new Vector();\r
- //REVERSE ORDER\r
- for (int i = frames.length-1; i > -1; i--)\r
+ long creation = System.currentTimeMillis();\r
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
+\r
+ if (frames == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ FileOutputStream fos = new FileOutputStream(statefile);\r
+ JarOutputStream jout = new JarOutputStream(fos);\r
+\r
+ //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
+ ////////////////////////////////////////////////////\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
+ "UTF-8"));\r
+\r
+ Vector shortNames = new Vector();\r
+\r
+ //REVERSE ORDER\r
+ for (int i = frames.length - 1; i > -1; i--)\r
+ {\r
+ if (frames[i] instanceof AlignFrame)\r
{\r
- if (frames[i] instanceof AlignFrame)\r
- {\r
- AlignFrame af = (AlignFrame) frames[i];\r
+ AlignFrame af = (AlignFrame) frames[i];\r
\r
- String shortName = af.getTitle();\r
+ String shortName = af.getTitle();\r
\r
- if(shortName.indexOf(File.separatorChar)>-1)\r
- shortName = shortName.substring(\r
- shortName.lastIndexOf(File.separatorChar)+1);\r
+ if (shortName.indexOf(File.separatorChar) > -1)\r
+ {\r
+ shortName = shortName.substring(shortName.lastIndexOf(\r
+ File.separatorChar) + 1);\r
+ }\r
\r
- int count=1;\r
- while( shortNames.contains(shortName) )\r
- {\r
- if(shortName.endsWith("_"+(count-1)))\r
- shortName = shortName.substring(0, shortName.lastIndexOf("_"));\r
+ int count = 1;\r
\r
- shortName = shortName.concat("_"+count);\r
- count++;\r
+ while (shortNames.contains(shortName))\r
+ {\r
+ if (shortName.endsWith("_" + (count - 1)))\r
+ {\r
+ shortName = shortName.substring(0,\r
+ shortName.lastIndexOf("_"));\r
}\r
- shortNames.addElement(shortName);\r
\r
- if(!shortName.endsWith(".xml"))\r
- shortName = shortName+".xml";\r
+ shortName = shortName.concat("_" + count);\r
+ count++;\r
+ }\r
+\r
+ shortNames.addElement(shortName);\r
+\r
+ if (!shortName.endsWith(".xml"))\r
+ {\r
+ shortName = shortName + ".xml";\r
+ }\r
\r
- SaveState( af, creation, shortName, jout, out);\r
- }\r
+ SaveState(af, creation, shortName, jout, out);\r
}\r
- out.close();\r
- jout.close();\r
}\r
- catch(Exception ex){ex.printStackTrace();}\r
+\r
+ out.close();\r
+ jout.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
\r
// USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
- public static void SaveState( AlignFrame af, String jarFile, String fileName)\r
+ public static void SaveState(AlignFrame af, String jarFile, String fileName)\r
{\r
- try{\r
+ try\r
+ {\r
FileOutputStream fos = new FileOutputStream(jarFile);\r
JarOutputStream jout = new JarOutputStream(fos);\r
+\r
//NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
////////////////////////////////////////////////////\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
+ "UTF-8"));\r
\r
SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
out.close();\r
jout.close();\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
\r
- public static void SaveState( AlignFrame af, long timeStamp,\r
- String fileName, JarOutputStream jout, PrintWriter out)\r
+ public static void SaveState(AlignFrame af, long timeStamp,\r
+ String fileName, JarOutputStream jout,\r
+ PrintWriter out)\r
{\r
-\r
Vector seqids = new Vector();\r
Vector userColours = new Vector();\r
\r
AlignViewport av = af.viewport;\r
\r
JalviewModel object = new JalviewModel();\r
- object.setVamsasModel( new VamsasModel() );\r
+ object.setVamsasModel(new VamsasModel());\r
\r
- object.setCreationDate( new java.util.Date(timeStamp) );\r
+ object.setCreationDate(new java.util.Date(timeStamp));\r
\r
jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
\r
Sequence vamsasSeq;\r
JalviewModelSequence jms = new JalviewModelSequence();\r
\r
- vamsasSet.setGapChar(jal.getGapCharacter()+"");\r
+ vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
\r
JSeq jseq;\r
\r
-\r
//SAVE SEQUENCES\r
int id = 0;\r
- for(int i=0; i<jal.getHeight(); i++)\r
+\r
+ for (int i = 0; i < jal.getHeight(); i++)\r
{\r
seqids.add(jal.getSequenceAt(i));\r
\r
- vamsasSeq = new Sequence( );\r
- vamsasSeq.setId(id+"");\r
+ vamsasSeq = new Sequence();\r
+ vamsasSeq.setId(id + "");\r
vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
\r
\r
jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
\r
- jseq.setId( id );\r
+ jseq.setId(id);\r
\r
jms.addJSeq(jseq);\r
vamsasSet.addSequence(vamsasSeq);\r
}\r
\r
//SAVE TREES\r
- if(af.viewport.currentTree!=null)\r
+ if (af.viewport.currentTree != null)\r
{\r
object.getVamsasModel().addTree(af.viewport.currentTree.toString());\r
}\r
\r
//SAVE ANNOTATIONS\r
- if(jal.getAlignmentAnnotation()!=null)\r
+ if (jal.getAlignmentAnnotation() != null)\r
{\r
+ jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
\r
- jalview.datamodel.AlignmentAnnotation [] aa = jal.getAlignmentAnnotation();\r
- for(int i=0; i<aa.length; i++)\r
+ for (int i = 0; i < aa.length; i++)\r
{\r
- if(aa[i].label.equals("Quality")\r
- || aa[i].label.equals("Conservation")\r
- || aa[i].label.equals("Consensus"))\r
- { continue;}\r
+ if (aa[i].label.equals("Quality") ||\r
+ aa[i].label.equals("Conservation") ||\r
+ aa[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
\r
Annotation an = new Annotation();\r
an.setDescription(aa[i].description);\r
\r
AnnotationElement ae;\r
\r
- for(int a=0; a<aa[i].annotations.length; a++)\r
+ for (int a = 0; a < aa[i].annotations.length; a++)\r
{\r
- if(aa[i]==null || aa[i].annotations[a]==null)\r
+ if ( (aa[i] == null) || (aa[i].annotations[a] == null))\r
+ {\r
continue;\r
+ }\r
\r
ae = new AnnotationElement();\r
ae.setDescription(aa[i].annotations[a].description);\r
ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
ae.setValue(aa[i].annotations[a].value);\r
ae.setPosition(a);\r
- ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure+"");\r
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
+ "");\r
an.addAnnotationElement(ae);\r
}\r
\r
vamsasSet.addAnnotation(an);\r
}\r
-\r
}\r
\r
//SAVE GROUPS\r
- if(jal.getGroups()!=null)\r
+ if (jal.getGroups() != null)\r
{\r
- JGroup [] groups = new JGroup[jal.getGroups().size()];\r
- for(int i=0; i<groups.length; i++)\r
+ JGroup[] groups = new JGroup[jal.getGroups().size()];\r
+\r
+ for (int i = 0; i < groups.length; i++)\r
{\r
groups[i] = new JGroup();\r
- jalview.datamodel.SequenceGroup sg\r
- = (jalview.datamodel.SequenceGroup)jal.getGroups().elementAt(i);\r
- groups[i].setStart( sg.getStartRes() );\r
- groups[i].setEnd( sg.getEndRes() );\r
- groups[i].setName( sg.getName());\r
\r
- if(sg.cs instanceof ConservationColourScheme)\r
- groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);\r
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)\r
+ jal.getGroups()\r
+ .elementAt(i);\r
+ groups[i].setStart(sg.getStartRes());\r
+ groups[i].setEnd(sg.getEndRes());\r
+ groups[i].setName(sg.getName());\r
+\r
+ if (sg.cs instanceof ConservationColourScheme)\r
+ {\r
+ groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);\r
+ }\r
\r
if (sg.cs instanceof ResidueColourScheme)\r
- groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).getThreshold());\r
+ {\r
+ groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).\r
+ getThreshold());\r
+ }\r
else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());\r
-\r
+ }\r
\r
if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours, jms));\r
+ {\r
+ groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
+ jms));\r
+ }\r
else\r
- groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));\r
+ {\r
+ groups[i].setColour(ColourSchemeProperty.getColourName(\r
+ sg.cs));\r
+ }\r
\r
groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
groups[i].setDisplayText(sg.getDisplayText());\r
groups[i].setColourText(sg.getColourText());\r
\r
- for(int s=0; s<sg.getSize(); s++)\r
+ for (int s = 0; s < sg.getSize(); s++)\r
{\r
- jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);\r
+ jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.\r
+ getSequenceAt(s);\r
int index = seqids.indexOf(seq);\r
groups[i].addSeq(index);\r
}\r
-\r
}\r
- jms.setJGroup(groups);\r
\r
+ jms.setJGroup(groups);\r
}\r
\r
///////////SAVE VIEWPORT\r
Viewport view = new Viewport();\r
- view.setTitle(af.getTitle());\r
- view.setXpos(af.getX());\r
- view.setYpos(af.getY());\r
- view.setWidth(af.getWidth());\r
- view.setHeight(af.getHeight());\r
- view.setStartRes(av.startRes);\r
- view.setStartSeq(av.startSeq);\r
-\r
-\r
- if( av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
- view.setBgColour( SetUserColourScheme(av.getGlobalColourScheme(),\r
- userColours, jms) );\r
- else\r
- view.setBgColour( ColourSchemeProperty.getColourName\r
- ( av.getGlobalColourScheme()));\r
-\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme)\r
- view.setConsThreshold( ((ConservationColourScheme)cs).inc);\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());\r
- else if (cs instanceof ScoreColourScheme)\r
- view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());\r
-\r
-\r
- view.setConservationSelected(av.getConservationSelected());\r
- view.setPidSelected(av.getAbovePIDThreshold());\r
- view.setFontName(av.font.getFontName());\r
- view.setFontSize(av.font.getSize());\r
- view.setFontStyle(av.font.getStyle());\r
- view.setRenderGaps(av.renderGaps);\r
- view.setShowAnnotation(av.getShowAnnotation());\r
- view.setShowBoxes(av.getShowBoxes());\r
- view.setShowColourText(av.getColourText());\r
- view.setShowConservation(av.showConservation);\r
- view.setShowFullId(av.getShowFullId());\r
- view.setShowIdentity(av.showIdentity);\r
- view.setShowQuality(av.showQuality);\r
- view.setShowSequenceFeatures(av.showSequenceFeatures);\r
- view.setShowText(av.getShowText());\r
- view.setWrapAlignment(av.getWrapAlignment());\r
-\r
- jms.addViewport( view );\r
+ view.setTitle(af.getTitle());\r
+ view.setXpos(af.getX());\r
+ view.setYpos(af.getY());\r
+ view.setWidth(af.getWidth());\r
+ view.setHeight(af.getHeight());\r
+ view.setStartRes(av.startRes);\r
+ view.setStartSeq(av.startSeq);\r
+\r
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
+ {\r
+ view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
+ userColours, jms));\r
+ }\r
+ else\r
+ {\r
+ view.setBgColour(ColourSchemeProperty.getColourName(\r
+ av.getGlobalColourScheme()));\r
+ }\r
+\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ view.setConsThreshold( ( (ConservationColourScheme) cs).inc);\r
+ }\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ {\r
+ view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());\r
+ }\r
+\r
+ view.setConservationSelected(av.getConservationSelected());\r
+ view.setPidSelected(av.getAbovePIDThreshold());\r
+ view.setFontName(av.font.getFontName());\r
+ view.setFontSize(av.font.getSize());\r
+ view.setFontStyle(av.font.getStyle());\r
+ view.setRenderGaps(av.renderGaps);\r
+ view.setShowAnnotation(av.getShowAnnotation());\r
+ view.setShowBoxes(av.getShowBoxes());\r
+ view.setShowColourText(av.getColourText());\r
+ view.setShowConservation(av.showConservation);\r
+ view.setShowFullId(av.getShowFullId());\r
+ view.setShowIdentity(av.showIdentity);\r
+ view.setShowQuality(av.showQuality);\r
+ view.setShowSequenceFeatures(av.showSequenceFeatures);\r
+ view.setShowText(av.getShowText());\r
+ view.setWrapAlignment(av.getWrapAlignment());\r
+\r
+ jms.addViewport(view);\r
\r
object.setJalviewModelSequence(jms);\r
object.getVamsasModel().addSequenceSet(vamsasSet);\r
\r
-\r
try\r
{\r
- if(!fileName.endsWith(".xml"))\r
- fileName = fileName+".xml";\r
+ if (!fileName.endsWith(".xml"))\r
+ {\r
+ fileName = fileName + ".xml";\r
+ }\r
\r
- JarEntry entry = new JarEntry(fileName);\r
- jout.putNextEntry(entry);\r
+ JarEntry entry = new JarEntry(fileName);\r
+ jout.putNextEntry(entry);\r
\r
object.marshal(out);\r
}\r
Vector userColours,\r
JalviewModelSequence jms)\r
{\r
- String id=null;\r
- jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)cs;\r
+ String id = null;\r
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)\r
+ cs;\r
+\r
if (!userColours.contains(ucs))\r
{\r
userColours.add(ucs);\r
- java.awt.Color [] colours = ucs.getColours();\r
+\r
+ java.awt.Color[] colours = ucs.getColours();\r
jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
- jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();\r
- for(int i=0; i<colours.length; i++)\r
+ jalview.binding.UserColourScheme jbucs = new jalview.binding.\r
+ UserColourScheme();\r
+\r
+ for (int i = 0; i < colours.length; i++)\r
{\r
- jalview.binding.Colour col = new jalview.binding.Colour();\r
- col.setRGB( jalview.util.Format.getHexString(colours[i]) );\r
- jbucs.addColour(col);\r
+ jalview.binding.Colour col = new jalview.binding.Colour();\r
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
+ jbucs.addColour(col);\r
}\r
- id = "ucs"+userColours.indexOf(ucs);\r
+\r
+ id = "ucs" + userColours.indexOf(ucs);\r
uc.setId(id);\r
uc.setUserColourScheme(jbucs);\r
jms.addUserColours(uc);\r
}\r
+\r
return id;\r
}\r
\r
- static jalview.schemes.UserColourScheme GetUserColourScheme(JalviewModelSequence jms, String id)\r
+ static jalview.schemes.UserColourScheme GetUserColourScheme(\r
+ JalviewModelSequence jms, String id)\r
{\r
- UserColours [] uc = jms.getUserColours();\r
- UserColours colours=null;\r
- for(int i=0; i<uc.length; i++)\r
+ UserColours[] uc = jms.getUserColours();\r
+ UserColours colours = null;\r
+\r
+ for (int i = 0; i < uc.length; i++)\r
{\r
- if(uc[i].getId().equals(id))\r
- { colours = uc[i]; break; }\r
+ if (uc[i].getId().equals(id))\r
+ {\r
+ colours = uc[i];\r
+\r
+ break;\r
+ }\r
}\r
- int csize = colours.getUserColourScheme().getColourCount();\r
- java.awt.Color [] newColours = new java.awt.Color[csize];\r
\r
- for(int i=0; i<csize;i++)\r
- newColours[i] = new java.awt.Color(\r
- Integer.parseInt( colours.getUserColourScheme().getColour(i).getRGB(), 16) );\r
+ int csize = colours.getUserColourScheme().getColourCount();\r
+ java.awt.Color[] newColours = new java.awt.Color[csize];\r
\r
- return new jalview.schemes.UserColourScheme(newColours);\r
+ for (int i = 0; i < csize; i++)\r
+ {\r
+ newColours[i] = new java.awt.Color(Integer.parseInt(\r
+ colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
+ }\r
\r
+ return new jalview.schemes.UserColourScheme(newColours);\r
}\r
\r
-\r
public static void LoadJalviewAlign(String file)\r
{\r
JalviewModel object = new JalviewModel();\r
- try{\r
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
\r
+ try\r
+ {\r
+ //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
URL url = null;\r
- if( file.startsWith("http://"))\r
- url = new URL(file);\r
+\r
+ if (file.startsWith("http://"))\r
+ {\r
+ url = new URL(file);\r
+ }\r
\r
JarInputStream jin = null;\r
- JarEntry jarentry=null;\r
+ JarEntry jarentry = null;\r
int entryCount = 1;\r
- do{\r
+\r
+ do\r
+ {\r
if (url != null)\r
+ {\r
jin = new JarInputStream(url.openStream());\r
+ }\r
else\r
+ {\r
jin = new JarInputStream(new FileInputStream(file));\r
+ }\r
\r
- for(int i=0; i<entryCount; i++)\r
+ for (int i = 0; i < entryCount; i++)\r
+ {\r
jarentry = jin.getNextJarEntry();\r
+ }\r
\r
- if(jarentry!=null)\r
+ if (jarentry != null)\r
{\r
InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
object = (JalviewModel) object.unmarshal(in);\r
LoadFromObject(object);\r
entryCount++;\r
}\r
- }while(jarentry!=null);\r
-\r
+ }\r
+ while (jarentry != null);\r
}\r
- catch(Exception ex)\r
- { System.err.println("Exception whilst loading jalview XML file : "+ex+"\n");\r
- ex.printStackTrace(); return; }\r
+ catch (Exception ex)\r
+ {\r
+ System.err.println("Exception whilst loading jalview XML file : " +\r
+ ex + "\n");\r
+ ex.printStackTrace();\r
\r
+ return;\r
+ }\r
}\r
\r
static void LoadFromObject(JalviewModel object)\r
{\r
- Vector seqids = new Vector();\r
- SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
- Sequence [] vamsasSeq = vamsasSet.getSequence();\r
-\r
- JalviewModelSequence jms = object.getJalviewModelSequence();\r
- //////////////////////////////////\r
- //LOAD SEQUENCES\r
- jalview.datamodel.Sequence [] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
- JSeq [] JSEQ = object.getJalviewModelSequence().getJSeq();\r
- for(int i=0; i<vamsasSeq.length; i++)\r
- {\r
- jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
- vamsasSeq[i].getSequence());\r
-\r
- jseqs[i].setStart( JSEQ[i].getStart());\r
- jseqs[i].setEnd( JSEQ[i].getEnd());\r
- jseqs[i].setColor( new java.awt.Color(JSEQ[i].getColour()) );\r
- seqids.add(jseqs[i]);\r
- }\r
-\r
- /////////////////////////////////\r
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
- /////////////////////////////////\r
-\r
- //////////////////////////////////\r
- //LOAD ANNOTATIONS\r
- if(vamsasSet.getAnnotation()!=null)\r
- {\r
- Annotation[] an = vamsasSet.getAnnotation();\r
- for (int i = 0; i < an.length; i++)\r
- {\r
- AnnotationElement[] ae = an[i].getAnnotationElement();\r
- jalview.datamodel.Annotation anot[]\r
- = new jalview.datamodel.Annotation[al.getWidth()];\r
- for (int aa = 0; aa < ae.length; aa++)\r
- {\r
- anot[ae[aa].getPosition()]\r
- = new jalview.datamodel.Annotation(\r
- ae[aa].getDisplayCharacter(),\r
- ae[aa].getDescription(),\r
- ae[aa].getSecondaryStructure().charAt(0),\r
- ae[aa].getValue()\r
- );\r
- }\r
-\r
-\r
- jalview.datamodel.AlignmentAnnotation jaa = null;\r
- if(an[i].getGraph())\r
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot,\r
- 0,0,1);\r
- else\r
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot);\r
- al.addAnnotation(jaa);\r
- }\r
- }\r
-\r
- /////////////////////////////////\r
- // LOAD VIEWPORT\r
- Viewport[] views = jms.getViewport();\r
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
-\r
- AlignFrame af = new AlignFrame(al);\r
- // af.changeColour() );\r
+ Vector seqids = new Vector();\r
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
+ Sequence[] vamsasSeq = vamsasSet.getSequence();\r
+\r
+ JalviewModelSequence jms = object.getJalviewModelSequence();\r
+\r
+ //////////////////////////////////\r
+ //LOAD SEQUENCES\r
+ jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[\r
+ vamsasSeq.length];\r
+ JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
+\r
+ for (int i = 0; i < vamsasSeq.length; i++)\r
+ {\r
+ jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
+ vamsasSeq[i].getSequence());\r
+\r
+ jseqs[i].setStart(JSEQ[i].getStart());\r
+ jseqs[i].setEnd(JSEQ[i].getEnd());\r
+ jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
+ seqids.add(jseqs[i]);\r
+ }\r
+\r
+ /////////////////////////////////\r
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
+\r
+ /////////////////////////////////\r
+ //////////////////////////////////\r
+ //LOAD ANNOTATIONS\r
+ if (vamsasSet.getAnnotation() != null)\r
+ {\r
+ Annotation[] an = vamsasSet.getAnnotation();\r
+\r
+ for (int i = 0; i < an.length; i++)\r
+ {\r
+ AnnotationElement[] ae = an[i].getAnnotationElement();\r
+ jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[\r
+ al.getWidth()];\r
+\r
+ for (int aa = 0; aa < ae.length; aa++)\r
+ {\r
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].\r
+ getDisplayCharacter(),\r
+ ae[aa].getDescription(),\r
+ ae[aa].getSecondaryStructure().charAt(0),\r
+ ae[aa].getValue());\r
+ }\r
+\r
+ jalview.datamodel.AlignmentAnnotation jaa = null;\r
+\r
+ if (an[i].getGraph())\r
+ {\r
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
+ an[i].getDescription(), anot, 0, 0, 1);\r
+ }\r
+ else\r
+ {\r
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
+ an[i].getDescription(), anot);\r
+ }\r
+\r
+ al.addAnnotation(jaa);\r
+ }\r
+ }\r
\r
+ /////////////////////////////////\r
+ // LOAD VIEWPORT\r
+ Viewport[] views = jms.getViewport();\r
+ Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
+\r
+ AlignFrame af = new AlignFrame(al);\r
+\r
+ // af.changeColour() );\r
/////////////////////////\r
//LOAD GROUPS\r
- if (jms.getJGroupCount()>0)\r
+ if (jms.getJGroupCount() > 0)\r
{\r
JGroup[] groups = jms.getJGroup();\r
+\r
for (int i = 0; i < groups.length; i++)\r
{\r
- ColourSchemeI cs=null;\r
- if(groups[i].getColour()!=null)\r
- {\r
- if (groups[i].getColour().startsWith("ucs"))\r
- cs = GetUserColourScheme(jms, groups[i].getColour());\r
- else\r
- cs = ColourSchemeProperty.getColour(al, groups[i].getColour());\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
- }\r
-\r
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup\r
- (groups[i].getName(),\r
- cs,\r
- groups[i].getDisplayBoxes(),\r
- groups[i].getDisplayText(),\r
- groups[i].getColourText(),\r
- groups[i].getStart(),\r
- groups[i].getEnd()) ;\r
- sg.setOutlineColour( new java.awt.Color(groups[i].getOutlineColour()));\r
- int [] ids = groups[i].getSeq();\r
- for(int s=0; s<ids.length; s++)\r
- sg.addSequence( (jalview.datamodel.SequenceI)seqids.elementAt( ids[s] ));\r
-\r
- if(groups[i].getConsThreshold()!=0)\r
+ ColourSchemeI cs = null;\r
+\r
+ if (groups[i].getColour() != null)\r
+ {\r
+ if (groups[i].getColour().startsWith("ucs"))\r
+ {\r
+ cs = GetUserColourScheme(jms, groups[i].getColour());\r
+ }\r
+ else\r
+ {\r
+ cs = ColourSchemeProperty.getColour(al,\r
+ groups[i].getColour());\r
+ }\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ {\r
+ ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
+ }\r
+ }\r
+\r
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.\r
+ SequenceGroup(groups[i].getName(),\r
+ cs, groups[i].getDisplayBoxes(),\r
+ groups[i].getDisplayText(), groups[i].getColourText(),\r
+ groups[i].getStart(), groups[i].getEnd());\r
+ sg.setOutlineColour(new java.awt.Color(\r
+ groups[i].getOutlineColour()));\r
+\r
+ int[] ids = groups[i].getSeq();\r
+\r
+ for (int s = 0; s < ids.length; s++)\r
+ {\r
+ sg.addSequence( (jalview.datamodel.SequenceI) seqids.elementAt(\r
+ ids[s]));\r
+ }\r
+\r
+ if (groups[i].getConsThreshold() != 0)\r
{\r
- jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
+ "All",\r
+ ResidueProperties.propHash, 3, sg.sequences, 0,\r
sg.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, 25);\r
sg.cs = cs;\r
}\r
\r
-\r
al.addGroup(sg);\r
}\r
}\r
\r
-\r
- Desktop.addInternalFrame(af, view.getTitle(), AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight());\r
- af.viewport.setStartRes( view.getStartRes() );\r
- af.viewport.setStartSeq( view.getStartSeq() );\r
+ Desktop.addInternalFrame(af, view.getTitle(),\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
+ view.getHeight());\r
+ af.viewport.setStartRes(view.getStartRes());\r
+ af.viewport.setStartSeq(view.getStartSeq());\r
af.viewport.showConservation = view.getShowConservation();\r
af.viewport.showQuality = view.getShowQuality();\r
- af.viewport.showIdentity= view.getShowIdentity();\r
- af.viewport.setAbovePIDThreshold( view.getPidSelected() );\r
- af.viewport.setColourText( view.getShowColourText() );\r
- af.viewport.setConservationSelected( view.getConservationSelected());\r
- af.viewport.setShowFullId( view.getShowFullId());\r
- af.viewport.setFont( new java.awt.Font( view.getFontName(),\r
- view.getFontStyle(),\r
- view.getFontSize()));\r
+ af.viewport.showIdentity = view.getShowIdentity();\r
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
+ af.viewport.setColourText(view.getShowColourText());\r
+ af.viewport.setConservationSelected(view.getConservationSelected());\r
+ af.viewport.setShowFullId(view.getShowFullId());\r
+ af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
+ view.getFontStyle(), view.getFontSize()));\r
af.alignPanel.fontChanged();\r
\r
af.sequenceFeatures_actionPerformed(null);\r
- af.viewport.setRenderGaps( view.getRenderGaps() );\r
+ af.viewport.setRenderGaps(view.getRenderGaps());\r
\r
- af.viewport.setWrapAlignment( view.getWrapAlignment() );\r
- if(view.getWrapAlignment())\r
+ af.viewport.setWrapAlignment(view.getWrapAlignment());\r
+\r
+ if (view.getWrapAlignment())\r
{\r
af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
}\r
af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
}\r
\r
- af.viewport.setShowBoxes( view.getShowBoxes() );\r
- af.viewport.setShowText( view.getShowText() );\r
+ af.viewport.setShowBoxes(view.getShowBoxes());\r
+ af.viewport.setShowText(view.getShowText());\r
\r
- ColourSchemeI cs=null;\r
- if(view.getBgColour()!=null)\r
- {\r
+ ColourSchemeI cs = null;\r
\r
+ if (view.getBgColour() != null)\r
+ {\r
if (view.getBgColour().startsWith("ucs"))\r
+ {\r
cs = GetUserColourScheme(jms, view.getBgColour());\r
+ }\r
else\r
+ {\r
cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
+ }\r
\r
if (cs instanceof ConservationColourScheme)\r
+ {\r
( (ConservationColourScheme) cs).inc = view.getConsThreshold();\r
+ }\r
\r
if (cs instanceof ResidueColourScheme)\r
+ {\r
( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
+ }\r
else if (cs instanceof ScoreColourScheme)\r
+ {\r
( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
-\r
+ }\r
}\r
- af.viewport.setGlobalColourScheme( cs );\r
\r
+ af.viewport.setGlobalColourScheme(cs);\r
\r
af.viewport.setColourAppliesToAllGroups(false);\r
af.changeColour(af.viewport.getGlobalColourScheme());\r
af.viewport.setColourAppliesToAllGroups(true);\r
\r
System.out.println(view.getShowSequenceFeatures());\r
- if( view.getShowSequenceFeatures() );\r
+\r
+ if (view.getShowSequenceFeatures())\r
{\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, af.alignPanel);\r
+ ;\r
+ }\r
+\r
+ {\r
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al,\r
+ af.alignPanel);\r
}\r
\r
//LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE\r
- if(object.getVamsasModel().getTreeCount()>0)\r
+ if (object.getVamsasModel().getTreeCount() > 0)\r
{\r
- try{\r
+ try\r
+ {\r
af.ShowNewickTree(new jalview.io.NewickFile(\r
- (String)object.getVamsasModel().getTree(0)), "Tree");\r
- }catch(Exception ex){ex.printStackTrace();}\r
+ (String) object.getVamsasModel().getTree(0)), "Tree");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
-\r
}\r
}\r
-\r
-\r
-\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import javax.swing.*;\r
+import java.awt.*;\r
import java.awt.event.*;\r
import java.awt.image.*;\r
-import java.awt.*;\r
+import javax.swing.*;\r
\r
-public class OverviewPanel extends JPanel implements Runnable\r
+public class OverviewPanel\r
+ extends JPanel implements Runnable\r
{\r
BufferedImage miniMe;\r
AlignViewport av;\r
AlignmentPanel ap;\r
float scalew = 1f;\r
float scaleh = 1f;\r
-\r
- int width, sequencesHeight;\r
- int graphHeight=30;\r
- int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;\r
-\r
+ int width;\r
+ int sequencesHeight;\r
+ int graphHeight = 30;\r
+ int boxX = -1;\r
+ int boxY = -1;\r
+ int boxWidth = -1;\r
+ int boxHeight = -1;\r
boolean resizing = false;\r
\r
public OverviewPanel(AlignmentPanel ap)\r
setLayout(null);\r
\r
// scale the initial size of overviewpanel to shape of alignment\r
- float initialScale = (float)av.alignment.getWidth()/(float)av.alignment.getHeight();\r
- if(av.alignment.getWidth() > av.alignment.getHeight())\r
+ float initialScale = (float) av.alignment.getWidth() /\r
+ (float) av.alignment.getHeight();\r
+\r
+ if (av.alignment.getWidth() > av.alignment.getHeight())\r
{\r
// wider\r
width = 400;\r
- sequencesHeight = (int)(400f/initialScale);\r
+ sequencesHeight = (int) (400f / initialScale);\r
}\r
else\r
{\r
// taller\r
- width = (int)(400f*initialScale);\r
+ width = (int) (400f * initialScale);\r
sequencesHeight = 300;\r
- if(width<120)\r
+\r
+ if (width < 120)\r
+ {\r
width = 120;\r
+ }\r
}\r
\r
addComponentListener(new ComponentAdapter()\r
- {\r
-\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- if( getWidth()!=width || getHeight()!=sequencesHeight+graphHeight)\r
- {\r
- updateOverviewImage();\r
- }\r
- }\r
- });\r
+ {\r
+ public void componentResized(ComponentEvent evt)\r
+ {\r
+ if ( (getWidth() != width) ||\r
+ (getHeight() != (sequencesHeight + graphHeight)))\r
+ {\r
+ updateOverviewImage();\r
+ }\r
+ }\r
+ });\r
\r
addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- { doMouseDragged(evt);}\r
- });\r
+ {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ doMouseDragged(evt);\r
+ }\r
+ });\r
\r
addMouseListener(new MouseAdapter()\r
{\r
public void mousePressed(MouseEvent evt)\r
- { doMousePressed(evt);}\r
+ {\r
+ doMousePressed(evt);\r
+ }\r
+\r
public void mouseReleased(MouseEvent evt)\r
- { doMouseReleased(evt);}\r
+ {\r
+ doMouseReleased(evt);\r
+ }\r
});\r
\r
updateOverviewImage();\r
-\r
}\r
\r
public void doMousePressed(MouseEvent evt)\r
boxX = evt.getX();\r
boxY = evt.getY();\r
checkValid();\r
- if(!resizing)\r
- ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),\r
- (int)(boxY/scaleh/av.getCharHeight()) );\r
+\r
+ if (!resizing)\r
+ {\r
+ ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
+ (int) (boxY / scaleh / av.getCharHeight()));\r
+ }\r
}\r
\r
public void doMouseDragged(MouseEvent evt)\r
boxX = evt.getX();\r
boxY = evt.getY();\r
checkValid();\r
- if(!resizing)\r
- ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),\r
- (int)(boxY/scaleh/av.getCharHeight()) );\r
+\r
+ if (!resizing)\r
+ {\r
+ ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
+ (int) (boxY / scaleh / av.getCharHeight()));\r
+ }\r
}\r
\r
void checkValid()\r
{\r
if (boxY < 0)\r
+ {\r
boxY = 0;\r
+ }\r
\r
- if (boxY > sequencesHeight - boxHeight)\r
- boxY = sequencesHeight - boxHeight+1;\r
+ if (boxY > (sequencesHeight - boxHeight))\r
+ {\r
+ boxY = sequencesHeight - boxHeight + 1;\r
+ }\r
\r
if (boxX < 0)\r
+ {\r
boxX = 0;\r
+ }\r
\r
- if (boxX > width - boxWidth)\r
+ if (boxX > (width - boxWidth))\r
+ {\r
boxX = width - boxWidth;\r
+ }\r
}\r
\r
public void updateOverviewImage()\r
{\r
- if(resizing)\r
+ if (resizing)\r
{\r
return;\r
}\r
\r
resizing = true;\r
+\r
Thread thread = new Thread(this);\r
thread.start();\r
repaint();\r
public void run()\r
{\r
miniMe = null;\r
+\r
int alwidth = av.alignment.getWidth();\r
int alheight = av.alignment.getHeight();\r
\r
- if(getWidth()>0 && getHeight()>0)\r
+ if ( (getWidth() > 0) && (getHeight() > 0))\r
{\r
width = getWidth();\r
sequencesHeight = getHeight() - graphHeight;\r
}\r
\r
- setPreferredSize (new Dimension(width, sequencesHeight+graphHeight));\r
+ setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
\r
- int fullsizeWidth = alwidth * av.getCharWidth();\r
+ int fullsizeWidth = alwidth * av.getCharWidth();\r
int fullsizeHeight = alheight * av.getCharHeight();\r
\r
scalew = (float) width / (float) fullsizeWidth;\r
BufferedImage.TYPE_INT_RGB);\r
\r
Graphics mg = miniMe.getGraphics();\r
- BufferedImage consensus = new BufferedImage(fullsizeWidth,\r
- 60,\r
- BufferedImage.TYPE_3BYTE_BGR);\r
+ BufferedImage consensus = new BufferedImage(fullsizeWidth, 60,\r
+ BufferedImage.TYPE_3BYTE_BGR);\r
Graphics g = consensus.getGraphics();\r
ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);\r
mg.drawImage(consensus, 0, sequencesHeight, width,\r
- sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
-\r
+ sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
\r
boolean oldRenderGaps = av.renderGaps;\r
- try{\r
- // We'll have to draw the full size alignment in chunks, as an image of the\r
- // whole alignment requires too much memory\r
\r
+ try\r
+ {\r
+ // We'll have to draw the full size alignment in chunks, as an image of the\r
+ // whole alignment requires too much memory\r
// Max size depends on the font size, the following is a\r
// guess at a size which works\r
- int maxSize = 2000 / av.getFont().getSize();\r
+ int maxSize = 2000 / av.getFont().getSize();\r
BufferedImage block;\r
- int blockx=0, blocky=0, blockw=0, blockh=0, eRes=0, eSeq=0;\r
+ int blockx = 0;\r
+ int blocky = 0;\r
+ int blockw = 0;\r
+ int blockh = 0;\r
+ int eRes = 0;\r
+ int eSeq = 0;\r
\r
av.setRenderGaps(false);\r
- for(int sRes=0, chunkx=0; sRes<alwidth; sRes+=maxSize, chunkx++)\r
+\r
+ for (int sRes = 0, chunkx = 0; sRes < alwidth;\r
+ sRes += maxSize, chunkx++)\r
{\r
- eSeq = 0;\r
- eRes+=maxSize;\r
- if(eRes>alwidth)\r
- eRes = alwidth;\r
+ eSeq = 0;\r
+ eRes += maxSize;\r
\r
- for(int sSeq=0, chunky=0; sSeq<alheight; sSeq+=maxSize, chunky++)\r
- {\r
- eSeq+=maxSize;\r
- if(eSeq>alheight)\r
- eSeq = alheight;\r
+ if (eRes > alwidth)\r
+ {\r
+ eRes = alwidth;\r
+ }\r
\r
- blocky = 0;\r
- blockx = (int)((float)sRes/(float)alwidth * width);\r
+ for (int sSeq = 0, chunky = 0; sSeq < alheight;\r
+ sSeq += maxSize, chunky++)\r
+ {\r
+ eSeq += maxSize;\r
\r
- block = new BufferedImage((eRes-sRes)*av.charWidth,\r
- (eSeq-sSeq)*av.charHeight,\r
- BufferedImage.TYPE_3BYTE_BGR);\r
- g = block.getGraphics();\r
+ if (eSeq > alheight)\r
+ {\r
+ eSeq = alheight;\r
+ }\r
\r
- ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);\r
+ blocky = 0;\r
+ blockx = (int) ( (float) sRes / (float) alwidth * width);\r
\r
- blockh = (int)( (float)(eSeq-sSeq)/(float)alheight * sequencesHeight )+1 ;\r
- blockw = (int)( (float)(eRes-sRes)/(float)alwidth * width )+1;\r
+ block = new BufferedImage( (eRes - sRes) * av.charWidth,\r
+ (eSeq - sSeq) * av.charHeight,\r
+ BufferedImage.TYPE_3BYTE_BGR);\r
+ g = block.getGraphics();\r
\r
- blocky += (int) ((float)sSeq/(float)alheight* sequencesHeight);\r
+ ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq,\r
+ sRes, sSeq, 0);\r
\r
- mg.drawImage(block, blockx,\r
- blocky ,\r
- blockx + blockw,\r
- blocky + blockh,\r
+ blockh = (int) ( (float) (eSeq - sSeq) / (float) alheight *\r
+ sequencesHeight) +\r
+ 1;\r
+ blockw = (int) ( (float) (eRes - sRes) / (float) alwidth * width) +\r
+ 1;\r
\r
- 0, 0, block.getWidth(),block.getHeight(), this);\r
+ blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);\r
\r
- block = null;\r
- }\r
+ mg.drawImage(block, blockx, blocky, blockx + blockw,\r
+ blocky + blockh, 0, 0, block.getWidth(),\r
+ block.getHeight(), this);\r
\r
+ block = null;\r
+ }\r
}\r
-\r
- }catch(OutOfMemoryError error)\r
- { System.err.println("Out of memory when trying to calculate the overview window image!"); }\r
-\r
+ }\r
+ catch (OutOfMemoryError error)\r
+ {\r
+ System.err.println(\r
+ "Out of memory when trying to calculate the overview window image!");\r
+ }\r
\r
av.setRenderGaps(oldRenderGaps);\r
resizing = false;\r
\r
public void setBoxPosition()\r
{\r
- boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
- boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
- boxWidth = (int) ((av.getEndRes()-av.getStartRes()+1)* av.getCharWidth() * scalew) ;\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;\r
- repaint();\r
+ boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
+ boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
+ boxWidth = (int) ( (av.getEndRes() - av.getStartRes() + 1) *\r
+ av.getCharWidth() * scalew);\r
+ boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -\r
+ boxY;\r
+ repaint();\r
}\r
\r
-\r
public void paintComponent(Graphics g)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(),getHeight());\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
g.setColor(Color.black);\r
\r
- if(resizing)\r
+ if (resizing)\r
{\r
g.setFont(new Font("Verdana", Font.BOLD, 15));\r
- g.drawString("Recalculating", 5, sequencesHeight/2);\r
- g.drawString("Overview.....", 5, sequencesHeight/2 +20);\r
+ g.drawString("Recalculating", 5, sequencesHeight / 2);\r
+ g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);\r
}\r
else\r
{\r
- if(miniMe!=null)\r
- g.drawImage(miniMe, 0,0,this);\r
+ if (miniMe != null)\r
+ {\r
+ g.drawImage(miniMe, 0, 0, this);\r
+ }\r
\r
g.setColor(Color.red);\r
g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2);\r
+ g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
}\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.PCA;\r
-import jalview.jbgui.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
\r
-public class PCAPanel extends GPCAPanel implements Runnable\r
+public class PCAPanel\r
+ extends GPCAPanel implements Runnable\r
{\r
PCA pca;\r
int top;\r
RotatableCanvas rc;\r
AlignViewport av;\r
\r
- public void run()\r
+ public PCAPanel(AlignViewport av, SequenceI[] s)\r
{\r
- // do stuff\r
- }\r
-\r
- public PCAPanel(AlignViewport av, SequenceI[] s) {\r
-\r
this.av = av;\r
- if(av.getSelectionGroup()!=null && av.getSelectionGroup().getSize()>3)\r
+\r
+ if ( (av.getSelectionGroup() != null) &&\r
+ (av.getSelectionGroup().getSize() > 3))\r
{\r
s = new Sequence[av.getSelectionGroup().getSize()];\r
- for(int i=0; i<s.length; i++)\r
+\r
+ for (int i = 0; i < s.length; i++)\r
+ {\r
s[i] = av.getSelectionGroup().getSequenceAt(i);\r
+ }\r
}\r
\r
-\r
- if(s==null)\r
+ if (s == null)\r
{\r
s = new Sequence[av.getAlignment().getHeight()];\r
+\r
for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
s[i] = av.getAlignment().getSequenceAt(i);\r
- }\r
+ }\r
+ }\r
\r
-//////////////////////This part was done in PCATHread originally. Is it too slow???\r
+ //////////////////////This part was done in PCATHread originally. Is it too slow???\r
pca = new PCA(s);\r
pca.run();\r
\r
// Now find the component coordinates\r
- int ii=0;\r
- while (ii < s.length && s[ii] != null)\r
+ int ii = 0;\r
+\r
+ while ( (ii < s.length) && (s[ii] != null))\r
{\r
ii++;\r
}\r
\r
double[][] comps = new double[ii][ii];\r
\r
- for (int i=0; i < ii; i++ )\r
+ for (int i = 0; i < ii; i++)\r
{\r
if (pca.getEigenvalue(i) > 1e-4)\r
{\r
- comps[i] = pca.component(i);\r
+ comps[i] = pca.component(i);\r
}\r
}\r
\r
//////////////////\r
-\r
xCombobox.setSelectedIndex(0);\r
yCombobox.setSelectedIndex(1);\r
zCombobox.setSelectedIndex(2);\r
\r
- top = pca.getM().rows-1;\r
+ top = pca.getM().rows - 1;\r
\r
Vector points = new Vector();\r
- float[][] scores = pca.getComponents(top-1,top-2,top-3,100);\r
+ float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);\r
\r
- for (int i =0; i < pca.getM().rows; i++ )\r
+ for (int i = 0; i < pca.getM().rows; i++)\r
{\r
- SequencePoint sp = new SequencePoint(s[i],scores[i]);\r
+ SequencePoint sp = new SequencePoint(s[i], scores[i]);\r
points.addElement(sp);\r
}\r
\r
- rc = new RotatableCanvas(av,points,pca.getM().rows);\r
+ rc = new RotatableCanvas(av, points, pca.getM().rows);\r
\r
//rc.printPoints();\r
-\r
add(rc, BorderLayout.CENTER);\r
}\r
\r
+ public void run()\r
+ {\r
+ // do stuff\r
+ }\r
\r
void doDimensionChange()\r
{\r
- if(top==0)\r
+ if (top == 0)\r
+ {\r
return;\r
+ }\r
\r
int dim1 = top - xCombobox.getSelectedIndex();\r
int dim2 = top - yCombobox.getSelectedIndex();\r
int dim3 = top - zCombobox.getSelectedIndex();\r
\r
- float[][] scores = pca.getComponents(dim1,dim2,dim3,100);\r
- for (int i=0; i < pca.getM().rows; i++) {\r
- ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];\r
+ float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);\r
+\r
+ for (int i = 0; i < pca.getM().rows; i++)\r
+ {\r
+ ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];\r
}\r
\r
rc.img = null;\r
{\r
doDimensionChange();\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
-import java.awt.*;\r
+\r
import java.util.*;\r
\r
+import java.awt.*;\r
+\r
public class PaintRefresher\r
{\r
static Vector components = new Vector();\r
\r
public static void Register(Component c)\r
{\r
- if(!components.contains(c))\r
+ if (!components.contains(c))\r
+ {\r
components.add(c);\r
+ }\r
else\r
+ {\r
components.remove(c);\r
+ }\r
}\r
\r
public static void Refresh(Component c)\r
{\r
Component temp;\r
Enumeration e = components.elements();\r
- while( e.hasMoreElements() )\r
+\r
+ while (e.hasMoreElements())\r
{\r
- temp = (Component)e.nextElement();\r
+ temp = (Component) e.nextElement();\r
\r
- if(!temp.isValid())\r
- components.removeElement( temp );\r
- else if( temp == c )\r
- continue;\r
+ if (!temp.isValid())\r
+ {\r
+ components.removeElement(temp);\r
+ }\r
+ else if (temp == c)\r
+ {\r
+ continue;\r
+ }\r
\r
temp.repaint();\r
}\r
-\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.jbgui.GPairwiseAlignPanel;\r
-import jalview.analysis.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
import java.util.*;\r
\r
+import java.awt.event.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
\r
-public class PairwiseAlignPanel extends GPairwiseAlignPanel\r
+public class PairwiseAlignPanel\r
+ extends GPairwiseAlignPanel\r
{\r
- Vector sequences = new Vector();\r
- AlignViewport av;\r
+ Vector sequences = new Vector();\r
+ AlignViewport av;\r
+\r
+ public PairwiseAlignPanel(AlignViewport av)\r
+ {\r
+ super();\r
+ this.av = av;\r
\r
- public PairwiseAlignPanel(AlignViewport av)\r
+ Vector selsubset = new Vector();\r
+\r
+ for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)\r
{\r
- super();\r
- this.av = av;\r
- Vector selsubset = new Vector();\r
- for (int i=0, j=av.getSelectionGroup().getSize(); i<j; i++)\r
- if (av.getAlignment().getSequences().contains(av.getSelectionGroup().getSequenceAt(i)))\r
- selsubset.add(av.getSelectionGroup().getSequenceAt(i));\r
- float scores[][] = new float[selsubset.size()][selsubset.size()];\r
- double totscore = 0;\r
- int count = selsubset.size();\r
-\r
- int acount = 0;\r
- for (int i = 1; i < count; i++)\r
+ if (av.getAlignment().getSequences().contains(av.getSelectionGroup()\r
+ .getSequenceAt(i)))\r
{\r
- for (int j = 0; j < i; j++)\r
- {\r
- acount++;\r
- AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),\r
- (SequenceI) selsubset.elementAt(j), "pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
- scores[i][j] = (float) as.getMaxScore() /\r
- (float) as.getASeq1().length;\r
- totscore = totscore + scores[i][j];\r
-\r
- textarea.append(as.getOutput());\r
- sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));\r
- sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));\r
- }\r
+ selsubset.add(av.getSelectionGroup().getSequenceAt(i));\r
}\r
- if (count > 2)\r
- {\r
- System.out.println("Pairwise alignment scaled similarity score matrix\n");\r
- for (int i = 0; i < count;i++)\r
- jalview.util.Format.print(System.out, "%s \n", (""+i)+" "+((SequenceI) selsubset.elementAt(i)).getName());\r
- System.out.println("\n");\r
- for (int i = 0; i < count;i++)\r
- for (int j = 0; j < i; j++)\r
- jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);\r
- System.out.println("\n");\r
+ }\r
+\r
+ float[][] scores = new float[selsubset.size()][selsubset.size()];\r
+ double totscore = 0;\r
+ int count = selsubset.size();\r
\r
+ int acount = 0;\r
+\r
+ for (int i = 1; i < count; i++)\r
+ {\r
+ for (int j = 0; j < i; j++)\r
+ {\r
+ acount++;\r
+\r
+ AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),\r
+ (SequenceI) selsubset.elementAt(j), "pep");\r
+ as.calcScoreMatrix();\r
+ as.traceAlignment();\r
+ as.printAlignment();\r
+ scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
+ totscore = totscore + scores[i][j];\r
+\r
+ textarea.append(as.getOutput());\r
+ sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));\r
+ sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));\r
}\r
}\r
\r
+ if (count > 2)\r
+ {\r
+ System.out.println(\r
+ "Pairwise alignment scaled similarity score matrix\n");\r
\r
- protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
- {\r
+ for (int i = 0; i < count; i++)\r
+ {\r
+ jalview.util.Format.print(System.out, "%s \n",\r
+ ("" + i) + " " +\r
+ ( (SequenceI) selsubset.elementAt(i)).getName());\r
+ }\r
\r
- Sequence [] seq = new Sequence[sequences.size()];\r
+ System.out.println("\n");\r
\r
- for (int i=0;i<sequences.size();i++)\r
- seq[i] = (Sequence) sequences.elementAt(i);\r
+ for (int i = 0; i < count; i++)\r
+ {\r
+ for (int j = 0; j < i; j++)\r
+ {\r
+ jalview.util.Format.print(System.out, "%7.3f",\r
+ scores[i][j] / totscore);\r
+ }\r
+ }\r
\r
+ System.out.println("\n");\r
+ }\r
+ }\r
\r
- AlignFrame af = new AlignFrame(new Alignment(seq));\r
- Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
+ protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
+ {\r
+ Sequence[] seq = new Sequence[sequences.size()];\r
\r
- }\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ seq[i] = (Sequence) sequences.elementAt(i);\r
+ }\r
\r
+ AlignFrame af = new AlignFrame(new Alignment(seq));\r
+ Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ }\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.schemes.*;\r
import java.awt.*;\r
-import javax.swing.*;\r
import java.awt.event.*;\r
-import jalview.io.*;\r
+import javax.swing.*;\r
+\r
import MCview.*;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.schemes.*;\r
\r
-public class PopupMenu extends JPopupMenu\r
+public class PopupMenu\r
+ extends JPopupMenu\r
{\r
JMenu groupMenu = new JMenu();\r
JMenuItem groupName = new JMenuItem();\r
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem hydrophobicityColour = new\r
+ JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
-\r
-\r
AlignmentPanel ap;\r
JMenu sequenceMenu = new JMenu();\r
JMenuItem sequenceName = new JMenuItem();\r
//\r
// If from the IDPanel, we must display the sequence menu\r
//////////////////////////////////////////////////////////\r
-\r
this.ap = ap;\r
sequence = seq;\r
\r
colours.add(BLOSUM62Colour);\r
\r
try\r
- { jbInit(); }\r
- catch(Exception e)\r
- { e.printStackTrace(); }\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg!=null)\r
+\r
+ if (sg != null)\r
{\r
groupName.setText(sg.getName());\r
- if(sg.cs instanceof ZappoColourScheme)\r
+\r
+ if (sg.cs instanceof ZappoColourScheme)\r
+ {\r
zappoColour.setSelected(true);\r
- else if(sg.cs instanceof TaylorColourScheme)\r
+ }\r
+ else if (sg.cs instanceof TaylorColourScheme)\r
+ {\r
taylorColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof PIDColourScheme)\r
+ {\r
PIDColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof Blosum62ColourScheme)\r
+ {\r
BLOSUM62Colour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof UserColourScheme)\r
+ {\r
userDefinedColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof HydrophobicColourScheme)\r
+ {\r
hydrophobicityColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof HelixColourScheme)\r
+ {\r
helixColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof StrandColourScheme)\r
+ {\r
strandColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof TurnColourScheme)\r
+ {\r
turnColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof BuriedColourScheme)\r
+ {\r
buriedColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof ClustalxColourScheme)\r
+ {\r
clustalColour.setSelected(true);\r
+ }\r
else\r
+ {\r
noColourmenuItem.setSelected(true);\r
+ }\r
\r
if (sg.cs instanceof ConservationColourScheme)\r
+ {\r
conservationMenuItem.setSelected(true);\r
+ }\r
\r
showText.setSelected(sg.getDisplayText());\r
showColourText.setSelected(sg.getColourText());\r
showBoxes.setSelected(sg.getDisplayBoxes());\r
}\r
\r
- if( !ap.av.alignment.getGroups().contains(sg))\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
+ {\r
unGroupMenuItem.setVisible(false);\r
+ }\r
else\r
+ {\r
groupMenu.insertSeparator(3);\r
+ }\r
\r
- if(seq==null)\r
- sequenceMenu.setVisible(false);\r
-\r
+ if (seq == null)\r
+ {\r
+ sequenceMenu.setVisible(false);\r
+ }\r
}\r
- private void jbInit() throws Exception\r
+\r
+ private void jbInit()\r
+ throws Exception\r
{\r
groupMenu.setText("Group");\r
groupMenu.setText("Define");\r
}\r
});\r
conservationMenuItem.setText("Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
-\r
-\r
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ conservationMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
}\r
\r
void refresh()\r
{\r
SequenceGroup sg = getGroup();\r
- SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
- if( superG !=null)\r
- superG.setSuperGroupProperties( sg );\r
+ SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
+\r
+ if (superG != null)\r
+ {\r
+ superG.setSuperGroupProperties(sg);\r
+ }\r
\r
ap.seqPanel.repaint();\r
}\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.sequences,\r
+ ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
refresh();\r
}\r
\r
-\r
protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
getGroup().cs = new HydrophobicColourScheme();\r
refresh();\r
}\r
\r
-\r
-\r
protected void abovePIDColour_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
+\r
if (abovePIDColour.isSelected())\r
{\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
ap.av.alignment.getWidth()));\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
+\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
+ getGroup().getName());\r
+\r
if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
+ {\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
\r
SliderPanel.showPIDSlider();\r
-\r
-\r
}\r
else // remove PIDColouring\r
{\r
}\r
\r
refresh();\r
-\r
}\r
\r
-\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- new UserDefinedColours( ap, getGroup());\r
+ new UserDefinedColours(ap, getGroup());\r
}\r
\r
protected void PIDColour_actionPerformed(ActionEvent e)\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ ap.av.alignment.getWidth()));\r
\r
refresh();\r
}\r
\r
-\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
getGroup().cs = null;\r
refresh();\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
\r
- if(conservationMenuItem.isSelected())\r
+ if (conservationMenuItem.isSelected())\r
{\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ ap.av.alignment.getWidth());\r
\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
sg.cs = ccs;\r
\r
}\r
else // remove ConservationColouring\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
+ ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
+ sg.cs = ccs.cs;\r
}\r
\r
- refresh();\r
+ refresh();\r
}\r
\r
-\r
protected void groupName_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
- if(reply==null)\r
+ String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter new group name", "Edit group name",\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply == null)\r
+ {\r
return;\r
+ }\r
\r
sg.setName(reply);\r
groupName.setText(reply);\r
}\r
\r
-\r
protected void analyze_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for(int i=0; i<sg.sequences.size(); i++)\r
- {\r
- Sequence tmp = (Sequence)sg.sequences.get(i);\r
- sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText( sb.toString() );\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(cap);\r
+ Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
+\r
+ SequenceGroup sg = getGroup();\r
+ StringBuffer sb = new StringBuffer();\r
\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ Sequence tmp = (Sequence) sg.sequences.get(i);\r
+ sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
+ sb.append("\n");\r
+ }\r
+\r
+ sb.append("Something amazing will happen soon");\r
+ cap.setText(sb.toString());\r
}\r
\r
SequenceGroup getGroup()\r
void sequenceName_actionPerformed(ActionEvent e)\r
{\r
String id = sequence.getName();\r
- String s = (String)JOptionPane.showInternalInputDialog(\r
- ap,\r
- "Edit sequence name",\r
- "Edit sequence name ("+sequence.getName()+")",\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- null,\r
- id);\r
+ String s = (String) JOptionPane.showInternalInputDialog(ap,\r
+ "Edit sequence name",\r
+ "Edit sequence name (" + sequence.getName() + ")",\r
+ JOptionPane.PLAIN_MESSAGE, null, null, id);\r
\r
- if(s!=null)\r
+ if (s != null)\r
{\r
sequence.setName(s);\r
ap.repaint();\r
}\r
-\r
}\r
\r
void unGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
}\r
\r
void pdbMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if(sequence.getPDBId()==null)\r
+ if (sequence.getPDBId() == null)\r
+ {\r
return;\r
+ }\r
\r
try\r
{\r
EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
+ String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,\r
+ null);\r
\r
PDBfile pdb = new PDBfile(result);\r
\r
rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
JInternalFrame frame = new JInternalFrame();\r
frame.setContentPane(rc);\r
- Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
+ Desktop.addInternalFrame(frame,\r
+ sequence.getName() + " " + sequence.getPDBId(),\r
+ 400, 400);\r
}\r
catch (Exception ex)\r
{\r
protected void outline_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);\r
- if(col!=null)\r
+ Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
+ Color.BLUE);\r
+\r
+ if (col != null)\r
+ {\r
sg.setOutlineColour(col);\r
+ }\r
+\r
ap.repaint();\r
}\r
\r
getGroup().setColourText(showColourText.isSelected());\r
refresh();\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
-import jalview.io.*;\r
-\r
-import jalview.bin.Cache;\r
-import javax.swing.*;\r
-import java.awt.event.ActionEvent;\r
import java.awt.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
\r
+import jalview.bin.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
\r
-public class Preferences extends GPreferences\r
+public class Preferences\r
+ extends GPreferences\r
{\r
- static boolean preferencesLoaded=false;\r
-\r
- public static boolean showFullscreen=false;\r
- public static boolean showFullId=true;\r
- public static boolean showAnnotation=true;\r
- public static boolean showConservation=true;\r
- public static boolean showQuality=true;\r
- public static boolean showIdentity=true;\r
- public static String fontName="SansSerif";\r
- public static String fontSize="10";\r
- public static String fontStyle=Font.PLAIN+"";\r
- public static char gapSymbol='-';\r
- public static String defaultColour=null;\r
- public static boolean showStartupFile=true;\r
- public static String startupFile = "http://www.jalview.org/examples/exampleFile.jar";\r
-\r
+ static boolean preferencesLoaded = false;\r
+ public static boolean showFullscreen = false;\r
+ public static boolean showFullId = true;\r
+ public static boolean showAnnotation = true;\r
+ public static boolean showConservation = true;\r
+ public static boolean showQuality = true;\r
+ public static boolean showIdentity = true;\r
+ public static String fontName = "SansSerif";\r
+ public static String fontSize = "10";\r
+ public static String fontStyle = Font.PLAIN + "";\r
+ public static char gapSymbol = '-';\r
+ public static String defaultColour = null;\r
+ public static boolean showStartupFile = true;\r
+ public static String startupFile =\r
+ "http://www.jalview.org/examples/exampleFile.jar";\r
JInternalFrame frame;\r
\r
- public static void initPreferences()\r
- {\r
- String string = Cache.getProperty("SHOW_FULL_ID");\r
- if(string!=null)\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_FULLSCREEN");\r
- if(string!=null)\r
- showFullscreen = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_ANNOTATIONS");\r
- if(string!=null)\r
- showAnnotation = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_CONSERVATION");\r
- if(string!=null)\r
- showConservation = Boolean.valueOf(string).booleanValue();\r
- string = Cache.getProperty("SHOW_QUALITY");\r
- if(string!=null)\r
- showQuality = Boolean.valueOf(string).booleanValue();\r
- string = Cache.getProperty("SHOW_IDENTITY");\r
- if(string!=null)\r
- showIdentity = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("GAP_SYMBOL");\r
- if(string!=null)\r
- gapSymbol = string.charAt(0);\r
-\r
- string = Cache.getProperty("SHOW_FULL_ID");\r
- if(string!=null)\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("FONT_NAME");\r
- if (string != null)\r
- fontName = string;\r
-\r
- string = Cache.getProperty("FONT_STYLE");\r
- if (string != null)\r
- fontStyle = string;\r
-\r
- string = Cache.getProperty("FONT_SIZE");\r
- if (string != null)\r
- fontSize = string;\r
-\r
-\r
- string = Cache.getProperty("DEFAULT_COLOUR");\r
- if(string!=null)\r
- defaultColour = string;\r
-\r
- string = Cache.getProperty("STARTUP_FILE");\r
- if(string!=null)\r
- startupFile = string;\r
-\r
- string = Cache.getProperty("SHOW_STARTUP_FILE");\r
- if(string!=null)\r
- showStartupFile = Boolean.valueOf(string).booleanValue();\r
-\r
- preferencesLoaded = true;\r
- }\r
-\r
public Preferences()\r
{\r
initPreferences();\r
\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Preferences", 480,390 );\r
+ Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
\r
fullID.setSelected(showFullId);\r
+\r
String string = Cache.getProperty("SHOW_FULLSCREEN");\r
boolean value = false;\r
- if(string!=null)\r
- value = Boolean.valueOf(string).booleanValue();\r
+\r
+ if (string != null)\r
+ {\r
+ value = Boolean.valueOf(string).booleanValue();\r
+ }\r
\r
fullScreen.setSelected(value);\r
annotations.setSelected(showAnnotation);\r
quality.setSelected(showQuality);\r
identity.setSelected(showIdentity);\r
\r
- for(int i=0; i<12; i++)\r
- colour.addItem( ColourSchemeProperty.getColourName(i) );\r
+ for (int i = 0; i < 12; i++)\r
+ {\r
+ colour.addItem(ColourSchemeProperty.getColourName(i));\r
+ }\r
\r
string = Cache.getProperty("DEFAULT_COLOUR");\r
- if(string!=null)\r
- colour.setSelectedItem( string );\r
+\r
+ if (string != null)\r
+ {\r
+ colour.setSelectedItem(string);\r
+ }\r
else\r
- colour.setSelectedIndex( 11 );\r
+ {\r
+ colour.setSelectedIndex(11);\r
+ }\r
\r
- String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
- for(int i=0; i<fonts.length; i++)\r
+ String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
+ .getAvailableFontFamilyNames();\r
+\r
+ for (int i = 0; i < fonts.length; i++)\r
+ {\r
fontNameCB.addItem(fonts[i]);\r
+ }\r
+\r
+ for (int i = 1; i < 31; i++)\r
+ {\r
+ fontSizeCB.addItem(i + "");\r
+ }\r
+\r
+ fontStyleCB.addItem("plain");\r
+ fontStyleCB.addItem("bold");\r
+ fontStyleCB.addItem("italic");\r
+\r
+ fontNameCB.setSelectedItem(fontName);\r
+ fontSizeCB.setSelectedItem(fontSize);\r
+ fontStyleCB.setSelectedItem(fontStyle);\r
+\r
+ gapSymbolCB.addItem("-");\r
+ gapSymbolCB.addItem(".");\r
+\r
+ gapSymbolCB.setSelectedItem(gapSymbol + "");\r
+\r
+ startupCheckbox.setSelected(showStartupFile);\r
+ startupFileTextfield.setText(startupFile);\r
+ }\r
+\r
+ public static void initPreferences()\r
+ {\r
+ String string = Cache.getProperty("SHOW_FULL_ID");\r
\r
- for(int i=1; i<31; i++)\r
- fontSizeCB.addItem(i+"");\r
+ if (string != null)\r
+ {\r
+ showFullId = Boolean.valueOf(string).booleanValue();\r
+ }\r
+\r
+ string = Cache.getProperty("SHOW_FULLSCREEN");\r
+\r
+ if (string != null)\r
+ {\r
+ showFullscreen = Boolean.valueOf(string).booleanValue();\r
+ }\r
+\r
+ string = Cache.getProperty("SHOW_ANNOTATIONS");\r
+\r
+ if (string != null)\r
+ {\r
+ showAnnotation = Boolean.valueOf(string).booleanValue();\r
+ }\r
+\r
+ string = Cache.getProperty("SHOW_CONSERVATION");\r
+\r
+ if (string != null)\r
+ {\r
+ showConservation = Boolean.valueOf(string).booleanValue();\r
+ }\r
+\r
+ string = Cache.getProperty("SHOW_QUALITY");\r
+\r
+ if (string != null)\r
+ {\r
+ showQuality = Boolean.valueOf(string).booleanValue();\r
+ }\r
+\r
+ string = Cache.getProperty("SHOW_IDENTITY");\r
+\r
+ if (string != null)\r
+ {\r
+ showIdentity = Boolean.valueOf(string).booleanValue();\r
+ }\r
+\r
+ string = Cache.getProperty("GAP_SYMBOL");\r
+\r
+ if (string != null)\r
+ {\r
+ gapSymbol = string.charAt(0);\r
+ }\r
+\r
+ string = Cache.getProperty("SHOW_FULL_ID");\r
+\r
+ if (string != null)\r
+ {\r
+ showFullId = Boolean.valueOf(string).booleanValue();\r
+ }\r
+\r
+ string = Cache.getProperty("FONT_NAME");\r
\r
- fontStyleCB.addItem("plain");\r
- fontStyleCB.addItem("bold");\r
- fontStyleCB.addItem("italic");\r
+ if (string != null)\r
+ {\r
+ fontName = string;\r
+ }\r
+\r
+ string = Cache.getProperty("FONT_STYLE");\r
+\r
+ if (string != null)\r
+ {\r
+ fontStyle = string;\r
+ }\r
+\r
+ string = Cache.getProperty("FONT_SIZE");\r
+\r
+ if (string != null)\r
+ {\r
+ fontSize = string;\r
+ }\r
+\r
+ string = Cache.getProperty("DEFAULT_COLOUR");\r
\r
- fontNameCB.setSelectedItem(fontName);\r
- fontSizeCB.setSelectedItem(fontSize);\r
- fontStyleCB.setSelectedItem(fontStyle);\r
+ if (string != null)\r
+ {\r
+ defaultColour = string;\r
+ }\r
\r
- gapSymbolCB.addItem("-");\r
- gapSymbolCB.addItem(".");\r
+ string = Cache.getProperty("STARTUP_FILE");\r
\r
- gapSymbolCB.setSelectedItem( gapSymbol+"" );\r
+ if (string != null)\r
+ {\r
+ startupFile = string;\r
+ }\r
\r
- startupCheckbox.setSelected(showStartupFile);\r
- startupFileTextfield.setText(startupFile);\r
+ string = Cache.getProperty("SHOW_STARTUP_FILE");\r
\r
+ if (string != null)\r
+ {\r
+ showStartupFile = Boolean.valueOf(string).booleanValue();\r
+ }\r
+\r
+ preferencesLoaded = true;\r
}\r
\r
public void ok_actionPerformed(ActionEvent e)\r
{\r
- showFullId = fullID.isSelected() ;\r
+ showFullId = fullID.isSelected();\r
showFullscreen = fullScreen.isSelected();\r
showAnnotation = annotations.isSelected();\r
showConservation = conservation.isSelected();\r
showStartupFile = startupCheckbox.isSelected();\r
\r
Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));\r
- Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString( showFullscreen ) );\r
+ Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString(showFullscreen));\r
\r
- Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString( showAnnotation ));\r
- Cache.setProperty("SHOW_CONSERVATION", Boolean.toString( showConservation ));\r
- Cache.setProperty("SHOW_QUALITY", Boolean.toString( showQuality ));\r
- Cache.setProperty("SHOW_IDENTITY", Boolean.toString( showIdentity ));\r
+ Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString(showAnnotation));\r
+ Cache.setProperty("SHOW_CONSERVATION",\r
+ Boolean.toString(showConservation));\r
+ Cache.setProperty("SHOW_QUALITY", Boolean.toString(showQuality));\r
+ Cache.setProperty("SHOW_IDENTITY", Boolean.toString(showIdentity));\r
\r
Cache.setProperty("DEFAULT_COLOUR", defaultColour);\r
- Cache.setProperty("GAP_SYMBOL", gapSymbol+"");\r
+ Cache.setProperty("GAP_SYMBOL", gapSymbol + "");\r
\r
Cache.setProperty("FONT_NAME", fontName);\r
Cache.setProperty("FONT_STYLE", fontStyle);\r
Cache.setProperty("STARTUP_FILE", startupFile);\r
Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));\r
\r
-\r
-\r
- try {\r
+ try\r
+ {\r
frame.setClosed(true);\r
- } catch (Exception ex) {}\r
-\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
\r
public void startupFileTextfield_mouseClicked()\r
{\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}\r
- ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select startup file");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());\r
- startupFileTextfield.setText( chooser.getSelectedFile().getAbsolutePath() );\r
- }\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Select startup file");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
+ chooser.getSelectedFormat());\r
+ startupFileTextfield.setText(chooser.getSelectedFile()\r
+ .getAbsolutePath());\r
+ }\r
}\r
\r
-\r
public void cancel_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
frame.setClosed(true);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
\r
public void annotations_actionPerformed(ActionEvent e)\r
quality.setEnabled(annotations.isSelected());\r
identity.setEnabled(annotations.isSelected());\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.*;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
import java.util.*;\r
+\r
+import java.awt.event.*;\r
import javax.swing.event.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+\r
public class RedundancyPanel\r
extends GSliderPanel\r
{\r
slider.setMinimum(0);\r
slider.setMaximum(100);\r
slider.setValue(100);\r
-\r
}\r
\r
public void applyButton_actionPerformed(ActionEvent e)\r
float threshold = slider.getValue();\r
Vector del;\r
HistoryItem it;\r
- historyList.push(it=new HistoryItem("Remove redundancy",\r
- ap.av.alignment, HistoryItem.HIDE));\r
- if (historyList.size()==1\r
- || !af.historyList.contains(historyList.firstElement())) {\r
- af.addHistoryItem((HistoryItem) historyList.firstElement());\r
+ historyList.push(it = new HistoryItem("Remove redundancy",\r
+ ap.av.alignment, HistoryItem.HIDE));\r
+\r
+ if ( (historyList.size() == 1) ||\r
+ !af.historyList.contains(historyList.firstElement()))\r
+ {\r
+ af.addHistoryItem( (HistoryItem) historyList.firstElement());\r
af.updateEditMenuBar();\r
}\r
+\r
undoButton.setEnabled(true);\r
+\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg != null && sg.getSize() >= 1)\r
- {\r
\r
+ if ( (sg != null) && (sg.getSize() >= 1))\r
+ {\r
del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
+\r
for (int i = 0; i < del.size(); i++)\r
{\r
if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
sg.deleteSequence( (SequenceI) del.elementAt(i));\r
}\r
}\r
-\r
}\r
else\r
{\r
Vector s = new Vector();\r
int i = 0;\r
+\r
while (i < ap.av.alignment.getHeight())\r
{\r
s.addElement(ap.av.alignment.getSequenceAt(i));\r
i++;\r
}\r
+\r
del = ap.av.alignment.removeRedundancy(threshold, s);\r
}\r
\r
// This has to be done before the restoreHistoryItem method of alignFrame will\r
// actually restore these sequences.\r
-\r
- if (del.size()>0)\r
- for (int i=0,j=del.size(); i<j; i++) {\r
+ if (del.size() > 0)\r
+ {\r
+ for (int i = 0, j = del.size(); i < j; i++)\r
+ {\r
SequenceI sq = (SequenceI) del.elementAt(i);\r
- sq.deleteChars(0,sq.getLength());\r
+ sq.deleteChars(0, sq.getLength());\r
}\r
+ }\r
\r
ap.av.firePropertyChange("alignment", null,\r
ap.av.getAlignment().getSequences());\r
ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
+\r
if (ap.av.getAlignment().getHeight() < 1)\r
{\r
try\r
af.setClosed(true);\r
}\r
catch (Exception ex)\r
- {}\r
+ {\r
+ }\r
}\r
+\r
ap.av.updateConservation();\r
ap.av.updateConsensus();\r
af.updateEditMenuBar();\r
ap.repaint();\r
-\r
}\r
\r
public void undoButton_actionPerformed(ActionEvent e)\r
{\r
HistoryItem hi = (HistoryItem) historyList.pop();\r
af.restoreHistoryItem(hi);\r
+\r
if (historyList.size() == 0)\r
{\r
undoButton.setEnabled(false);\r
+\r
if (af.historyList.contains(hi))\r
{\r
af.historyList.remove(hi);\r
}\r
}\r
}\r
+\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
try\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.math.*;\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
+import java.util.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
-import java.util.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.math.*;\r
+import jalview.util.*;\r
\r
-public class RotatableCanvas extends JPanel implements MouseListener,\r
- MouseMotionListener,\r
- KeyListener\r
- //RubberbandListener,\r
- //SequenceSelectionListener\r
+public class RotatableCanvas\r
+ extends JPanel implements MouseListener,\r
+ MouseMotionListener, KeyListener\r
+//RubberbandListener,\r
+//SequenceSelectionListener\r
{\r
- RotatableMatrix idmat = new RotatableMatrix(3,3);\r
- RotatableMatrix objmat = new RotatableMatrix(3,3);\r
- RotatableMatrix rotmat = new RotatableMatrix(3,3);\r
+ RotatableMatrix idmat = new RotatableMatrix(3, 3);\r
+ RotatableMatrix objmat = new RotatableMatrix(3, 3);\r
+ RotatableMatrix rotmat = new RotatableMatrix(3, 3);\r
\r
//RubberbandRectangle rubberband;\r
-\r
boolean drawAxes = true;\r
-\r
int omx = 0;\r
int mx = 0;\r
int omy = 0;\r
int my = 0;\r
-\r
Image img;\r
Graphics ig;\r
-\r
Dimension prefsize;\r
-\r
- float centre[] = new float[3];\r
- float width[] = new float[3];\r
-\r
- float max[] = new float[3];\r
- float min[] = new float[3];\r
-\r
+ float[] centre = new float[3];\r
+ float[] width = new float[3];\r
+ float[] max = new float[3];\r
+ float[] min = new float[3];\r
float maxwidth;\r
float scale;\r
-\r
int npoint;\r
-\r
Vector points;\r
float[][] orig;\r
float[][] axes;\r
-\r
int startx;\r
int starty;\r
-\r
int lastx;\r
int lasty;\r
-\r
int rectx1;\r
int recty1;\r
int rectx2;\r
int recty2;\r
-\r
float scalefactor = 1;\r
-\r
AlignViewport av;\r
-// Controller controller;\r
-\r
\r
- public RotatableCanvas(AlignViewport av,\r
- Vector points, int npoint) {\r
+ // Controller controller;\r
+ public RotatableCanvas(AlignViewport av, Vector points, int npoint)\r
+ {\r
this.points = points;\r
this.npoint = npoint;\r
this.av = av;\r
ToolTipManager.sharedInstance().registerComponent(this);\r
PaintRefresher.Register(this);\r
-//\r
+\r
+ //\r
prefsize = getPreferredSize();\r
orig = new float[npoint][3];\r
\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- for (int j=0; j < 3; j++) {\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
orig[i][j] = sp.coord[j];\r
}\r
}\r
- //Initialize the matrices to identity\r
\r
- for (int i = 0; i < 3; i++) {\r
- for (int j = 0; j < 3 ; j++) {\r
- if (i != j) {\r
- idmat.addElement(i,j,0);\r
- objmat.addElement(i,j,0);\r
- rotmat.addElement(i,j,0);\r
- } else {\r
- idmat.addElement(i,j,0);\r
- objmat.addElement(i,j,0);\r
- rotmat.addElement(i,j,0);\r
+ //Initialize the matrices to identity\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
+ if (i != j)\r
+ {\r
+ idmat.addElement(i, j, 0);\r
+ objmat.addElement(i, j, 0);\r
+ rotmat.addElement(i, j, 0);\r
+ }\r
+ else\r
+ {\r
+ idmat.addElement(i, j, 0);\r
+ objmat.addElement(i, j, 0);\r
+ rotmat.addElement(i, j, 0);\r
}\r
}\r
}\r
scale = findScale();\r
\r
// System.out.println("Scale factor = " + scale);\r
-\r
addMouseListener(this);\r
addKeyListener(this);\r
- // if (getParent() != null) {\r
- // getParent().addKeyListener(this);\r
+\r
+ // if (getParent() != null) {\r
+ // getParent().addKeyListener(this);\r
//}\r
addMouseMotionListener(this);\r
\r
// Add rubberband\r
- // rubberband = new RubberbandRectangle(this);\r
- // rubberband.setActive(true);\r
- // rubberband.addListener(this);\r
- }\r
-\r
- /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {\r
- redrawneeded = true;\r
- repaint();\r
- return true;\r
+ // rubberband = new RubberbandRectangle(this);\r
+ // rubberband.setActive(true);\r
+ // rubberband.addListener(this);\r
}\r
\r
- public void removeNotify() {\r
- controller.removeListener(this);\r
- super.removeNotify();\r
- }*/\r
-\r
- public void initAxes() {\r
- for (int i = 0; i < 3; i++) {\r
- for (int j=0; j < 3; j++) {\r
- if (i != j) {\r
+ /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {\r
+ redrawneeded = true;\r
+ repaint();\r
+ return true;\r
+ }\r
+\r
+ public void removeNotify() {\r
+ controller.removeListener(this);\r
+ super.removeNotify();\r
+ }*/\r
+ public void initAxes()\r
+ {\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
+ if (i != j)\r
+ {\r
axes[i][j] = 0;\r
- } else {\r
+ }\r
+ else\r
+ {\r
axes[i][j] = 1;\r
}\r
}\r
}\r
}\r
\r
- public void findWidth() {\r
+ public void findWidth()\r
+ {\r
max = new float[3];\r
min = new float[3];\r
\r
- max[0] = (float)-1e30;\r
- max[1] = (float)-1e30;\r
- max[2] = (float)-1e30;\r
+ max[0] = (float) - 1e30;\r
+ max[1] = (float) - 1e30;\r
+ max[2] = (float) - 1e30;\r
+\r
+ min[0] = (float) 1e30;\r
+ min[1] = (float) 1e30;\r
+ min[2] = (float) 1e30;\r
\r
- min[0] = (float)1e30;\r
- min[1] = (float)1e30;\r
- min[2] = (float)1e30;\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ for (int j = 0; j < npoint; j++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(j);\r
\r
- for (int i = 0; i < 3; i++) {\r
- for (int j = 0; j < npoint; j++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(j);\r
- if (sp.coord[i] >= max[i]) {\r
+ if (sp.coord[i] >= max[i])\r
+ {\r
max[i] = sp.coord[i];\r
}\r
- if (sp.coord[i] <= min[i]) {\r
+\r
+ if (sp.coord[i] <= min[i])\r
+ {\r
min[i] = sp.coord[i];\r
}\r
}\r
// System.out.println("xmax " + max[0] + " min " + min[0]);\r
//System.out.println("ymax " + max[1] + " min " + min[1]);\r
//System.out.println("zmax " + max[2] + " min " + min[2]);\r
-\r
width[0] = Math.abs(max[0] - min[0]);\r
width[1] = Math.abs(max[1] - min[1]);\r
width[2] = Math.abs(max[2] - min[2]);\r
maxwidth = width[0];\r
\r
if (width[1] > width[0])\r
+ {\r
maxwidth = width[1];\r
+ }\r
+\r
if (width[2] > width[1])\r
+ {\r
maxwidth = width[2];\r
+ }\r
\r
//System.out.println("Maxwidth = " + maxwidth);\r
}\r
\r
- public float findScale() {\r
- int dim, width, height;\r
- if (getWidth() != 0) {\r
+ public float findScale()\r
+ {\r
+ int dim;\r
+ int width;\r
+ int height;\r
+\r
+ if (getWidth() != 0)\r
+ {\r
width = getWidth();\r
height = getHeight();\r
- } else {\r
+ }\r
+ else\r
+ {\r
width = prefsize.width;\r
height = prefsize.height;\r
}\r
\r
- if (width < height) {\r
+ if (width < height)\r
+ {\r
dim = width;\r
- } else {\r
+ }\r
+ else\r
+ {\r
dim = height;\r
}\r
\r
- return (float)(dim*scalefactor/(2*maxwidth));\r
+ return (float) ( (dim * scalefactor) / (2 * maxwidth));\r
}\r
\r
- public void findCentre() {\r
+ public void findCentre()\r
+ {\r
//Find centre coordinate\r
findWidth();\r
\r
- centre[0] = (max[0] + min[0])/2;\r
- centre[1] = (max[1] + min[1])/2;\r
- centre[2] = (max[2] + min[2])/2;\r
+ centre[0] = (max[0] + min[0]) / 2;\r
+ centre[1] = (max[1] + min[1]) / 2;\r
+ centre[2] = (max[2] + min[2]) / 2;\r
\r
// System.out.println("Centre x " + centre[0]);\r
//System.out.println("Centre y " + centre[1]);\r
//System.out.println("Centre z " + centre[2]);\r
}\r
\r
- public Dimension getPreferredSize() {\r
- if (prefsize != null) {\r
+ public Dimension getPreferredSize()\r
+ {\r
+ if (prefsize != null)\r
+ {\r
return prefsize;\r
- } else {\r
- return new Dimension(400,400);\r
+ }\r
+ else\r
+ {\r
+ return new Dimension(400, 400);\r
}\r
}\r
\r
- public Dimension getMinimumSize() {\r
+ public Dimension getMinimumSize()\r
+ {\r
return getPreferredSize();\r
}\r
\r
- public void paintComponent(Graphics g) {\r
+ public void paintComponent(Graphics g)\r
+ {\r
//Only create the image at the beginning -\r
- if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {\r
+ if ( (img == null) || (prefsize.width != getWidth()) ||\r
+ (prefsize.height != getHeight()))\r
+ {\r
prefsize.width = getWidth();\r
prefsize.height = getHeight();\r
\r
scale = findScale();\r
\r
// System.out.println("New scale = " + scale);\r
- img = createImage(getWidth(),getHeight());\r
+ img = createImage(getWidth(), getHeight());\r
ig = img.getGraphics();\r
-\r
}\r
\r
+ drawBackground(ig, Color.black);\r
+ drawScene(ig);\r
\r
- drawBackground(ig,Color.black);\r
- drawScene(ig);\r
- if (drawAxes == true)\r
- {\r
- drawAxes(ig);\r
- }\r
-\r
+ if (drawAxes == true)\r
+ {\r
+ drawAxes(ig);\r
+ }\r
\r
- g.drawImage(img,0,0,this);\r
+ g.drawImage(img, 0, 0, this);\r
}\r
\r
- public void drawAxes(Graphics g) {\r
-\r
+ public void drawAxes(Graphics g)\r
+ {\r
g.setColor(Color.yellow);\r
- for (int i=0; i < 3 ; i++) {\r
- g.drawLine(getWidth()/2,getHeight()/2,\r
- (int)(axes[i][0]*scale*max[0] + getWidth()/2),\r
- (int)(axes[i][1]*scale*max[1] + getHeight()/2));\r
+\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ g.drawLine(getWidth() / 2, getHeight() / 2,\r
+ (int) ( (axes[i][0] * scale * max[0]) + (getWidth() / 2)),\r
+ (int) ( (axes[i][1] * scale * max[1]) + (getHeight() / 2)));\r
}\r
}\r
\r
- public void drawBackground(Graphics g, Color col) {\r
+ public void drawBackground(Graphics g, Color col)\r
+ {\r
g.setColor(col);\r
- g.fillRect(0,0,prefsize.width,prefsize.height);\r
+ g.fillRect(0, 0, prefsize.width, prefsize.height);\r
}\r
\r
-\r
- public void drawScene(Graphics g) {\r
+ public void drawScene(Graphics g)\r
+ {\r
boolean darker = false;\r
\r
- int halfwidth = getWidth()/2;\r
- int halfheight = getHeight()/2;\r
+ int halfwidth = getWidth() / 2;\r
+ int halfheight = getHeight() / 2;\r
\r
- for (int i = 0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- int x = (int)((float)(sp.coord[0] - centre[0])*scale) + halfwidth;\r
- int y = (int)((float)(sp.coord[1] - centre[1])*scale) + halfheight;\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ int x = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +\r
+ halfwidth;\r
+ int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +\r
+ halfheight;\r
float z = sp.coord[1] - centre[2];\r
\r
-\r
-\r
-\r
if (sp.sequence.getColor() == Color.black)\r
- g.setColor(Color.white);\r
+ {\r
+ g.setColor(Color.white);\r
+ }\r
else\r
- g.setColor(sp.sequence.getColor());\r
-\r
+ {\r
+ g.setColor(sp.sequence.getColor());\r
+ }\r
\r
if (av.getSelectionGroup() != null)\r
{\r
- if (av.getSelectionGroup().sequences.contains(((SequencePoint)points.elementAt(i)).sequence))\r
+ if (av.getSelectionGroup().sequences.contains(\r
+ ( (SequencePoint) points.elementAt(i)).sequence))\r
+ {\r
g.setColor(Color.gray);\r
+ }\r
}\r
+\r
if (z < 0)\r
+ {\r
g.setColor(g.getColor().darker());\r
+ }\r
\r
-\r
- g.fillRect(x-3,y-3,6,6);\r
+ g.fillRect(x - 3, y - 3, 6, 6);\r
g.setColor(Color.red);\r
}\r
-// //Now the rectangle\r
-// if (rectx2 != -1 && recty2 != -1) {\r
-// g.setColor(Color.white);\r
-//\r
-// g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);\r
-// }\r
+\r
+ // //Now the rectangle\r
+ // if (rectx2 != -1 && recty2 != -1) {\r
+ // g.setColor(Color.white);\r
+ //\r
+ // g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);\r
+ // }\r
}\r
\r
- public Dimension minimumsize() {\r
+ public Dimension minimumsize()\r
+ {\r
return prefsize;\r
}\r
\r
- public Dimension preferredsize() {\r
+ public Dimension preferredsize()\r
+ {\r
return prefsize;\r
}\r
\r
- public void keyTyped(KeyEvent evt) { }\r
- public void keyReleased(KeyEvent evt) { }\r
+ public void keyTyped(KeyEvent evt)\r
+ {\r
+ }\r
\r
- public void keyPressed(KeyEvent evt) {\r
+ public void keyReleased(KeyEvent evt)\r
+ {\r
+ }\r
+\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
requestFocus();\r
- if (evt.getKeyCode() == KeyEvent.VK_UP) {\r
- scalefactor = (float)(scalefactor * 1.1);\r
+\r
+ if (evt.getKeyCode() == KeyEvent.VK_UP)\r
+ {\r
+ scalefactor = (float) (scalefactor * 1.1);\r
scale = findScale();\r
- } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {\r
- scalefactor = (float)(scalefactor * 0.9);\r
+ }\r
+ else if (evt.getKeyCode() == KeyEvent.VK_DOWN)\r
+ {\r
+ scalefactor = (float) (scalefactor * 0.9);\r
scale = findScale();\r
- } else if (evt.getKeyChar() == 's') {\r
+ }\r
+ else if (evt.getKeyChar() == 's')\r
+ {\r
System.err.println("DEBUG: Rectangle selection"); // log.debug\r
- if (rectx2 != -1 && recty2 != -1) {\r
- rectSelect(rectx1,recty1,rectx2,recty2);\r
\r
+ if ( (rectx2 != -1) && (recty2 != -1))\r
+ {\r
+ rectSelect(rectx1, recty1, rectx2, recty2);\r
}\r
}\r
+\r
repaint();\r
}\r
\r
- public void printPoints() {\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- Format.print(System.out,"%5d ", i);\r
- for (int j=0; j < 3;j++) {\r
- Format.print(System.out,"%13.3f ",sp.coord[j]);\r
+ public void printPoints()\r
+ {\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ Format.print(System.out, "%5d ", i);\r
+\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
+ Format.print(System.out, "%13.3f ", sp.coord[j]);\r
}\r
+\r
System.out.println();\r
}\r
}\r
\r
- public void mouseClicked(MouseEvent evt) { }\r
- public void mouseEntered(MouseEvent evt) { }\r
- public void mouseExited(MouseEvent evt) { }\r
- public void mouseReleased(MouseEvent evt) { }\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ }\r
\r
- public void mousePressed(MouseEvent evt) {\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
int x = evt.getX();\r
int y = evt.getY();\r
\r
rectx2 = -1;\r
recty2 = -1;\r
\r
- SequenceI found = findPoint(x,y);\r
+ SequenceI found = findPoint(x, y);\r
\r
if (found != null)\r
{\r
}\r
else\r
{\r
- av.setSelectionGroup(new SequenceGroup());\r
- av.getSelectionGroup().addOrRemove(found);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth());\r
-\r
+ av.setSelectionGroup(new SequenceGroup());\r
+ av.getSelectionGroup().addOrRemove(found);\r
+ av.getSelectionGroup().setEndRes(av.alignment.getWidth());\r
}\r
}\r
+\r
repaint();\r
}\r
\r
- // private void fireSequenceSelectionEvent(Selection sel) {\r
- // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));\r
+ // private void fireSequenceSelectionEvent(Selection sel) {\r
+ // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));\r
//}\r
-\r
public void mouseMoved(MouseEvent evt)\r
{\r
- SequenceI found = findPoint(evt.getX(), evt.getY());\r
- if (found != null)\r
- this.setToolTipText(found.getName());\r
- else\r
- this.setToolTipText(null);\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt) {\r
+ SequenceI found = findPoint(evt.getX(), evt.getY());\r
+\r
+ if (found != null)\r
+ {\r
+ this.setToolTipText(found.getName());\r
+ }\r
+ else\r
+ {\r
+ this.setToolTipText(null);\r
+ }\r
+ }\r
+\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
mx = evt.getX();\r
my = evt.getY();\r
+\r
//Check if this is a rectangle drawing drag\r
- if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0) {\r
-// rectx2 = evt.getX();\r
-// recty2 = evt.getY();\r
- } else {\r
+ if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)\r
+ {\r
+ // rectx2 = evt.getX();\r
+ // recty2 = evt.getY();\r
+ }\r
+ else\r
+ {\r
rotmat.setIdentity();\r
\r
- rotmat.rotate((float)(my-omy),'x');\r
- rotmat.rotate((float)(mx-omx),'y');\r
+ rotmat.rotate( (float) (my - omy), 'x');\r
+ rotmat.rotate( (float) (mx - omx), 'y');\r
\r
- for (int i = 0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
sp.coord[0] -= centre[0];\r
sp.coord[1] -= centre[1];\r
sp.coord[2] -= centre[2];\r
\r
//Now apply the rotation matrix\r
- sp.coord= rotmat.vectorMultiply(sp.coord);\r
+ sp.coord = rotmat.vectorMultiply(sp.coord);\r
\r
//Now translate back again\r
sp.coord[0] += centre[0];\r
sp.coord[2] += centre[2];\r
}\r
\r
- for (int i=0; i < 3; i++) {\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
axes[i] = rotmat.vectorMultiply(axes[i]);\r
}\r
+\r
omx = mx;\r
omy = my;\r
\r
paint(this.getGraphics());\r
}\r
-\r
}\r
\r
- public void rectSelect(int x1, int y1, int x2, int y2) {\r
+ public void rectSelect(int x1, int y1, int x2, int y2)\r
+ {\r
boolean changedSel = false;\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- int tmp1 = (int)((sp.coord[0] - centre[0])*scale + (float)getWidth()/2.0);\r
- int tmp2 = (int)((sp.coord[1] - centre[1])*scale + (float)getHeight()/2.0);\r
\r
- if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) {\r
- if (av != null) {\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ int tmp1 = (int) ( ( (sp.coord[0] - centre[0]) * scale) +\r
+ ( (float) getWidth() / 2.0));\r
+ int tmp2 = (int) ( ( (sp.coord[1] - centre[1]) * scale) +\r
+ ( (float) getHeight() / 2.0));\r
+\r
+ if ( (tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))\r
+ {\r
+ if (av != null)\r
+ {\r
if (!av.getSelectionGroup().sequences.contains(sp.sequence))\r
{\r
changedSel = true;\r
}\r
}\r
}\r
- // if (changedSel) {\r
- // fireSequenceSelectionEvent(av.getSelection());\r
- // }\r
+\r
+ // if (changedSel) {\r
+ // fireSequenceSelectionEvent(av.getSelection());\r
+ // }\r
}\r
- public SequenceI findPoint(int x, int y) {\r
\r
- int halfwidth = getWidth()/2;\r
- int halfheight = getHeight()/2;\r
+ public SequenceI findPoint(int x, int y)\r
+ {\r
+ int halfwidth = getWidth() / 2;\r
+ int halfheight = getHeight() / 2;\r
\r
int found = -1;\r
\r
- for (int i=0; i < npoint; i++) {\r
-\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- int px = (int)((float)(sp.coord[0] - centre[0])*scale) + halfwidth;\r
- int py = (int)((float)(sp.coord[1] - centre[1])*scale) + halfheight;\r
-\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +\r
+ halfwidth;\r
+ int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +\r
+ halfheight;\r
\r
- if (Math.abs(px-x)<3 && Math.abs(py - y) < 3 ) {\r
+ if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))\r
+ {\r
found = i;\r
}\r
}\r
- if (found != -1) {\r
- return ((SequencePoint)points.elementAt(found)).sequence;\r
- } else {\r
+\r
+ if (found != -1)\r
+ {\r
+ return ( (SequencePoint) points.elementAt(found)).sequence;\r
+ }\r
+ else\r
+ {\r
return null;\r
}\r
}\r
-/* public boolean handleRubberbandEvent(RubberbandEvent evt) {\r
- System.out.println("Rubberband handler called in RotatableCanvas with " +\r
- evt.getBounds());\r
\r
- Rubberband rb = (Rubberband)evt.getSource();\r
+ /* public boolean handleRubberbandEvent(RubberbandEvent evt) {\r
+ System.out.println("Rubberband handler called in RotatableCanvas with " +\r
+ evt.getBounds());\r
\r
- // Clear the current selection (instance variable)\r
- //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {\r
- // clearSelection();\r
- //}\r
+ Rubberband rb = (Rubberband)evt.getSource();\r
\r
- if (rb.getComponent() == this) {\r
- Rectangle bounds = evt.getBounds();\r
- rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);\r
- }\r
+ // Clear the current selection (instance variable)\r
+ //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {\r
+ // clearSelection();\r
+ //}\r
\r
- redrawneeded = true;\r
- paint(this.getGraphics());\r
+ if (rb.getComponent() == this) {\r
+ Rectangle bounds = evt.getBounds();\r
+ rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);\r
+ }\r
\r
- return true;\r
- }*/\r
+ redrawneeded = true;\r
+ paint(this.getGraphics());\r
\r
+ return true;\r
+ }*/\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
\r
-public class ScalePanel extends JPanel\r
-{\r
+import jalview.datamodel.*;\r
\r
+public class ScalePanel\r
+ extends JPanel\r
+{\r
protected int offy = 4;\r
- public int width;\r
-\r
+ public int width;\r
protected AlignViewport av;\r
AlignmentPanel ap;\r
-\r
boolean stretchingGroup = false;\r
\r
public ScalePanel(AlignViewport av, AlignmentPanel ap)\r
{\r
- this.av = av;\r
+ this.av = av;\r
this.ap = ap;\r
\r
addMouseListener(new MouseAdapter()\r
{\r
doMousePressed(evt);\r
}\r
+\r
public void mouseReleased(MouseEvent evt)\r
{\r
doMouseReleased(evt);\r
}\r
-\r
});\r
addMouseMotionListener(new MouseMotionAdapter()\r
{\r
doMouseDragged(evt);\r
}\r
});\r
-\r
}\r
\r
-\r
- public void doMousePressed(MouseEvent evt) {\r
+ public void doMousePressed(MouseEvent evt)\r
+ {\r
int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
+ int res = (x / av.getCharWidth()) + av.getStartRes();\r
SequenceGroup sg = null;\r
\r
if (av.getColumnSelection().contains(res))\r
+ {\r
av.getColumnSelection().removeElement(res);\r
+ }\r
else\r
{\r
av.getColumnSelection().addElement(res);\r
\r
sg = new SequenceGroup();\r
+\r
for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
+ {\r
sg.addSequence(av.alignment.getSequenceAt(i));\r
+ }\r
\r
sg.setStartRes(res);\r
sg.setEndRes(res);\r
\r
ap.annotationPanel.addEditableColumn(res);\r
}\r
+\r
av.setSelectionGroup(sg);\r
ap.repaint();\r
}\r
\r
public void doMouseReleased(MouseEvent evt)\r
{\r
- if(!stretchingGroup)\r
+ if (!stretchingGroup)\r
+ {\r
return;\r
+ }\r
\r
int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
+ int res = (x / av.getCharWidth()) + av.getStartRes();\r
\r
- if (! av.getColumnSelection().contains(res))\r
- av.getColumnSelection().addElement(res);\r
+ if (!av.getColumnSelection().contains(res))\r
+ {\r
+ av.getColumnSelection().addElement(res);\r
+ }\r
\r
- SequenceGroup sg = av.getSelectionGroup();\r
+ SequenceGroup sg = av.getSelectionGroup();\r
\r
- if(res>sg.getStartRes())\r
- sg.setEndRes(res);\r
- else if(res<sg.getStartRes())\r
- sg.setStartRes(res);\r
+ if (res > sg.getStartRes())\r
+ {\r
+ sg.setEndRes(res);\r
+ }\r
+ else if (res < sg.getStartRes())\r
+ {\r
+ sg.setStartRes(res);\r
+ }\r
\r
- stretchingGroup = false;\r
- ap.repaint();\r
+ stretchingGroup = false;\r
+ ap.repaint();\r
}\r
\r
public void doMouseDragged(MouseEvent evt)\r
{\r
int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
+ int res = (x / av.getCharWidth()) + av.getStartRes();\r
\r
SequenceGroup sg = av.getSelectionGroup();\r
- if(sg!=null)\r
+\r
+ if (sg != null)\r
{\r
stretchingGroup = true;\r
+\r
if (res > sg.getStartRes())\r
+ {\r
sg.setEndRes(res);\r
+ }\r
else if (res < sg.getStartRes())\r
+ {\r
sg.setStartRes(res);\r
+ }\r
\r
- ap.annotationPanel.addEditableColumn(res);\r
+ ap.annotationPanel.addEditableColumn(res);\r
ap.repaint();\r
}\r
}\r
drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());\r
}\r
\r
-// scalewidth will normally be screenwidth,\r
- public void drawScale(Graphics g, int startx, int endx, int width, int height)\r
+ // scalewidth will normally be screenwidth,\r
+ public void drawScale(Graphics g, int startx, int endx, int width,\r
+ int height)\r
{\r
- Graphics2D gg = (Graphics2D)g;\r
+ Graphics2D gg = (Graphics2D) g;\r
gg.setFont(av.getFont());\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
//Fill in the background\r
gg.setColor(Color.white);\r
- gg.fillRect(0,0,width, height);\r
+ gg.fillRect(0, 0, width, height);\r
gg.setColor(Color.black);\r
\r
-\r
//Fill the selected columns\r
ColumnSelection cs = av.getColumnSelection();\r
- gg.setColor(new Color(220,0,0));\r
- for (int i=0; i<cs.size(); i++)\r
+ gg.setColor(new Color(220, 0, 0));\r
+\r
+ for (int i = 0; i < cs.size(); i++)\r
{\r
- int sel = cs.columnAt(i);\r
- if ( sel >= startx && sel <= endx)\r
- gg.fillRect((sel-startx)*av.charWidth,0,av.charWidth,getHeight());\r
- }\r
+ int sel = cs.columnAt(i);\r
\r
+ if ( (sel >= startx) && (sel <= endx))\r
+ {\r
+ gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,\r
+ getHeight());\r
+ }\r
+ }\r
\r
// Draw the scale numbers\r
gg.setColor(Color.black);\r
- int scalestartx = (startx/10) * 10;\r
+\r
+ int scalestartx = (startx / 10) * 10;\r
\r
FontMetrics fm = gg.getFontMetrics(av.getFont());\r
- int y = av.charHeight -fm.getDescent();\r
+ int y = av.charHeight - fm.getDescent();\r
\r
- if(scalestartx%10==0)\r
- scalestartx+=5;\r
+ if ( (scalestartx % 10) == 0)\r
+ {\r
+ scalestartx += 5;\r
+ }\r
\r
- for (int i=scalestartx;i < endx; i+= 5)\r
+ for (int i = scalestartx; i < endx; i += 5)\r
{\r
- if(i%10==0)\r
+ if ( (i % 10) == 0)\r
{\r
- gg.drawString(String.valueOf(i), (i - startx - 1) * av.charWidth, y);\r
- gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y+2,\r
- (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y+fm.getDescent()*2);\r
+ gg.drawString(String.valueOf(i),\r
+ (i - startx - 1) * av.charWidth, y);\r
+ gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +\r
+ (av.charWidth / 2)), y + 2,\r
+ (int) ( ( (i - startx - 1) * av.charWidth) +\r
+ (av.charWidth / 2)), y + (fm.getDescent() * 2));\r
}\r
else\r
- gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y+fm.getDescent(),\r
- (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y+fm.getDescent()*2);\r
-\r
-\r
+ {\r
+ gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +\r
+ (av.charWidth / 2)), y + fm.getDescent(),\r
+ (int) ( ( (i - startx - 1) * av.charWidth) +\r
+ (av.charWidth / 2)), y + (fm.getDescent() * 2));\r
+ }\r
}\r
}\r
-\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
import java.awt.*;\r
import java.awt.image.*;\r
import javax.swing.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
\r
-public class SeqCanvas extends JComponent\r
+public class SeqCanvas\r
+ extends JComponent\r
{\r
- FeatureRenderer fr;\r
- SequenceRenderer sr;\r
- BufferedImage img;\r
- Graphics2D gg;\r
- int imgWidth;\r
- int imgHeight;\r
-\r
- AlignViewport av;\r
-\r
- boolean showScores = false;\r
- boolean displaySearch = false;\r
- int [] searchResults = null;\r
-\r
- int chunkHeight;\r
- int chunkWidth;\r
-\r
- boolean fastPaint = false;\r
-\r
-\r
- public SeqCanvas(AlignViewport av)\r
- {\r
- this.av = av;\r
- fr = new FeatureRenderer(av);\r
- sr = new SequenceRenderer(av);\r
- setLayout(new BorderLayout());\r
- PaintRefresher.Register(this);\r
-\r
- }\r
+ FeatureRenderer fr;\r
+ SequenceRenderer sr;\r
+ BufferedImage img;\r
+ Graphics2D gg;\r
+ int imgWidth;\r
+ int imgHeight;\r
+ AlignViewport av;\r
+ boolean showScores = false;\r
+ boolean displaySearch = false;\r
+ int[] searchResults = null;\r
+ int chunkHeight;\r
+ int chunkWidth;\r
+ boolean fastPaint = false;\r
+ int LABEL_WEST;\r
+ int LABEL_EAST;\r
+\r
+ public SeqCanvas(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ fr = new FeatureRenderer(av);\r
+ sr = new SequenceRenderer(av);\r
+ setLayout(new BorderLayout());\r
+ PaintRefresher.Register(this);\r
+ }\r
\r
- void drawNorthScale(Graphics g, int startx, int endx,int ypos) {\r
- int scalestartx = startx - startx % 10 + 10;\r
+ void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ int scalestartx = startx - (startx % 10) + 10;\r
\r
g.setColor(Color.black);\r
\r
{\r
String string = String.valueOf(i);\r
g.drawString(string, (i - startx - 1) * av.charWidth,\r
- ypos - av.charHeight / 2);\r
-\r
- g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,\r
- ypos + 2 - av.charHeight / 2,\r
- (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);\r
+ ypos - (av.charHeight / 2));\r
\r
+ g.drawLine( ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
+ (ypos + 2) - (av.charHeight / 2),\r
+ ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -\r
+ 2);\r
}\r
}\r
\r
void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
{\r
FontMetrics fm = getFontMetrics(av.getFont());\r
- ypos+= av.charHeight;\r
- // EAST SCALE\r
+ ypos += av.charHeight;\r
+\r
+ // EAST SCALE\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
SequenceI seq = av.alignment.getSequenceAt(i);\r
int index = startx;\r
int value = -1;\r
+\r
while (index < endx)\r
{\r
if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
{\r
index++;\r
+\r
continue;\r
}\r
\r
value = av.alignment.getSequenceAt(i).findPosition(index);\r
+\r
break;\r
}\r
- if(value!=-1)\r
+\r
+ if (value != -1)\r
{\r
- int x = LABEL_WEST - fm.stringWidth(value+"");\r
- g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5);\r
+ int x = LABEL_WEST - fm.stringWidth(value + "");\r
+ g.drawString(value + "", x,\r
+ (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
}\r
}\r
}\r
\r
void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
-{\r
- ypos+= av.charHeight;\r
- // EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
- int index = endx;\r
- int value = -1;\r
- while (index > startx)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
- {\r
- index--;\r
- continue;\r
- }\r
+ ypos += av.charHeight;\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
- break;\r
- }\r
- if(value!=-1)\r
- g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5);\r
- }\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
\r
-}\r
+ while (index > startx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index--;\r
\r
+ continue;\r
+ }\r
\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
\r
+ break;\r
+ }\r
\r
+ if (value != -1)\r
+ {\r
+ g.drawString(value + "", 0,\r
+ (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
+ }\r
+ }\r
+ }\r
\r
-public void fastPaint(int horizontal, int vertical)\r
-{\r
- if (horizontal == 0 && vertical == 0 || gg==null)\r
+ public void fastPaint(int horizontal, int vertical)\r
+ {\r
+ if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null))\r
+ {\r
return;\r
+ }\r
\r
gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
-vertical * av.charHeight);\r
\r
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,\r
- transX = 0, transY = 0;\r
+ int sr = av.startRes;\r
+ int er = av.endRes;\r
+ int ss = av.startSeq;\r
+ int es = av.endSeq;\r
+ int transX = 0;\r
+ int transY = 0;\r
+\r
if (horizontal > 0) // scrollbar pulled right, image to the left\r
{\r
transX = (er - sr - horizontal) * av.charWidth;\r
sr = er - horizontal;\r
}\r
else if (horizontal < 0)\r
+ {\r
er = sr - horizontal;\r
-\r
+ }\r
else if (vertical > 0) // scroll down\r
{\r
ss = es - vertical;\r
- if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time\r
+\r
+ if (ss < av.startSeq)\r
+ { // ie scrolling too fast, more than a page at a time\r
ss = av.startSeq;\r
+ }\r
else\r
- transY = imgHeight - vertical * av.charHeight;\r
+ {\r
+ transY = imgHeight - (vertical * av.charHeight);\r
+ }\r
}\r
else if (vertical < 0)\r
{\r
es = ss - vertical;\r
- if(es > av.endSeq)\r
+\r
+ if (es > av.endSeq)\r
+ {\r
es = av.endSeq;\r
+ }\r
}\r
\r
-\r
gg.translate(transX, transY);\r
\r
gg.setColor(Color.white);\r
- gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);\r
+ gg.fillRect(0, 0, (er - sr + 1) * av.charWidth,\r
+ (es - ss) * av.charHeight);\r
drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
gg.translate( -transX, -transY);\r
\r
fastPaint = true;\r
repaint();\r
+ }\r
\r
-}\r
-\r
-/**\r
- * Definitions of startx and endx (hopefully):\r
- * SMJS This is what I'm working towards!\r
- * startx is the first residue (starting at 0) to display.\r
- * endx is the last residue to display (starting at 0).\r
- * starty is the first sequence to display (starting at 0).\r
- * endy is the last sequence to display (starting at 0).\r
- * NOTE 1: The av limits are set in setFont in this class and\r
- * in the adjustment listener in SeqPanel when the scrollbars move.\r
- */\r
-\r
+ /**\r
+ * Definitions of startx and endx (hopefully):\r
+ * SMJS This is what I'm working towards!\r
+ * startx is the first residue (starting at 0) to display.\r
+ * endx is the last residue to display (starting at 0).\r
+ * starty is the first sequence to display (starting at 0).\r
+ * endy is the last sequence to display (starting at 0).\r
+ * NOTE 1: The av limits are set in setFont in this class and\r
+ * in the adjustment listener in SeqPanel when the scrollbars move.\r
+ */\r
public void paintComponent(Graphics g)\r
{\r
g.setColor(Color.white);\r
{\r
g.drawImage(img, 0, 0, this);\r
fastPaint = false;\r
+\r
return;\r
}\r
\r
// this draws the whole of the alignment\r
- imgWidth = getWidth();\r
- imgHeight = getHeight();\r
+ imgWidth = getWidth();\r
+ imgHeight = getHeight();\r
\r
- imgWidth -= imgWidth%av.charWidth;\r
- imgHeight-= imgHeight%av.charHeight;\r
+ imgWidth -= (imgWidth % av.charWidth);\r
+ imgHeight -= (imgHeight % av.charHeight);\r
\r
- if(imgWidth<1 || imgHeight<1)\r
- return;\r
+ if ( (imgWidth < 1) || (imgHeight < 1))\r
+ {\r
+ return;\r
+ }\r
\r
- img = new BufferedImage(imgWidth,imgHeight,BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D)img.getGraphics();\r
- gg.setFont(av.getFont());\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);\r
+ gg = (Graphics2D) img.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0,0,imgWidth,imgHeight);\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
- chunkWidth = getWrappedCanvasWidth( getWidth() );\r
- chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
+ chunkWidth = getWrappedCanvasWidth(getWidth());\r
+ chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
\r
av.setChunkHeight(chunkHeight);\r
av.setChunkWidth(chunkWidth);\r
\r
-\r
if (av.getWrapAlignment())\r
+ {\r
drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
+ }\r
else\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);\r
+ {\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,\r
+ av.startRes, av.startSeq, 0);\r
+ }\r
\r
g.drawImage(img, 0, 0, this);\r
-\r
}\r
\r
- int LABEL_WEST, LABEL_EAST;\r
public int getWrappedCanvasWidth(int cwidth)\r
{\r
FontMetrics fm = getFontMetrics(av.getFont());\r
LABEL_EAST = 0;\r
LABEL_WEST = 0;\r
\r
- if(av.scaleRightWrapped)\r
- LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");\r
+ }\r
\r
- if(av.scaleLeftWrapped)\r
- LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");\r
+ }\r
\r
- return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
}\r
\r
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)\r
+ public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
+ int startRes)\r
{\r
- AlignmentI al = av.getAlignment();\r
+ AlignmentI al = av.getAlignment();\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ int LABEL_EAST = 0;\r
+\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(al.getWidth() + "000");\r
+ }\r
\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ int LABEL_WEST = 0;\r
\r
- int LABEL_EAST = 0;\r
- if(av.scaleRightWrapped)\r
- LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );\r
- int LABEL_WEST = 0;\r
- if(av.scaleLeftWrapped)\r
- LABEL_WEST = fm.stringWidth(al.getWidth()+"0");\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(al.getWidth() + "0");\r
+ }\r
\r
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
\r
- int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
+ av.endRes = av.startRes + cWidth;\r
\r
- av.endRes = av.startRes + cWidth;\r
+ int endx = (startRes + cWidth) - 1;\r
+ int ypos = 2 * av.charHeight;\r
\r
- int endx = startRes+cWidth-1;\r
- int ypos = 2*av.charHeight;\r
+ while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
+ {\r
+ g.setColor(Color.black);\r
\r
- while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )\r
+ if (av.scaleLeftWrapped)\r
{\r
- g.setColor(Color.black);\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
\r
- if(av.scaleLeftWrapped)\r
- drawWestScale(g, startRes, endx, ypos);\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);\r
+ }\r
\r
- if(av.scaleRightWrapped)\r
- {\r
- g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);\r
- drawEastScale(g, startRes, endx, ypos);\r
- g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);\r
- }\r
+ g.translate(LABEL_WEST, 0);\r
\r
- g.translate(LABEL_WEST,0);\r
- if(av.scaleAboveWrapped)\r
- drawNorthScale(g, startRes, endx, ypos);\r
-\r
-\r
- // When printing we have an extra clipped region,\r
- // the Printable page which we need to account for here\r
- Shape clip = g.getClip();\r
- if(clip==null)\r
- g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);\r
- else\r
- g.setClip(0,\r
- (int)clip.getBounds().getY(),\r
- cWidth*av.charWidth,\r
- (int)clip.getBounds().getHeight()\r
- );\r
-\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
- g.setClip(clip);\r
- g.translate(-LABEL_WEST,0);\r
-\r
- ypos += cHeight;\r
- startRes += cWidth;\r
- endx = startRes + cWidth - 1;\r
-\r
- if (endx > al.getWidth())\r
- endx = al.getWidth();\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ drawNorthScale(g, startRes, endx, ypos);\r
}\r
\r
- }\r
+ // When printing we have an extra clipped region,\r
+ // the Printable page which we need to account for here\r
+ Shape clip = g.getClip();\r
+\r
+ if (clip == null)\r
+ {\r
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
+ }\r
+ else\r
+ {\r
+ g.setClip(0, (int) clip.getBounds().getY(),\r
+ cWidth * av.charWidth, (int) clip.getBounds().getHeight());\r
+ }\r
\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+ g.setClip(clip);\r
+ g.translate( -LABEL_WEST, 0);\r
\r
- synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
+ ypos += cHeight;\r
+ startRes += cWidth;\r
+ endx = (startRes + cWidth) - 1;\r
+\r
+ if (endx > al.getWidth())\r
+ {\r
+ endx = al.getWidth();\r
+ }\r
+ }\r
+ }\r
\r
- Graphics2D g = (Graphics2D)g1;\r
+ synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
+ int y2, int startx, int starty, int offset)\r
+ {\r
+ Graphics2D g = (Graphics2D) g1;\r
g.setFont(av.getFont());\r
sr.renderGaps(av.renderGaps);\r
\r
-\r
SequenceI nextSeq;\r
\r
/// First draw the sequences\r
/////////////////////////////\r
- for (int i = y1 ; i < y2 ;i++)\r
+ for (int i = y1; i < y2; i++)\r
{\r
- nextSeq = av.alignment.getSequenceAt(i);\r
-\r
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,\r
- (x1 - startx) * av.charWidth,\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth,av.charHeight);\r
-\r
- if(av.showSequenceFeatures)\r
- {\r
- fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,\r
- (x1 - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth, av.charHeight);\r
- }\r
+ nextSeq = av.alignment.getSequenceAt(i);\r
+\r
+ sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
+ x1, x2, (x1 - startx) * av.charWidth,\r
+ offset +\r
+ AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+ av.charWidth, av.charHeight);\r
+\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.drawSequence(g, nextSeq,\r
+ av.alignment.findAllGroups(nextSeq), x1, x2,\r
+ (x1 - startx) * av.charWidth,\r
+ offset +\r
+ AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+ av.charWidth, av.charHeight);\r
+ }\r
}\r
+\r
//\r
/////////////////////////////////////\r
-\r
// Now outline any areas if necessary\r
/////////////////////////////////////\r
SequenceGroup group = av.getSelectionGroup();\r
java.util.Vector groups = av.alignment.getGroups();\r
\r
- int sx = -1, sy = -1, ex = -1;\r
+ int sx = -1;\r
+ int sy = -1;\r
+ int ex = -1;\r
int groupIndex = -1;\r
- if (group == null && groups.size() > 0)\r
+\r
+ if ( (group == null) && (groups.size() > 0))\r
{\r
group = (SequenceGroup) groups.elementAt(0);\r
groupIndex = 0;\r
}\r
\r
if (group != null)\r
+ {\r
do\r
{\r
int oldY = -1;\r
int i = 0;\r
boolean inGroup = false;\r
- int top=-1, bottom =-1;\r
+ int top = -1;\r
+ int bottom = -1;\r
+\r
for (i = y1; i < y2; i++)\r
{\r
sx = (group.getStartRes() - startx) * av.charWidth;\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;\r
-\r
- if (sx < getWidth()\r
- && ex > 0\r
- && group.sequences.contains(av.alignment.getSequenceAt(i)))\r
+ sy = offset +\r
+ AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+ ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *\r
+ av.charWidth) -\r
+ 1;\r
+\r
+ if ( (sx < getWidth()) && (ex > 0) &&\r
+ group.sequences.contains(av.alignment.getSequenceAt(\r
+ i)))\r
{\r
- if (bottom == -1 &&\r
- !group.sequences.contains(av.alignment.getSequenceAt(i + 1)))\r
- bottom = sy + av.charHeight ;\r
+ if ( (bottom == -1) &&\r
+ !group.sequences.contains(\r
+ av.alignment.getSequenceAt(i + 1)))\r
+ {\r
+ bottom = sy + av.charHeight;\r
+ }\r
\r
if (!inGroup)\r
{\r
- if (top == -1 && i==0 ||\r
- !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))\r
+ if ( ( (top == -1) && (i == 0)) ||\r
+ !group.sequences.contains(\r
+ av.alignment.getSequenceAt(i - 1)))\r
+ {\r
top = sy;\r
-\r
+ }\r
\r
oldY = sy;\r
inGroup = true;\r
+\r
if (group == av.getSelectionGroup())\r
{\r
- g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,3f}, 0f ));\r
+ g.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_BUTT,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[]\r
+ {5f, 3f}, 0f));\r
g.setColor(Color.RED);\r
}\r
else\r
{\r
if (inGroup)\r
{\r
- g.drawLine(sx, oldY, sx, sy );\r
- g.drawLine(sx+ex, oldY, sx+ex, sy );\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
\r
if (top != -1)\r
{\r
g.drawLine(sx, top, sx + ex, top);\r
- top =-1;\r
+ top = -1;\r
}\r
+\r
if (bottom != -1)\r
{\r
g.drawLine(sx, bottom, sx + ex, bottom);\r
bottom = -1;\r
}\r
\r
-\r
inGroup = false;\r
}\r
}\r
\r
if (inGroup)\r
{\r
-\r
- if(top!=-1)\r
+ if (top != -1)\r
{\r
g.drawLine(sx, top, sx + ex, top);\r
- top =-1;\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
}\r
- if(bottom!=-1)\r
- {\r
- g.drawLine(sx, bottom-1, sx + ex, bottom-1);\r
- bottom = -1;\r
-\r
- }\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- g.drawLine(sx, oldY, sx, sy );\r
- g.drawLine(sx+ex, oldY, sx+ex, sy );\r
+\r
+ sy = offset +\r
+ AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
inGroup = false;\r
}\r
+\r
groupIndex++;\r
+\r
if (groupIndex >= groups.size())\r
+ {\r
break;\r
+ }\r
\r
group = (SequenceGroup) groups.elementAt(groupIndex);\r
-\r
}\r
while (groupIndex < groups.size());\r
-\r
+ }\r
\r
/// Highlight search Results once all sequences have been drawn\r
//////////////////////////////////////////////////////////\r
- if(displaySearch)\r
+ if (displaySearch)\r
{\r
- for(int r=0; r<searchResults.length; r+=3)\r
+ for (int r = 0; r < searchResults.length; r += 3)\r
{\r
int searchSeq = searchResults[r];\r
\r
- if (searchSeq >= y1 && searchSeq < y2)\r
+ if ( (searchSeq >= y1) && (searchSeq < y2))\r
{\r
SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
\r
- int searchStart = seq.findIndex( searchResults[r+1] )-1;\r
- int searchEnd = seq.findIndex( searchResults[r+2] )-1;\r
+ int searchStart = seq.findIndex(searchResults[r + 1]) - 1;\r
+ int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;\r
\r
SequenceRenderer ssr = (SequenceRenderer) sr;\r
- if(searchStart<x1)\r
+\r
+ if (searchStart < x1)\r
+ {\r
searchStart = x1;\r
- if(searchEnd > x2)\r
+ }\r
+\r
+ if (searchEnd > x2)\r
+ {\r
searchEnd = x2;\r
+ }\r
\r
- ssr.drawHighlightedText(seq,\r
- searchStart,\r
- searchEnd,\r
+ ssr.drawHighlightedText(seq, searchStart, searchEnd,\r
(searchStart - startx) * av.charWidth,\r
offset +\r
- AlignmentUtil.getPixelHeight(starty, searchSeq,\r
- av.charHeight),\r
- av.charWidth,\r
- av.charHeight);\r
+ AlignmentUtil.getPixelHeight(starty,\r
+ searchSeq,\r
+ av.charHeight), av.charWidth, av.charHeight);\r
}\r
}\r
}\r
-\r
}\r
\r
-\r
-\r
- public void highlightSearchResults(int [] results)\r
+ public void highlightSearchResults(int[] results)\r
{\r
// results are in the order sequence, startRes, endRes\r
- if(results==null)\r
+ if (results == null)\r
+ {\r
displaySearch = false;\r
+ }\r
else\r
+ {\r
displaySearch = true;\r
+ }\r
\r
searchResults = results;\r
\r
repaint();\r
}\r
-\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import jalview.datamodel.*;\r
import javax.swing.*;\r
-import java.util.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import jalview.analysis.Conservation;\r
\r
-public class SeqPanel extends JPanel\r
+public class SeqPanel\r
+ extends JPanel\r
{\r
-\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel ap;\r
-\r
+ public SeqCanvas seqCanvas;\r
+ public AlignmentPanel ap;\r
protected int lastres;\r
protected int startseq;\r
- int startEdit=-1;\r
- int endEdit=-1;\r
-\r
+ int startEdit = -1;\r
+ int endEdit = -1;\r
protected AlignViewport av;\r
\r
// if character is inserted or deleted, we will need to recalculate the conservation\r
int seqEditOccurred = -1;\r
-\r
ScrollThread scrollThread = null;\r
boolean mouseDragging = false;\r
-\r
boolean editingSeqs = false;\r
boolean groupEditing = false;\r
\r
+ //////////////////////////////////////////\r
+ /////Everything below this is for defining the boundary of the rubberband\r
+ //////////////////////////////////////////\r
+ int oldSeq = -1;\r
+ boolean changeEndSeq = false;\r
+ boolean changeStartSeq = false;\r
+ boolean changeEndRes = false;\r
+ boolean changeStartRes = false;\r
+ SequenceGroup stretchGroup = null;\r
+ boolean remove = false;\r
\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
- this.av = avp;\r
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+ {\r
+ this.av = avp;\r
\r
- seqCanvas = new SeqCanvas(avp);\r
+ seqCanvas = new SeqCanvas(avp);\r
setLayout(new BorderLayout());\r
add(seqCanvas, BorderLayout.CENTER);\r
\r
ap = p;\r
\r
- addMouseMotionListener( new MouseMotionAdapter()\r
+ addMouseMotionListener(new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- doMouseMoved(evt); }\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+\r
+ doMouseMoved(evt);\r
+ }\r
\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if( editingSeqs )\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (editingSeqs)\r
+ {\r
doMouseDragged(evt);\r
+ }\r
else\r
+ {\r
doMouseDraggedDefineMode(evt);\r
+ }\r
}\r
});\r
\r
- addMouseListener( new MouseAdapter()\r
+ addMouseListener(new MouseAdapter()\r
{\r
public void mouseReleased(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if(editingSeqs)\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (editingSeqs)\r
+ {\r
doMouseReleased(evt);\r
+ }\r
else\r
+ {\r
doMouseReleasedDefineMode(evt);\r
-\r
+ }\r
}\r
+\r
public void mousePressed(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if (av.getWrapAlignment())\r
{\r
- if(evt.isAltDown() || evt.isControlDown())\r
+ return;\r
+ }\r
+\r
+ if (evt.isShiftDown() || evt.isAltDown() ||\r
+ evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown() || evt.isControlDown())\r
+ {\r
groupEditing = true;\r
+ }\r
\r
editingSeqs = true;\r
doMousePressed(evt);\r
}\r
else\r
+ {\r
doMousePressedDefineMode(evt);\r
+ }\r
}\r
+\r
public void mouseExited(MouseEvent evt)\r
{\r
if (av.getWrapAlignment() || editingSeqs)\r
- return;\r
- doMouseExitedDefineMode(evt);\r
+ {\r
+ return;\r
+ }\r
\r
+ doMouseExitedDefineMode(evt);\r
}\r
+\r
public void mouseEntered(MouseEvent evt)\r
{\r
if (av.getWrapAlignment() || editingSeqs)\r
+ {\r
return;\r
+ }\r
+\r
doMouseEnteredDefineMode(evt);\r
}\r
-\r
});\r
repaint();\r
}\r
\r
-\r
- public void doMouseReleased(MouseEvent evt) {\r
-\r
- if(seqEditOccurred>-1)\r
+ public void doMouseReleased(MouseEvent evt)\r
+ {\r
+ if (seqEditOccurred > -1)\r
+ {\r
editOccurred(seqEditOccurred);\r
+ }\r
\r
startseq = -1;\r
- lastres = -1;\r
+ lastres = -1;\r
seqEditOccurred = -1;\r
- editingSeqs = false;\r
+ editingSeqs = false;\r
groupEditing = false;\r
\r
ap.repaint();\r
}\r
\r
- public void doMousePressed(MouseEvent evt) {\r
-\r
- ap.alignFrame.addHistoryItem( new HistoryItem(\r
- "Edit Sequence",av.alignment, HistoryItem.EDIT));\r
+ public void doMousePressed(MouseEvent evt)\r
+ {\r
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
\r
int seq;\r
int res;\r
int x = evt.getX();\r
int y = evt.getY();\r
\r
- res = x/av.getCharWidth() + av.getStartRes();\r
- seq = y/av.getCharHeight() + av.getStartSeq();\r
+ res = (x / av.getCharWidth()) + av.getStartRes();\r
+ seq = (y / av.getCharHeight()) + av.getStartSeq();\r
\r
- if (seq < av.getAlignment().getHeight() &&\r
- res < av.getAlignment().getSequenceAt(seq).getLength())\r
+ if ( (seq < av.getAlignment().getHeight()) &&\r
+ (res < av.getAlignment().getSequenceAt(seq).getLength()))\r
{\r
startseq = seq;\r
lastres = res;\r
\r
public void doMouseMoved(MouseEvent evt)\r
{\r
- int res=0, seq=0;\r
+ int res = 0;\r
+ int seq = 0;\r
int x = evt.getX();\r
int y = evt.getY();\r
- if(av.wrapAlignment)\r
+\r
+ if (av.wrapAlignment)\r
{\r
- y -= 2*av.charHeight;\r
- int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;\r
+ y -= (2 * av.charHeight);\r
\r
+ int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
\r
- res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();\r
+ res = (int) ( (y / chunkHeight) * (getWidth() / av.charWidth)) +\r
+ (x / av.getCharWidth()) + av.getStartRes();\r
\r
y %= chunkHeight;\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
-\r
+ seq = (y / av.getCharHeight()) + av.getStartSeq();\r
}\r
else\r
{\r
- res = x / av.getCharWidth() + av.getStartRes();\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
+ res = (x / av.getCharWidth()) + av.getStartRes();\r
+ seq = (y / av.getCharHeight()) + av.getStartSeq();\r
}\r
\r
-\r
- if(seq>=av.getAlignment().getHeight())\r
+ if (seq >= av.getAlignment().getHeight())\r
+ {\r
return;\r
+ }\r
\r
SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
- if(res>sequence.getLength())\r
+\r
+ if (res > sequence.getLength())\r
+ {\r
return;\r
+ }\r
\r
- Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
+ Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +\r
+ "");\r
String aa = "";\r
- if(obj!=null)\r
- aa = obj.toString();\r
\r
- StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());\r
- if(aa!="")\r
- text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
+ if (obj != null)\r
+ {\r
+ aa = obj.toString();\r
+ }\r
+\r
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+ sequence.getName());\r
+\r
+ if (aa != "")\r
+ {\r
+ text.append(" Residue: " + aa + " (" +\r
+ av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+ }\r
\r
ap.alignFrame.statusBar.setText(text.toString());\r
\r
// use aa to see if the mouse pointer is on a\r
- if( av.showSequenceFeatures)\r
+ if (av.showSequenceFeatures)\r
{\r
Vector features = sequence.getSequenceFeatures();\r
Enumeration e = features.elements();\r
StringBuffer sbuffer = new StringBuffer();\r
\r
-\r
while (e.hasMoreElements())\r
{\r
SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getStart() <= sequence.findPosition(res) &&\r
- sf.getEnd() >= sequence.findPosition(res))\r
+\r
+ if ( (sf.getStart() <= sequence.findPosition(res)) &&\r
+ (sf.getEnd() >= sequence.findPosition(res)))\r
{\r
- if(sbuffer.length()>0)\r
+ if (sbuffer.length() > 0)\r
+ {\r
sbuffer.append("; ");\r
+ }\r
+\r
sbuffer.append(sf.getType() + " " + sf.getDescription());\r
- if(sf.getStatus().length()>0)\r
- sbuffer.append(" ("+sf.getStatus()+")");\r
- }\r
\r
+ if (sf.getStatus().length() > 0)\r
+ {\r
+ sbuffer.append(" (" + sf.getStatus() + ")");\r
+ }\r
+ }\r
}\r
\r
ToolTipManager.sharedInstance().registerComponent(this);\r
this.setToolTipText(sbuffer.toString());\r
}\r
-\r
-\r
}\r
\r
- public void doMouseDragged(MouseEvent evt) {\r
-\r
+ public void doMouseDragged(MouseEvent evt)\r
+ {\r
// If we're dragging we're editing\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+\r
if (res < 0)\r
+ {\r
res = 0;\r
+ }\r
\r
- if (lastres == -1 || lastres == res)\r
+ if ( (lastres == -1) || (lastres == res))\r
+ {\r
return;\r
+ }\r
\r
boolean dragRight = true;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
- dragRight = false;\r
\r
+ if ( (res < av.getAlignment().getWidth()) && (res < lastres))\r
+ {\r
+ dragRight = false;\r
+ }\r
\r
if (res != lastres)\r
{\r
- // Group editing\r
- if (groupEditing)\r
+ // Group editing\r
+ if (groupEditing)\r
+ {\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+\r
+ if (sg == null)\r
{\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg==null)\r
- {\r
- lastres=-1;\r
- return;\r
- }\r
+ lastres = -1;\r
\r
- // drag to right\r
- if(dragRight)\r
- sg.setEndRes(sg.getEndRes() + (res-lastres));\r
+ return;\r
+ }\r
\r
- // drag to left\r
- else\r
+ // drag to right\r
+ if (dragRight)\r
+ {\r
+ sg.setEndRes(sg.getEndRes() + (res - lastres));\r
+ }\r
+ // drag to left\r
+ else\r
+ {\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+ boolean deleteAllowed = false;\r
+\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(s);\r
+\r
+ for (int j = res; j < lastres; j++)\r
{\r
- /// Are we able to delete?\r
- // ie are all columns blank?\r
- boolean deleteAllowed = false;\r
- for (int s = 0; s < sg.getSize(); s++)\r
+ if (seq.getSequence().length() <= j)\r
{\r
- SequenceI seq = sg.getSequenceAt(s);\r
- for (int j=res; j<lastres; j++)\r
- {\r
- if(seq.getSequence().length()<=j)\r
- continue;\r
-\r
- if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- res=j+1;\r
- deleteAllowed = false;\r
- continue;\r
- }\r
- deleteAllowed = true;\r
- }\r
+ continue;\r
}\r
\r
- if(!deleteAllowed)\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getSequence().charAt(j)))\r
{\r
- lastres = -1;\r
- return;\r
+ // Not a gap, block edit not valid\r
+ res = j + 1;\r
+ deleteAllowed = false;\r
+\r
+ continue;\r
}\r
\r
- sg.setEndRes(sg.getEndRes() - (lastres-res));\r
+ deleteAllowed = true;\r
}\r
+ }\r
\r
+ if (!deleteAllowed)\r
+ {\r
+ lastres = -1;\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
+ return;\r
+ }\r
+\r
+ sg.setEndRes(sg.getEndRes() - (lastres - res));\r
+ }\r
\r
- // drag to right\r
- if (dragRight)\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, k);\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI s = sg.getSequenceAt(i);\r
+ int k = av.alignment.findIndex(s);\r
\r
- // drag to left\r
- else\r
+ // drag to right\r
+ if (dragRight)\r
+ {\r
+ for (int j = lastres; j < res; j++)\r
+ {\r
+ insertChar(j, k);\r
+ }\r
+ }\r
+ // drag to left\r
+ else\r
+ {\r
+ for (int j = res; j < lastres; j++)\r
+ {\r
+ if (s.getLength() > j)\r
{\r
- for (int j = res; j < lastres; j++)\r
- {\r
- if(s.getLength()>j)\r
- deleteChar(res, k);\r
- }\r
+ deleteChar(res, k);\r
}\r
}\r
+ }\r
}\r
- else /////Editing a single sequence///////////\r
+ }\r
+ else /////Editing a single sequence///////////\r
+ {\r
+ if ( (res < av.getAlignment().getWidth()) && (res > lastres))\r
{\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
+ // dragging to the right\r
+ for (int j = lastres; j < res; j++)\r
{\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, startseq);\r
+ insertChar(j, startseq);\r
}\r
- else if (res < av.getAlignment().getWidth() && res < lastres)\r
+ }\r
+ else if ( (res < av.getAlignment().getWidth()) &&\r
+ (res < lastres))\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > res; j--)\r
{\r
- // dragging to the left\r
- for (int j = lastres; j > res; j--)\r
+ if (jalview.util.Comparison.isGap(\r
+ av.alignment.getSequenceAt(startseq)\r
+ .getSequence().charAt(res)))\r
{\r
- if( jalview.util.Comparison.isGap(\r
- av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
-\r
deleteChar(res, startseq);\r
- else\r
- {\r
-\r
- break;\r
- }\r
+ }\r
+ else\r
+ {\r
+ break;\r
}\r
}\r
-\r
}\r
+ }\r
}\r
\r
endEdit = res;\r
repaint();\r
}\r
\r
- public void drawChars(int seqstart, int seqend, int start) {\r
- seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);\r
+ public void drawChars(int seqstart, int seqend, int start)\r
+ {\r
+ seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,\r
+ seqend, av.getStartRes(), av.getStartSeq(), 0);\r
repaint();\r
}\r
\r
public void insertChar(int j, int seq)\r
{\r
av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred=seq;\r
+ seqEditOccurred = seq;\r
}\r
\r
public void deleteChar(int j, int seq)\r
{\r
av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
- seqEditOccurred=seq;\r
+ seqEditOccurred = seq;\r
\r
av.alignment.getWidth();\r
repaint();\r
}\r
\r
-\r
void editOccurred(int i)\r
{\r
- if(endEdit==startEdit)\r
+ if (endEdit == startEdit)\r
{\r
ap.alignFrame.historyList.pop();\r
ap.alignFrame.updateEditMenuBar();\r
\r
// Y O Y CLUSTALX\r
ColourSchemeI cs = av.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme)\r
+\r
+ if (cs instanceof ConservationColourScheme)\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
- if(ccs.cs instanceof ClustalxColourScheme)\r
- {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
+\r
+ if (ccs.cs instanceof ClustalxColourScheme)\r
+ {\r
Conservation c = new Conservation("All",\r
ResidueProperties.propHash, 3,\r
av.alignment.getSequences(), 0,\r
c.calculate();\r
c.verdict(false, av.ConsPercGaps);\r
\r
- ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;\r
- cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());\r
+ ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;\r
+ cxs.resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
ccs = new ConservationColourScheme(c, cxs);\r
av.setGlobalColourScheme(ccs);\r
- }\r
+ }\r
}\r
\r
- if(cs instanceof ClustalxColourScheme)\r
+ if (cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
+ ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
av.setGlobalColourScheme(cs);\r
}\r
-\r
}\r
\r
-//////////////////////////////////////////\r
-/////Everything below this is for defining the boundary of the rubberband\r
-//////////////////////////////////////////\r
- int oldSeq = -1;\r
public void doMousePressedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+ int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();\r
oldSeq = seq;\r
\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
\r
- if(sequence==null || res>sequence.getLength())\r
+ if ( (sequence == null) || (res > sequence.getLength()))\r
+ {\r
return;\r
+ }\r
\r
stretchGroup = av.getSelectionGroup();\r
\r
- if(stretchGroup == null)\r
- {\r
- stretchGroup = av.alignment.findGroup( sequence );\r
- if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
- av.setSelectionGroup(stretchGroup);\r
- else\r
- stretchGroup = null;\r
- }\r
-\r
- else if(!stretchGroup.sequences.contains(sequence)\r
- || stretchGroup.getStartRes()>res\r
- || stretchGroup.getEndRes()<res)\r
- {\r
- stretchGroup = null;\r
-\r
- SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );\r
-\r
- if (allGroups != null)\r
- for (int i = 0; i < allGroups.length; i++)\r
- if (allGroups[i].getStartRes() <= res &&\r
- allGroups[i].getEndRes() >= res)\r
- {\r
- stretchGroup = allGroups[i];\r
- av.setSelectionGroup(stretchGroup);\r
- break;\r
- }\r
- }\r
-\r
- if(stretchGroup==null)\r
+ if (stretchGroup == null)\r
+ {\r
+ stretchGroup = av.alignment.findGroup(sequence);\r
+\r
+ if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&\r
+ (res < stretchGroup.getEndRes()))\r
+ {\r
+ av.setSelectionGroup(stretchGroup);\r
+ }\r
+ else\r
+ {\r
+ stretchGroup = null;\r
+ }\r
+ }\r
+ else if (!stretchGroup.sequences.contains(sequence) ||\r
+ (stretchGroup.getStartRes() > res) ||\r
+ (stretchGroup.getEndRes() < res))\r
+ {\r
+ stretchGroup = null;\r
+\r
+ SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
+\r
+ if (allGroups != null)\r
+ {\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ {\r
+ if ( (allGroups[i].getStartRes() <= res) &&\r
+ (allGroups[i].getEndRes() >= res))\r
+ {\r
+ stretchGroup = allGroups[i];\r
+ av.setSelectionGroup(stretchGroup);\r
+\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (stretchGroup == null)\r
{\r
// define a new group here\r
SequenceGroup sg = new SequenceGroup();\r
sg.setStartRes(res);\r
sg.setEndRes(res);\r
- sg.addSequence( sequence );\r
- av.setSelectionGroup( sg );\r
+ sg.addSequence(sequence);\r
+ av.setSelectionGroup(sg);\r
stretchGroup = sg;\r
\r
- if(av.getConservationSelected())\r
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
- if(av.getAbovePIDThreshold())\r
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
+ if (av.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(ap,\r
+ av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
\r
+ if (av.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
}\r
- else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
+ else if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
{\r
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);\r
- pop.show(this, evt.getX(), evt.getY());\r
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);\r
+ pop.show(this, evt.getX(), evt.getY());\r
\r
- // edit the properties of existing group\r
+ // edit the properties of existing group\r
}\r
\r
- if(stretchGroup!=null && stretchGroup.getEndRes()==res)\r
+ if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
+ {\r
// Edit end res position of selected group\r
changeEndRes = true;\r
-\r
- else if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
+ }\r
+ else if ( (stretchGroup != null) && (stretchGroup.getStartRes() == res))\r
+ {\r
// Edit end res position of selected group\r
changeStartRes = true;\r
+ }\r
\r
stretchGroup.getWidth();\r
\r
repaint();\r
-\r
}\r
\r
- boolean changeEndSeq = false;\r
- boolean changeStartSeq = false;\r
- boolean changeEndRes = false;\r
- boolean changeStartRes = false;\r
- SequenceGroup stretchGroup = null;\r
-\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
mouseDragging = false;\r
\r
- if(stretchGroup==null)\r
+ if (stretchGroup == null)\r
+ {\r
return;\r
+ }\r
\r
- if(stretchGroup.cs instanceof ClustalxColourScheme)\r
+ if (stretchGroup.cs instanceof ClustalxColourScheme)\r
{\r
- stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
+ stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,\r
+ av.alignment.getWidth());\r
repaint();\r
}\r
-\r
- else if(stretchGroup.cs instanceof ConservationColourScheme)\r
+ else if (stretchGroup.cs instanceof ConservationColourScheme)\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
- stretchGroup.cs = ccs;\r
- SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
+ ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;\r
+ stretchGroup.cs = ccs;\r
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
\r
- repaint();\r
+ repaint();\r
}\r
else\r
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
-\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
+ }\r
\r
changeEndRes = false;\r
changeStartRes = false;\r
ap.idPanel.repaint();\r
}\r
\r
-\r
- boolean remove = false;\r
public void doMouseDraggedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+ int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();\r
\r
- if(stretchGroup==null)\r
+ if (stretchGroup == null)\r
+ {\r
return;\r
+ }\r
\r
- if(res>av.alignment.getWidth())\r
- res = av.alignment.getWidth()-1;\r
-\r
+ if (res > av.alignment.getWidth())\r
+ {\r
+ res = av.alignment.getWidth() - 1;\r
+ }\r
\r
- if(stretchGroup.getEndRes()==res)\r
+ if (stretchGroup.getEndRes() == res)\r
+ {\r
// Edit end res position of selected group\r
changeEndRes = true;\r
-\r
- else if(stretchGroup.getStartRes()==res)\r
+ }\r
+ else if (stretchGroup.getStartRes() == res)\r
+ {\r
// Edit start res position of selected group\r
changeStartRes = true;\r
+ }\r
\r
-\r
- if(res<av.getStartRes())\r
+ if (res < av.getStartRes())\r
+ {\r
res = av.getStartRes();\r
- else if(res>av.getEndRes())\r
+ }\r
+ else if (res > av.getEndRes())\r
+ {\r
res = av.getEndRes();\r
+ }\r
\r
- if(changeEndRes)\r
+ if (changeEndRes)\r
{\r
- if(res>stretchGroup.getStartRes()-1)\r
- stretchGroup.setEndRes( res );\r
+ if (res > (stretchGroup.getStartRes() - 1))\r
+ {\r
+ stretchGroup.setEndRes(res);\r
+ }\r
}\r
- else if(changeStartRes)\r
+ else if (changeStartRes)\r
{\r
- if(res<stretchGroup.getEndRes()+1)\r
- stretchGroup.setStartRes( res );\r
+ if (res < (stretchGroup.getEndRes() + 1))\r
+ {\r
+ stretchGroup.setStartRes(res);\r
+ }\r
}\r
\r
int dragDirection = 0;\r
+\r
if (y > oldSeq)\r
+ {\r
dragDirection = 1;\r
+ }\r
else if (y < oldSeq)\r
+ {\r
dragDirection = -1;\r
+ }\r
\r
- while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())\r
+ while ( (y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))\r
{\r
// This routine ensures we don't skip any sequences, as the\r
// selection is quite slow.\r
Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
\r
oldSeq += dragDirection;\r
+\r
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
\r
if (stretchGroup.sequences.contains(nextSeq))\r
}\r
else\r
{\r
- if(seq!=null)\r
- stretchGroup.addSequence(seq);\r
+ if (seq != null)\r
+ {\r
+ stretchGroup.addSequence(seq);\r
+ }\r
+\r
stretchGroup.addSequence(nextSeq);\r
}\r
}\r
+\r
oldSeq = y;\r
mouseDragging = true;\r
- if(scrollThread!=null)\r
+\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.setEvent(evt);\r
+ }\r
\r
repaint();\r
}\r
public void doMouseEnteredDefineMode(MouseEvent e)\r
{\r
if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
}\r
\r
public void doMouseExitedDefineMode(MouseEvent e)\r
{\r
if (av.getWrapAlignment())\r
+ {\r
return;\r
+ }\r
\r
- if(mouseDragging)\r
+ if (mouseDragging)\r
+ {\r
scrollThread = new ScrollThread();\r
-\r
+ }\r
}\r
+\r
// this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread extends Thread\r
+ class ScrollThread\r
+ extends Thread\r
{\r
MouseEvent evt;\r
boolean running = false;\r
+\r
public ScrollThread()\r
{\r
start();\r
public void run()\r
{\r
running = true;\r
+\r
while (running)\r
{\r
- if(evt!=null)\r
+ if (evt != null)\r
{\r
-\r
- if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+ if (mouseDragging && (evt.getY() < 0) &&\r
+ (av.getStartSeq() > 0))\r
+ {\r
running = ap.scrollUp(true);\r
+ }\r
\r
- if (mouseDragging && evt.getY() >= getHeight() &&\r
- av.alignment.getHeight() > av.getEndSeq())\r
+ if (mouseDragging && (evt.getY() >= getHeight()) &&\r
+ (av.alignment.getHeight() > av.getEndSeq()))\r
+ {\r
running = ap.scrollUp(false);\r
+ }\r
\r
- if (mouseDragging && evt.getX() < 0)\r
+ if (mouseDragging && (evt.getX() < 0))\r
+ {\r
running = ap.scrollRight(true);\r
-\r
- else if (mouseDragging && evt.getX() >= getWidth())\r
+ }\r
+ else if (mouseDragging && (evt.getX() >= getWidth()))\r
+ {\r
running = ap.scrollRight(false);\r
+ }\r
}\r
\r
try\r
Thread.sleep(75);\r
}\r
catch (Exception ex)\r
- {}\r
+ {\r
+ }\r
}\r
}\r
+ }\r
}\r
-\r
-\r
-\r
-}\r
-\r
-\r
-\r
-\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
+import java.awt.*;\r
+\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import java.awt.*;\r
\r
public class SequenceRenderer\r
{\r
FontMetrics fm;\r
boolean renderGaps = true;\r
SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
+ SequenceGroup[] allGroups = null;\r
Color resBoxColour;\r
Graphics graphics;\r
\r
this.av = av;\r
}\r
\r
-\r
public void renderGaps(boolean b)\r
{\r
renderGaps = b;\r
public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
{\r
getBoxColour(cs, seq, i);\r
+\r
return resBoxColour;\r
}\r
\r
void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
{\r
- if (cs != null)\r
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
- else\r
- resBoxColour = Color.white;\r
+ if (cs != null)\r
+ {\r
+ resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
+ }\r
+ else\r
+ {\r
+ resBoxColour = Color.white;\r
+ }\r
}\r
\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)\r
+ public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int x1, int y1, int width,\r
+ int height)\r
{\r
allGroups = sg;\r
\r
drawBoxes(seq, start, end, x1, y1, (int) width, height);\r
\r
fm = g.getFontMetrics();\r
- drawText(seq,start,end,x1,y1,(int)width,height);\r
-\r
+ drawText(seq, start, end, x1, y1, (int) width, height);\r
}\r
\r
- public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height) {\r
- int i = start;\r
+ public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,\r
+ int width, int height)\r
+ {\r
+ int i = start;\r
int length = seq.getLength();\r
\r
int curStart = -1;\r
int curWidth = width;\r
\r
Color tempColour = null;\r
- while (i <= end && i < length)\r
+\r
+ while ( (i <= end) && (i < length))\r
{\r
- if(inCurrentSequenceGroup(i))\r
+ if (inCurrentSequenceGroup(i))\r
{\r
- if( currentSequenceGroup.getDisplayBoxes())\r
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
else\r
- resBoxColour = Color.white;\r
+ {\r
+ resBoxColour = Color.white;\r
+ }\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.getGlobalColourScheme(), seq, i);\r
}\r
- else if(av.getShowBoxes())\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
else\r
+ {\r
resBoxColour = Color.white;\r
-\r
+ }\r
\r
if (resBoxColour != tempColour)\r
{\r
- if(tempColour!=null)\r
- graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
+ if (tempColour != null)\r
+ {\r
+ graphics.fillRect(x1 + (width * (curStart - start)), y1,\r
+ curWidth, height);\r
+ }\r
+\r
graphics.setColor(resBoxColour);\r
\r
curStart = i;\r
curWidth = width;\r
tempColour = resBoxColour;\r
-\r
}\r
else\r
+ {\r
curWidth += width;\r
+ }\r
\r
i++;\r
}\r
\r
-\r
- graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
+ graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,\r
+ height);\r
}\r
\r
- public void drawText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r
+ public void drawText(SequenceI seq, int start, int end, int x1, int y1,\r
+ int width, int height)\r
{\r
- int pady = height/5;\r
- int charOffset=0;\r
+ int pady = height / 5;\r
+ int charOffset = 0;\r
char s;\r
- // Need to find the sequence position here.\r
\r
+ // Need to find the sequence position here.\r
+ String sequence = seq.getSequence();\r
\r
- String sequence = seq.getSequence();\r
for (int i = start; i <= end; i++)\r
{\r
- graphics.setColor(Color.black);\r
+ graphics.setColor(Color.black);\r
\r
- if(i<sequence.length())\r
- s = sequence.charAt(i);\r
- else\r
- s = ' ';\r
+ if (i < sequence.length())\r
+ {\r
+ s = sequence.charAt(i);\r
+ }\r
+ else\r
+ {\r
+ s = ' ';\r
+ }\r
\r
- if(!renderGaps && jalview.util.Comparison.isGap(s))\r
- continue;\r
+ if (!renderGaps && jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (!currentSequenceGroup.getDisplayText())\r
+ {\r
+ continue;\r
+ }\r
\r
- if (inCurrentSequenceGroup(i))\r
+ if (currentSequenceGroup.getColourText())\r
{\r
- if(!currentSequenceGroup.getDisplayText())\r
- continue;\r
-\r
- if (currentSequenceGroup.getColourText())\r
- {\r
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
- graphics.setColor(resBoxColour.darker());\r
- }\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ graphics.setColor(resBoxColour.darker());\r
}\r
- else\r
+ }\r
+ else\r
+ {\r
+ if (!av.getShowText())\r
{\r
- if(!av.getShowText())\r
- continue;\r
-\r
- if(av.getColourText())\r
- {\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
- if(av.getShowBoxes())\r
- graphics.setColor(resBoxColour.darker());\r
- else\r
- graphics.setColor(resBoxColour);\r
- }\r
+ continue;\r
}\r
\r
- charOffset = (width - fm.charWidth(s))/2;\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i - start),\r
- y1 + height - pady);\r
+ if (av.getColourText())\r
+ {\r
+ getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+\r
+ if (av.getShowBoxes())\r
+ {\r
+ graphics.setColor(resBoxColour.darker());\r
+ }\r
+ else\r
+ {\r
+ graphics.setColor(resBoxColour);\r
+ }\r
}\r
+ }\r
\r
-\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - pady);\r
+ }\r
}\r
\r
boolean inCurrentSequenceGroup(int res)\r
{\r
- if(allGroups ==null)\r
+ if (allGroups == null)\r
+ {\r
return false;\r
+ }\r
\r
- for(int i=0; i<allGroups.length; i++)\r
- if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ {\r
+ if ( (allGroups[i].getStartRes() <= res) &&\r
+ (allGroups[i].getEndRes() >= res))\r
{\r
- currentSequenceGroup = allGroups[i];\r
- return true;\r
+ currentSequenceGroup = allGroups[i];\r
+\r
+ return true;\r
}\r
+ }\r
\r
return false;\r
}\r
\r
- public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1,\r
+ int y1, int width, int height)\r
{\r
- int pady = height/5;\r
- int charOffset=0;\r
+ int pady = height / 5;\r
+ int charOffset = 0;\r
graphics.setColor(Color.BLACK);\r
- graphics.fillRect(x1,y1,width*(end-start+1),height);\r
+ graphics.fillRect(x1, y1, width * (end - start + 1), height);\r
graphics.setColor(Color.white);\r
\r
- char s='~';\r
+ char s = '~';\r
+\r
// Need to find the sequence position here.\r
for (int i = start; i <= end; i++)\r
{\r
- if(i<seq.getLength())\r
- s = seq.getSequence().charAt(i);\r
+ if (i < seq.getLength())\r
+ {\r
+ s = seq.getSequence().charAt(i);\r
+ }\r
\r
- charOffset = (width - fm.charWidth(s))/2;\r
- graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - pady);\r
}\r
}\r
-\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
+\r
import java.awt.event.*;\r
-import javax.swing.event.*;\r
import javax.swing.*;\r
-import java.util.*;\r
+import javax.swing.event.*;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
\r
-public class SliderPanel extends GSliderPanel\r
+public class SliderPanel\r
+ extends GSliderPanel\r
{\r
+ static JInternalFrame conservationSlider;\r
+ static JInternalFrame PIDSlider;\r
AlignmentPanel ap;\r
boolean forConservation = true;\r
ColourSchemeI cs;\r
\r
- static JInternalFrame conservationSlider;\r
- static JInternalFrame PIDSlider;\r
+ public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,\r
+ ColourSchemeI cs)\r
+ {\r
+ this.ap = ap;\r
+ this.cs = cs;\r
+ forConservation = forConserve;\r
+ undoButton.setVisible(false);\r
+ applyButton.setVisible(false);\r
\r
- public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs, String source)\r
+ if (forConservation)\r
+ {\r
+ label.setText("Enter value to increase conservation visibility");\r
+ slider.setMinimum(0);\r
+ slider.setMaximum(50);\r
+ }\r
+ else\r
+ {\r
+ label.setText("Enter % identity above which to colour residues");\r
+ slider.setMinimum(0);\r
+ slider.setMaximum(100);\r
+ }\r
+\r
+ slider.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ valueField.setText(slider.getValue() + "");\r
+ valueChanged(slider.getValue());\r
+ }\r
+ });\r
+\r
+ slider.setValue(value);\r
+ valueField.setText(value + "");\r
+ }\r
+\r
+ public static int setConservationSlider(AlignmentPanel ap,\r
+ ColourSchemeI cs, String source)\r
{\r
SliderPanel sp = null;\r
- ConservationColourScheme ccs = (ConservationColourScheme)cs;\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
\r
- if(conservationSlider == null)\r
+ if (conservationSlider == null)\r
{\r
sp = new SliderPanel(ap, ccs.inc, true, cs);\r
conservationSlider = new JInternalFrame();\r
}\r
else\r
{\r
- sp = (SliderPanel)conservationSlider.getContentPane();\r
- sp.cs = cs;\r
+ sp = (SliderPanel) conservationSlider.getContentPane();\r
+ sp.cs = cs;\r
}\r
\r
- conservationSlider.setTitle("Conservation Colour Increment ("+source+")");\r
- if(ap.av.alignment.getGroups()!=null)\r
- sp.setAllGroupsCheckEnabled( true );\r
+ conservationSlider.setTitle("Conservation Colour Increment (" +\r
+ source + ")");\r
+\r
+ if (ap.av.alignment.getGroups() != null)\r
+ {\r
+ sp.setAllGroupsCheckEnabled(true);\r
+ }\r
else\r
- sp.setAllGroupsCheckEnabled( false);\r
+ {\r
+ sp.setAllGroupsCheckEnabled(false);\r
+ }\r
\r
return sp.getValue();\r
}\r
\r
public static void showConservationSlider()\r
{\r
- try{\r
+ try\r
+ {\r
PIDSlider.setClosed(true);\r
PIDSlider = null;\r
- }catch(Exception ex){}\r
-\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
- if(!conservationSlider.isVisible())\r
+ if (!conservationSlider.isVisible())\r
{\r
- Desktop.addInternalFrame(conservationSlider, conservationSlider.getTitle(), 420, 90, false);\r
+ Desktop.addInternalFrame(conservationSlider,\r
+ conservationSlider.getTitle(), 420, 90, false);\r
conservationSlider.addInternalFrameListener(new javax.swing.event.\r
InternalFrameAdapter()\r
{\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent e)\r
{\r
conservationSlider = null;\r
}\r
});\r
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
}\r
-\r
}\r
\r
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
- {\r
- SliderPanel pid = null;\r
-\r
- int threshold = 50;\r
- if (cs instanceof ResidueColourScheme)\r
- threshold = ( ( (ResidueColourScheme) cs).getThreshold());\r
- else if (cs instanceof ScoreColourScheme)\r
- threshold = ( ( (ScoreColourScheme) cs).getThreshold());\r
-\r
-\r
- if(PIDSlider == null)\r
- {\r
- pid = new SliderPanel(ap, threshold, false, cs);\r
- PIDSlider = new JInternalFrame();\r
- PIDSlider.setContentPane(pid);\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
- else\r
- {\r
- pid = (SliderPanel)PIDSlider.getContentPane();\r
- pid.cs = cs;\r
- }\r
- PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
-\r
- if (ap.av.alignment.getGroups() != null)\r
- pid.setAllGroupsCheckEnabled(true);\r
- else\r
- pid.setAllGroupsCheckEnabled(false);\r
-\r
- return pid.getValue();\r
-\r
- }\r
-\r
- public static void showPIDSlider()\r
- {\r
- try{\r
- conservationSlider.setClosed(true);\r
- conservationSlider = null;\r
- }catch(Exception ex){}\r
-\r
- if(!PIDSlider.isVisible())\r
- {\r
- Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90, false);\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- PIDSlider.addInternalFrameListener(new javax.swing.event.\r
- InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
- {\r
- PIDSlider = null;\r
- }\r
- });\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,\r
+ String source)\r
+ {\r
+ SliderPanel pid = null;\r
+\r
+ int threshold = 50;\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ {\r
+ threshold = ( ( (ResidueColourScheme) cs).getThreshold());\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ threshold = ( ( (ScoreColourScheme) cs).getThreshold());\r
}\r
\r
- }\r
+ if (PIDSlider == null)\r
+ {\r
+ pid = new SliderPanel(ap, threshold, false, cs);\r
+ PIDSlider = new JInternalFrame();\r
+ PIDSlider.setContentPane(pid);\r
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
+ else\r
+ {\r
+ pid = (SliderPanel) PIDSlider.getContentPane();\r
+ pid.cs = cs;\r
+ }\r
\r
+ PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");\r
\r
- public SliderPanel(AlignmentPanel ap, int value, boolean forConserve, ColourSchemeI cs)\r
- {\r
- this.ap = ap;\r
- this.cs = cs;\r
- forConservation = forConserve;\r
- undoButton.setVisible(false);\r
- applyButton.setVisible(false);\r
- if(forConservation)\r
+ if (ap.av.alignment.getGroups() != null)\r
{\r
- label.setText("Enter value to increase conservation visibility");\r
- slider.setMinimum(0);\r
- slider.setMaximum(50);\r
+ pid.setAllGroupsCheckEnabled(true);\r
}\r
else\r
{\r
- label.setText("Enter % identity above which to colour residues");\r
- slider.setMinimum(0);\r
- slider.setMaximum(100);\r
+ pid.setAllGroupsCheckEnabled(false);\r
}\r
\r
+ return pid.getValue();\r
+ }\r
\r
+ public static void showPIDSlider()\r
+ {\r
+ try\r
+ {\r
+ conservationSlider.setClosed(true);\r
+ conservationSlider = null;\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
- slider.addChangeListener( new ChangeListener()\r
+ if (!PIDSlider.isVisible())\r
{\r
- public void stateChanged(ChangeEvent evt)\r
+ Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,\r
+ false);\r
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ PIDSlider.addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
{\r
- valueField.setText( slider.getValue()+"" );\r
- valueChanged( slider.getValue() );\r
- }\r
- });\r
-\r
- slider.setValue(value);\r
- valueField.setText(value+"");\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent e)\r
+ {\r
+ PIDSlider = null;\r
+ }\r
+ });\r
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
}\r
\r
public void valueChanged(int i)\r
{\r
- if(cs == null)\r
+ if (cs == null)\r
+ {\r
return;\r
+ }\r
\r
ColourSchemeI toChange = null;\r
Vector allGroups = null;\r
int groupIndex = 0;\r
\r
- if(allGroupsCheck.isSelected())\r
+ if (allGroupsCheck.isSelected())\r
{\r
allGroups = ap.av.alignment.getGroups();\r
- groupIndex = allGroups.size()-1;\r
+ groupIndex = allGroups.size() - 1;\r
}\r
else\r
+ {\r
toChange = cs;\r
+ }\r
\r
-\r
- while( groupIndex > -1 )\r
+ while (groupIndex > -1)\r
{\r
- if(allGroups!=null)\r
- toChange = ((SequenceGroup)allGroups.get(groupIndex)).cs;\r
+ if (allGroups != null)\r
+ {\r
+ toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;\r
+ }\r
\r
if (forConservation)\r
{\r
if (toChange instanceof ConservationColourScheme)\r
+ {\r
( (ConservationColourScheme) toChange).inc = i;\r
+ }\r
}\r
else\r
{\r
- ( (ResidueColourScheme) toChange).setThreshold(i);\r
+ ( (ResidueColourScheme) toChange).setThreshold(i);\r
}\r
\r
groupIndex--;\r
}\r
\r
ap.seqPanel.seqCanvas.repaint();\r
-\r
}\r
\r
public void setAllGroupsCheckEnabled(boolean b)\r
allGroupsCheck.setEnabled(b);\r
}\r
\r
-\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
int i = Integer.parseInt(valueField.getText());\r
slider.setValue(i);\r
}\r
- catch(Exception ex)\r
+ catch (Exception ex)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
+ valueField.setText(slider.getValue() + "");\r
}\r
}\r
\r
{\r
slider.setValue(value);\r
}\r
+\r
public int getValue()\r
{\r
return Integer.parseInt(valueField.getText());\r
}\r
-\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import javax.swing.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
+import javax.swing.*;\r
\r
-public class SplashScreen extends JPanel implements Runnable\r
+public class SplashScreen\r
+ extends JPanel implements Runnable\r
{\r
boolean visible = true;\r
JInternalFrame iframe;\r
Image image;\r
+ int fontSize = 11;\r
+ int yoffset = 30;\r
\r
public SplashScreen(JInternalFrame iframe, Image i)\r
{\r
this.iframe = iframe;\r
image = i;\r
+\r
Thread t = new Thread(this);\r
t.start();\r
addMouseListener(new MouseAdapter()\r
- { public void mousePressed(MouseEvent evt)\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
{\r
try\r
- { closeSplash(); }\r
+ {\r
+ closeSplash();\r
+ }\r
catch (Exception ex)\r
- {}\r
+ {\r
+ }\r
}\r
- });\r
+ });\r
}\r
\r
-\r
public void run()\r
{\r
- long startTime = System.currentTimeMillis()/1000;\r
+ long startTime = System.currentTimeMillis() / 1000;\r
\r
- while( visible )\r
+ while (visible)\r
{\r
- if( System.currentTimeMillis()/1000 - startTime > 5)\r
+ if ( ( (System.currentTimeMillis() / 1000) - startTime) > 5)\r
+ {\r
visible = false;\r
+ }\r
\r
- try{\r
+ try\r
+ {\r
Thread.sleep(1000);\r
}\r
- catch(Exception ex){}\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
+\r
closeSplash();\r
}\r
\r
iframe.setClosed(true);\r
}\r
catch (Exception ex)\r
- {}\r
-\r
+ {\r
+ }\r
}\r
\r
- int fontSize = 11;\r
- int yoffset = 30;\r
public void paintComponent(Graphics g)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(),getHeight());\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
g.setColor(Color.black);\r
- g.setFont( new Font("Verdana", Font.BOLD, fontSize+6));\r
- if(image!=null)\r
- g.drawImage(image, 5,yoffset+12,this);\r
- g.drawString("JalView 2005 ", 50,yoffset);\r
- g.setFont( new Font("Verdana", Font.BOLD, fontSize+2));\r
- g.drawString("Version "+jalview.bin.Cache.VERSION+"; Last updated: "+jalview.bin.Cache.BUILD_DATE, 180,yoffset);\r
- g.setFont( new Font("Verdana", Font.BOLD, fontSize));\r
- g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",50,yoffset+20);\r
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",50,yoffset+24+fontSize);\r
- g.drawString("If you use JalView, please cite: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),",50,yoffset+28+fontSize*2);\r
- g.drawString("\"The Jalview Java Alignment Editor\" Bioinformatics, 2004 12;426-7.",50,yoffset+32+fontSize*3);\r
+ g.setFont(new Font("Verdana", Font.BOLD, fontSize + 6));\r
\r
- }\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, 5, yoffset + 12, this);\r
+ }\r
\r
+ g.drawString("JalView 2005 ", 50, yoffset);\r
+ g.setFont(new Font("Verdana", Font.BOLD, fontSize + 2));\r
+ g.drawString("Version " + jalview.bin.Cache.VERSION +\r
+ "; Last updated: " + jalview.bin.Cache.BUILD_DATE, 180,\r
+ yoffset);\r
+ g.setFont(new Font("Verdana", Font.BOLD, fontSize));\r
+ g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
+ 50, yoffset + 20);\r
+ g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
+ 50, yoffset + 24 + fontSize);\r
+ g.drawString("If you use JalView, please cite: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),",\r
+ 50, yoffset + 28 + (fontSize * 2));\r
+ g.drawString(\r
+ "\"The Jalview Java Alignment Editor\" Bioinformatics, 2004 12;426-7.",\r
+ 50, yoffset + 32 + (fontSize * 3));\r
+ }\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
+import java.util.*;\r
\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-import jalview.schemes.*;\r
-import javax.swing.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
import java.awt.print.*;\r
+import javax.swing.*;\r
\r
-public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+import jalview.util.*;\r
+\r
+public class TreeCanvas\r
+ extends JPanel implements MouseListener, Runnable,\r
+ Printable\r
{\r
+ public static final String PLACEHOLDER = " * ";\r
NJTree tree;\r
JScrollPane scrollPane;\r
AlignViewport av;\r
- public static final String PLACEHOLDER=" * ";\r
Font font;\r
- int fontSize = 12;\r
-\r
+ int fontSize = 12;\r
boolean fitToWindow = true;\r
boolean showDistances = false;\r
boolean showBootstrap = false;\r
boolean markPlaceholders = false;\r
-\r
int offx = 20;\r
int offy = 20;\r
-\r
float threshold;\r
-\r
String longestName;\r
- int labelLength=-1;\r
+ int labelLength = -1;\r
\r
//RubberbandRectangle rubberband;\r
-\r
- Vector listeners;\r
-\r
+ Vector listeners;\r
Hashtable nameHash = new Hashtable();\r
Hashtable nodeHash = new Hashtable();\r
\r
- public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, String label)\r
+ public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,\r
+ String label)\r
{\r
this.av = av;\r
- this.tree = tree;\r
+ this.tree = tree;\r
scrollPane = scroller;\r
addMouseListener(this);\r
tree.findHeight(tree.getTopNode());\r
\r
PaintRefresher.Register(this);\r
}\r
+\r
public void TreeSelectionChanged(Sequence sequence)\r
- {\r
+ {\r
SequenceGroup selected = av.getSelectionGroup();\r
- if(selected == null)\r
+\r
+ if (selected == null)\r
{\r
selected = new SequenceGroup();\r
av.setSelectionGroup(selected);\r
selected.setEndRes(av.alignment.getWidth());\r
selected.addOrRemove(sequence);\r
\r
-\r
PaintRefresher.Refresh(this);\r
repaint();\r
- }\r
-\r
-\r
+ }\r
\r
- public void setTree(NJTree tree) {\r
+ public void setTree(NJTree tree)\r
+ {\r
this.tree = tree;\r
tree.findHeight(tree.getTopNode());\r
}\r
\r
- public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {\r
- if (node == null) {\r
+ public void drawNode(Graphics g, SequenceNode node, float chunk,\r
+ float scale, int width, int offx, int offy)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if (node.left() == null && node.right() == null) {\r
+ if ( (node.left() == null) && (node.right() == null))\r
+ {\r
// Drawing leaf node\r
-\r
float height = node.height;\r
- float dist = node.dist;\r
+ float dist = node.dist;\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\r
+ int xstart = (int) ( (height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
\r
- int ypos = (int)(node.ycount * chunk) + offy;\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
\r
if (node.element() instanceof SequenceI)\r
{\r
- if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() == Color.white)\r
- {\r
- g.setColor(Color.black);\r
- }\r
- else\r
- g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().\r
- darker());\r
-\r
+ if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() ==\r
+ Color.white)\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
+ else\r
+ {\r
+ g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor()\r
+ .darker());\r
+ }\r
}\r
else\r
- g.setColor(Color.black);\r
-\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
\r
// Draw horizontal line\r
- g.drawLine(xstart,ypos,xend,ypos);\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
\r
String nodeLabel = "";\r
- if (showDistances && node.dist > 0) {\r
+\r
+ if (showDistances && (node.dist > 0))\r
+ {\r
nodeLabel = new Format("%5.2f").form(node.dist);\r
}\r
- if (showBootstrap) {\r
- if (showDistances) {\r
+\r
+ if (showBootstrap)\r
+ {\r
+ if (showDistances)\r
+ {\r
nodeLabel = nodeLabel + " : ";\r
}\r
+\r
nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
}\r
- if (! nodeLabel.equals("")) {\r
- g.drawString(nodeLabel,xstart,ypos - 10);\r
+\r
+ if (!nodeLabel.equals(""))\r
+ {\r
+ g.drawString(nodeLabel, xstart, ypos - 10);\r
}\r
\r
- String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER+node.getName()) : node.getName();\r
+ String name = (markPlaceholders && node.isPlaceholder())\r
+ ? (PLACEHOLDER + node.getName()) : node.getName();\r
FontMetrics fm = g.getFontMetrics(font);\r
- int charWidth = fm.stringWidth(name) + 3;\r
+ int charWidth = fm.stringWidth(name) + 3;\r
int charHeight = fm.getHeight();\r
\r
- Rectangle rect = new Rectangle(xend+20,ypos-charHeight,\r
- charWidth,charHeight);\r
+ Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,\r
+ charWidth, charHeight);\r
\r
- nameHash.put((SequenceI)node.element(),rect);\r
+ nameHash.put( (SequenceI) node.element(), rect);\r
\r
// Colour selected leaves differently\r
SequenceGroup selected = av.getSelectionGroup();\r
- if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {\r
+\r
+ if ( (selected != null) &&\r
+ selected.sequences.contains( (SequenceI) node.element()))\r
+ {\r
g.setColor(Color.gray);\r
\r
- g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);\r
+ g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,\r
+ charHeight);\r
g.setColor(Color.white);\r
}\r
- g.drawString(name,xend+10,ypos);\r
+\r
+ g.drawString(name, xend + 10, ypos);\r
g.setColor(Color.black);\r
- } else {\r
- drawNode(g,(SequenceNode)node.left(), chunk,scale,width,offx,offy);\r
- drawNode(g,(SequenceNode)node.right(),chunk,scale,width,offx,offy);\r
+ }\r
+ else\r
+ {\r
+ drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,\r
+ offy);\r
+ drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,\r
+ offy);\r
\r
float height = node.height;\r
- float dist = node.dist;\r
+ float dist = node.dist;\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height *scale) + offx;\r
- int ypos = (int)(node.ycount *chunk) + offy;\r
+ int xstart = (int) ( (height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
\r
- g.setColor(((SequenceNode)node).color.darker());\r
+ g.setColor( ( (SequenceNode) node).color.darker());\r
\r
// Draw horizontal line\r
- g.drawLine(xstart,ypos,xend,ypos);\r
- g.fillRect(xend-2, ypos-2, 4,4);\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
+ g.fillRect(xend - 2, ypos - 2, 4, 4);\r
\r
- int ystart = (int)(((SequenceNode)node.left()) .ycount * chunk) + offy;\r
- int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;\r
+ int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) +\r
+ offy;\r
+ int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) +\r
+ offy;\r
\r
- Rectangle pos = new Rectangle(xend-2,ypos-2,5,5);\r
- nodeHash.put(node,pos);\r
+ Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);\r
+ nodeHash.put(node, pos);\r
\r
- g.drawLine((int)(height*scale) + offx, ystart,\r
- (int)(height*scale) + offx, yend);\r
+ g.drawLine( (int) (height * scale) + offx, ystart,\r
+ (int) (height * scale) + offx, yend);\r
\r
- if (showDistances && node.dist > 0) {\r
- g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);\r
+ if (showDistances && (node.dist > 0))\r
+ {\r
+ g.drawString(new Format("%5.2f").form(node.dist), xstart,\r
+ ypos - 5);\r
}\r
-\r
}\r
}\r
- public Object findElement(int x, int y) {\r
- Enumeration keys = nameHash.keys();\r
\r
- while (keys.hasMoreElements()) {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle)nameHash.get(ob);\r
+ public Object findElement(int x, int y)\r
+ {\r
+ Enumeration keys = nameHash.keys();\r
\r
- if (x >= rect.x && x <= (rect.x + rect.width) &&\r
- y >= rect.y && y <= (rect.y + rect.height)) {\r
- return ob;\r
- }\r
- }\r
- keys = nodeHash.keys();\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nameHash.get(ob);\r
\r
- while (keys.hasMoreElements()) {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle)nodeHash.get(ob);\r
+ if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&\r
+ (y <= (rect.y + rect.height)))\r
+ {\r
+ return ob;\r
+ }\r
+ }\r
\r
- if (x >= rect.x && x <= (rect.x + rect.width) &&\r
- y >= rect.y && y <= (rect.y + rect.height)) {\r
- return ob;\r
- }\r
+ keys = nodeHash.keys();\r
+\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nodeHash.get(ob);\r
+\r
+ if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&\r
+ (y <= (rect.y + rect.height)))\r
+ {\r
+ return ob;\r
+ }\r
}\r
- return null;\r
\r
+ return null;\r
}\r
\r
- public void pickNodes(Rectangle pickBox) {\r
- int width = getWidth();\r
+ public void pickNodes(Rectangle pickBox)\r
+ {\r
+ int width = getWidth();\r
int height = getHeight();\r
\r
SequenceNode top = tree.getTopNode();\r
\r
- float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()\r
-;\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
+ float wscale = (float) ( (width * .8) - (offx * 2)) / tree.getMaxHeight();\r
+\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ( (SequenceNode) top.left()).count +\r
+ ( (SequenceNode) top.right()).count;\r
}\r
- float chunk = (float)(height-offy*2)/top.count;\r
\r
- pickNode(pickBox,top,chunk,wscale,width,offx,offy);\r
+ float chunk = (float) (height - (offy * 2)) / top.count;\r
+\r
+ pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
}\r
\r
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {\r
- if (node == null) {\r
+ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,\r
+ float scale, int width, int offx, int offy)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if (node.left() == null && node.right() == null) {\r
+ if ( (node.left() == null) && (node.right() == null))\r
+ {\r
float height = node.height;\r
- float dist = node.dist;\r
+ float dist = node.dist;\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\r
+ int xstart = (int) ( (height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
\r
- int ypos = (int)(node.ycount * chunk) + offy;\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
\r
- if (pickBox.contains(new Point(xend,ypos))) {\r
- if (node.element() instanceof SequenceI) {\r
- SequenceI seq = (SequenceI)node.element();\r
+ if (pickBox.contains(new Point(xend, ypos)))\r
+ {\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ SequenceI seq = (SequenceI) node.element();\r
SequenceGroup sg = av.getSelectionGroup();\r
- if(sg!=null)\r
+\r
+ if (sg != null)\r
+ {\r
sg.addOrRemove(seq);\r
+ }\r
}\r
}\r
- } else {\r
- pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);\r
- pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);\r
+ }\r
+ else\r
+ {\r
+ pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,\r
+ offx, offy);\r
+ pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,\r
+ offx, offy);\r
}\r
}\r
\r
public void setColor(SequenceNode node, Color c)\r
{\r
if (node == null)\r
+ {\r
return;\r
+ }\r
\r
- if (node.left() == null && node.right() == null)\r
+ if ( (node.left() == null) && (node.right() == null))\r
{\r
node.color = c;\r
\r
if (node.element() instanceof SequenceI)\r
- ((SequenceI)node.element()).setColor(c);\r
- } else\r
+ {\r
+ ( (SequenceI) node.element()).setColor(c);\r
+ }\r
+ }\r
+ else\r
{\r
node.color = c;\r
- setColor((SequenceNode)node.left(),c);\r
- setColor((SequenceNode)node.right(),c);\r
+ setColor( (SequenceNode) node.left(), c);\r
+ setColor( (SequenceNode) node.right(), c);\r
}\r
}\r
\r
PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
\r
printJob.setPrintable(this, pf);\r
+\r
if (printJob.printDialog())\r
{\r
try\r
}\r
}\r
\r
-\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
+ public int print(Graphics pg, PageFormat pf, int pi)\r
+ throws PrinterException\r
{\r
-\r
pg.setFont(font);\r
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
+ pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());\r
+\r
int pwidth = (int) pf.getImageableWidth();\r
int pheight = (int) pf.getImageableHeight();\r
\r
int noPages = getHeight() / pheight;\r
- if(pi>noPages)\r
- return Printable.NO_SUCH_PAGE;\r
\r
+ if (pi > noPages)\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
\r
if (pwidth > getWidth())\r
- pwidth = getWidth();\r
+ {\r
+ pwidth = getWidth();\r
+ }\r
\r
- if(fitToWindow)\r
+ if (fitToWindow)\r
{\r
if (pheight > getHeight())\r
+ {\r
pheight = getHeight();\r
+ }\r
\r
noPages = 0;\r
}\r
else\r
{\r
-\r
- FontMetrics fm = pg.getFontMetrics(font);\r
- int height = fm.getHeight() * nameHash.size();\r
- pg.translate(0, -pi*pheight );\r
- pg.setClip(0,pi*pheight, pwidth,pi*pheight + pheight);\r
- // translate number of pages,\r
- // height is screen size as this is the\r
- // non overlapping text size\r
- pheight = height;\r
+ FontMetrics fm = pg.getFontMetrics(font);\r
+ int height = fm.getHeight() * nameHash.size();\r
+ pg.translate(0, -pi * pheight);\r
+ pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);\r
+\r
+ // translate number of pages,\r
+ // height is screen size as this is the\r
+ // non overlapping text size\r
+ pheight = height;\r
}\r
\r
draw(pg, pwidth, pheight);\r
\r
return Printable.PAGE_EXISTS;\r
-\r
}\r
\r
public void paintComponent(Graphics g)\r
{\r
-\r
- font = new Font("Verdana",Font.PLAIN,fontSize);\r
+ font = new Font("Verdana", Font.PLAIN, fontSize);\r
g.setFont(font);\r
\r
FontMetrics fm = g.getFontMetrics(font);\r
\r
- if(nameHash.size()==0)\r
+ if (nameHash.size() == 0)\r
+ {\r
repaint();\r
+ }\r
\r
-\r
- if( fitToWindow || (!fitToWindow && scrollPane.getHeight() > fm.getHeight() * nameHash.size()+offy ) )\r
- {\r
- draw(g,scrollPane.getWidth(),scrollPane.getHeight());\r
- setPreferredSize(null);\r
- }\r
+ if (fitToWindow ||\r
+ (!fitToWindow &&\r
+ (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +\r
+ offy))))\r
+ {\r
+ draw(g, scrollPane.getWidth(), scrollPane.getHeight());\r
+ setPreferredSize(null);\r
+ }\r
else\r
- {\r
- setPreferredSize(new Dimension(scrollPane.getWidth(), fm.getHeight() * nameHash.size()));\r
- draw( g,scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
- }\r
+ {\r
+ setPreferredSize(new Dimension(scrollPane.getWidth(),\r
+ fm.getHeight() * nameHash.size()));\r
+ draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
+ }\r
\r
scrollPane.revalidate();\r
}\r
- public int getFontSize() {\r
- return fontSize;\r
- }\r
- public void setFontSize(int fontSize) {\r
- this.fontSize = fontSize;\r
- repaint();\r
- }\r
- public void draw(Graphics g1, int width, int height) {\r
\r
- Graphics2D g2 = (Graphics2D)g1;\r
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);\r
- g2.setColor(Color.white);\r
- g2.fillRect(0,0,width,height);\r
+ public int getFontSize()\r
+ {\r
+ return fontSize;\r
+ }\r
\r
+ public void setFontSize(int fontSize)\r
+ {\r
+ this.fontSize = fontSize;\r
+ repaint();\r
+ }\r
\r
- labelLength = g2.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar\r
+ public void draw(Graphics g1, int width, int height)\r
+ {\r
+ Graphics2D g2 = (Graphics2D) g1;\r
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ g2.setColor(Color.white);\r
+ g2.fillRect(0, 0, width, height);\r
\r
- float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();\r
+ labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar\r
\r
- SequenceNode top = tree.getTopNode();\r
+ float wscale = (float) (width - labelLength - (offx * 2)) /\r
+ tree.getMaxHeight();\r
\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
- }\r
- float chunk = (float)(height-offy*2)/top.count ;\r
+ SequenceNode top = tree.getTopNode();\r
\r
- drawNode(g2,tree.getTopNode(),chunk,wscale,width,offx,offy);\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ( (SequenceNode) top.left()).count +\r
+ ( (SequenceNode) top.right()).count;\r
+ }\r
\r
- if (threshold != 0)\r
- {\r
- if(av.getCurrentTree() == tree)\r
- g2.setColor(Color.red);\r
- else\r
- g2.setColor(Color.gray);\r
+ float chunk = (float) (height - (offy * 2)) / top.count;\r
\r
- int x = (int)( threshold * (float)(getWidth()-labelLength - 2*offx) +offx ) ;\r
+ drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
\r
- g2.drawLine(x,0,x,getHeight());\r
+ if (threshold != 0)\r
+ {\r
+ if (av.getCurrentTree() == tree)\r
+ {\r
+ g2.setColor(Color.red);\r
}\r
-\r
- }\r
-\r
- public void mouseReleased(MouseEvent e) { }\r
- public void mouseEntered(MouseEvent e) { }\r
- public void mouseExited(MouseEvent e) { }\r
- public void mouseClicked(MouseEvent e) {\r
- }\r
-\r
- public void mousePressed(MouseEvent e) {\r
-\r
- av.setCurrentTree(tree);\r
-\r
- int x = e.getX();\r
- int y = e.getY();\r
-\r
- Object ob = findElement(x,y);\r
-\r
- if (ob instanceof SequenceI)\r
+ else\r
{\r
- TreeSelectionChanged((Sequence)ob);\r
- repaint();\r
- return;\r
-\r
- } else if (ob instanceof SequenceNode) {\r
- SequenceNode tmpnode = (SequenceNode)ob;\r
- tree.swapNodes(tmpnode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- } else {\r
- // Find threshold\r
+ g2.setColor(Color.gray);\r
+ }\r
\r
- if (tree.getMaxHeight() != 0) {\r
- threshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);\r
+ int x = (int) ( (threshold * (float) (getWidth() - labelLength -\r
+ (2 * offx))) + offx);\r
\r
- tree.getGroups().removeAllElements();\r
- tree.groupNodes(tree.getTopNode(),threshold);\r
- setColor(tree.getTopNode(),Color.black);\r
+ g2.drawLine(x, 0, x, getHeight());\r
+ }\r
+ }\r
\r
- av.setSelectionGroup(null);\r
- av.alignment.deleteAllGroups();\r
+ public void mouseReleased(MouseEvent e)\r
+ {\r
+ }\r
\r
- for (int i=0; i < tree.getGroups().size(); i++)\r
- {\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ }\r
\r
- Color col = new Color((int)(Math.random()*255),\r
- (int)(Math.random()*255),\r
- (int)(Math.random()*255));\r
- setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());\r
+ public void mouseExited(MouseEvent e)\r
+ {\r
+ }\r
\r
- Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());\r
- SequenceGroup sg = null;\r
- for (int j = 0; j < l.size(); j++)\r
- {\r
- SequenceNode sn = (SequenceNode) l.elementAt(j);\r
- if(sg==null)\r
- sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());\r
+ public void mouseClicked(MouseEvent e)\r
+ {\r
+ }\r
\r
- sg.addSequence( (Sequence) sn.element());\r
- }\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
+ av.setCurrentTree(tree);\r
\r
- if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, sg.getStartRes(),\r
- sg.getEndRes());\r
+ int x = e.getX();\r
+ int y = e.getY();\r
\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
+ Object ob = findElement(x, y);\r
\r
- sg.cs = ccs;\r
+ if (ob instanceof SequenceI)\r
+ {\r
+ TreeSelectionChanged( (Sequence) ob);\r
+ repaint();\r
\r
- }\r
+ return;\r
+ }\r
+ else if (ob instanceof SequenceNode)\r
+ {\r
+ SequenceNode tmpnode = (SequenceNode) ob;\r
+ tree.swapNodes(tmpnode);\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+ }\r
+ else\r
+ {\r
+ // Find threshold\r
+ if (tree.getMaxHeight() != 0)\r
+ {\r
+ threshold = (float) (x - offx) / (float) (getWidth() -\r
+ labelLength - (2 * offx));\r
+\r
+ tree.getGroups().removeAllElements();\r
+ tree.groupNodes(tree.getTopNode(), threshold);\r
+ setColor(tree.getTopNode(), Color.black);\r
+\r
+ av.setSelectionGroup(null);\r
+ av.alignment.deleteAllGroups();\r
+\r
+ for (int i = 0; i < tree.getGroups().size(); i++)\r
+ {\r
+ Color col = new Color( (int) (Math.random() * 255),\r
+ (int) (Math.random() * 255),\r
+ (int) (Math.random() * 255));\r
+ setColor( (SequenceNode) tree.getGroups().elementAt(i),\r
+ col.brighter());\r
+\r
+ Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()\r
+ .elementAt(i),\r
+ new Vector());\r
+ SequenceGroup sg = null;\r
+\r
+ for (int j = 0; j < l.size(); j++)\r
+ {\r
+ SequenceNode sn = (SequenceNode) l.elementAt(j);\r
+\r
+ if (sg == null)\r
+ {\r
+ sg = new SequenceGroup("TreeGroup",\r
+ av.getGlobalColourScheme(), true, true,\r
+ false, 0, av.alignment.getWidth());\r
+ }\r
\r
+ sg.addSequence( (Sequence) sn.element());\r
+ }\r
\r
+ if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) av.\r
+ getGlobalColourScheme();\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences,\r
+ sg.getStartRes(), sg.getEndRes());\r
\r
- av.alignment.addGroup(sg);\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
\r
- }\r
+ sg.cs = ccs;\r
}\r
- }\r
\r
- PaintRefresher.Refresh(this);\r
- repaint();\r
+ av.alignment.addGroup(sg);\r
+ }\r
+ }\r
+ }\r
\r
+ PaintRefresher.Refresh(this);\r
+ repaint();\r
}\r
\r
- public void setShowDistances(boolean state) {\r
- this.showDistances = state;\r
- repaint();\r
- }\r
+ public void setShowDistances(boolean state)\r
+ {\r
+ this.showDistances = state;\r
+ repaint();\r
+ }\r
\r
- public void setShowBootstrap(boolean state) {\r
- this.showBootstrap = state;\r
- repaint();\r
- }\r
- public void setMarkPlaceholders(boolean state) {\r
- this.markPlaceholders = state;\r
- repaint();\r
- }\r
+ public void setShowBootstrap(boolean state)\r
+ {\r
+ this.showBootstrap = state;\r
+ repaint();\r
+ }\r
\r
+ public void setMarkPlaceholders(boolean state)\r
+ {\r
+ this.markPlaceholders = state;\r
+ repaint();\r
+ }\r
}\r
-\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.jbgui.GTreePanel;\r
-import jalview.io.*;\r
-import java.awt.event.*;\r
-import java.util.*;\r
import java.io.*;\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.image.*;\r
-import org.jibble.epsgraphics.*;\r
+import java.util.*;\r
import javax.imageio.*;\r
\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import java.awt.image.*;\r
+import javax.swing.*;\r
\r
+import org.jibble.epsgraphics.*;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
\r
-public class TreePanel extends GTreePanel\r
+public class TreePanel\r
+ extends GTreePanel\r
{\r
SequenceI[] seq;\r
String type;\r
TreeCanvas treeCanvas;\r
NJTree tree;\r
\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
- public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
+ public TreePanel(AlignViewport av, Vector seqVector, String type,\r
+ String pwtype, int s, int e)\r
{\r
super();\r
\r
end = e;\r
\r
String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ seq = new Sequence[seqVector.size()];\r
+\r
+ for (int i = 0; i < seqVector.size(); i++)\r
{\r
seq[i] = (Sequence) seqVector.elementAt(i);\r
- if(seq[i].getName().length()>longestName.length())\r
+\r
+ if (seq[i].getName().length() > longestName.length())\r
+ {\r
longestName = seq[i].getName();\r
+ }\r
}\r
\r
tree = new NJTree(seq, type, pwtype, start, end);\r
tree.reCount(tree.getTopNode());\r
tree.findHeight(tree.getTopNode());\r
scrollPane.setViewportView(treeCanvas);\r
-\r
}\r
- private void setViewStateFromTreeCanvas(TreeCanvas tree) {\r
- // update view menu state from treeCanvas render state\r
- distanceMenu.setSelected(tree.showDistances);\r
- bootstrapMenu.setSelected(tree.showBootstrap);\r
- placeholdersMenu.setSelected(tree.markPlaceholders);\r
- }\r
-\r
- private void setTreeCanvasFromViewState(TreeCanvas tree) {\r
- // update view menu state from treeCanvas render state\r
- tree.showDistances = distanceMenu.isSelected();\r
- tree.showBootstrap = bootstrapMenu.isSelected();\r
- tree.markPlaceholders = placeholdersMenu.isSelected();\r
- }\r
-\r
\r
public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
String type, String pwtype)\r
+ {\r
+ super();\r
+\r
+ // These are probably only arbitrary strings reflecting source of tree\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
+\r
+ start = 0;\r
+ end = seqVector.size();\r
+\r
+ String longestName = "";\r
+ seq = new Sequence[seqVector.size()];\r
+\r
+ for (int i = 0; i < seqVector.size(); i++)\r
{\r
- super();\r
- // These are probably only arbitrary strings reflecting source of tree\r
- this.type = type;\r
- this.pwtype = pwtype;\r
+ seq[i] = (Sequence) seqVector.elementAt(i);\r
+ }\r
+\r
+ // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
+ tree = new NJTree(seq, newtree);\r
+\r
+ // Now have to calculate longest name based on the leaves\r
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
+ boolean has_placeholders = false;\r
\r
- start = 0;\r
- end = seqVector.size();\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ if (lf.isPlaceholder())\r
{\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
+ has_placeholders = true;\r
}\r
- // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
- tree = new NJTree(seq, newtree);\r
- // Now have to calculate longest name based on the leaves\r
- Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());\r
- boolean has_placeholders = false;\r
- for (int i=0;i < leaves.size();i++) {\r
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
- if (lf.isPlaceholder())\r
- has_placeholders = true;\r
- if (longestName.length()<((Sequence) lf.element()).getName().length())\r
- longestName = TreeCanvas.PLACEHOLDER+((Sequence) lf.element()).getName();\r
+\r
+ if (longestName.length() < ( (Sequence) lf.element()).getName()\r
+ .length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) lf.element()).getName();\r
}\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
-\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- scrollPane.setViewportView(treeCanvas);\r
- treeCanvas.setMarkPlaceholders(has_placeholders);\r
- setViewStateFromTreeCanvas(treeCanvas);\r
- // JBPNote TODO: preference for always marking placeholders in new associated tree\r
}\r
\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
\r
- public void textbox_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+ treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
+ treeCanvas.setShowDistances(newtree.HasDistances());\r
+ scrollPane.setViewportView(treeCanvas);\r
+ treeCanvas.setMarkPlaceholders(has_placeholders);\r
+ setViewStateFromTreeCanvas(treeCanvas);\r
+\r
+ // JBPNote TODO: preference for always marking placeholders in new associated tree\r
+ }\r
\r
- StringBuffer buffer = new StringBuffer();\r
+ public NJTree getTree()\r
+ {\r
+ return tree;\r
+ }\r
\r
- if(type.equals("AV"))\r
- buffer.append("Average distance tree using ");\r
- else\r
- buffer.append("Neighbour joining tree using ");\r
+ private void setViewStateFromTreeCanvas(TreeCanvas tree)\r
+ {\r
+ // update view menu state from treeCanvas render state\r
+ distanceMenu.setSelected(tree.showDistances);\r
+ bootstrapMenu.setSelected(tree.showBootstrap);\r
+ placeholdersMenu.setSelected(tree.markPlaceholders);\r
+ }\r
\r
- if(pwtype.equals("BL"))\r
- buffer.append("BLOSUM62");\r
- else\r
- buffer.append("PID");\r
+ private void setTreeCanvasFromViewState(TreeCanvas tree)\r
+ {\r
+ // update view menu state from treeCanvas render state\r
+ tree.showDistances = distanceMenu.isSelected();\r
+ tree.showBootstrap = bootstrapMenu.isSelected();\r
+ tree.markPlaceholders = placeholdersMenu.isSelected();\r
+ }\r
\r
- Desktop.addInternalFrame(cap,buffer.toString(), 500, 100);\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- cap.setText( fout.print(false,true) );\r
+ public void textbox_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
\r
- }\r
+ StringBuffer buffer = new StringBuffer();\r
\r
+ if (type.equals("AV"))\r
+ {\r
+ buffer.append("Average distance tree using ");\r
+ }\r
+ else\r
+ {\r
+ buffer.append("Neighbour joining tree using ");\r
+ }\r
\r
- public void saveAsNewick_actionPerformed(ActionEvent e)\r
+ if (pwtype.equals("BL"))\r
+ {\r
+ buffer.append("BLOSUM62");\r
+ }\r
+ else\r
{\r
+ buffer.append("PID");\r
+ }\r
\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty("LAST_DIRECTORY"));\r
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
+\r
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
+ cap.setText(fout.print(false, true));\r
+ }\r
+\r
+ public void saveAsNewick_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"));\r
chooser.setFileView(new JalviewFileView());\r
chooser.setDialogTitle("Save tree as newick file");\r
chooser.setToolTipText("Save");\r
+\r
int value = chooser.showSaveDialog(null);\r
- if (value == JalviewFileChooser.APPROVE_OPTION) {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- try{\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ try\r
+ {\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- String output = fout.print(false,true); // distances only\r
- java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );\r
+ String output = fout.print(false, true); // distances only\r
+ java.io.PrintWriter out = new java.io.PrintWriter(new java.io.\r
+ FileWriter(\r
+ choice));\r
out.println(output);\r
out.close();\r
}\r
- catch (Exception ex) {\r
+ catch (Exception ex)\r
+ {\r
ex.printStackTrace();\r
}\r
}\r
\r
protected void printMenu_actionPerformed(ActionEvent e)\r
{\r
-\r
//Putting in a thread avoids Swing painting problems\r
treeCanvas.startPrinting();\r
}\r
repaint();\r
}\r
\r
-\r
protected void fontSize_actionPerformed(ActionEvent e)\r
{\r
- if( treeCanvas==null )\r
- return;\r
-\r
- String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);\r
-\r
- Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Select font size",\r
- "Font size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
- ,"Font Size - "+size);\r
- if(selection!=null)\r
- {\r
- fontSize.setText("Font Size - " + selection);\r
-\r
- int i = Integer.parseInt(selection.toString());\r
- treeCanvas.setFontSize(i);\r
- }\r
- scrollPane.setViewportView(treeCanvas);\r
+ if (treeCanvas == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +\r
+ 1);\r
+\r
+ Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ new String[]\r
+ {\r
+ "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"\r
+ }, "Font Size - " + size);\r
\r
+ if (selection != null)\r
+ {\r
+ fontSize.setText("Font Size - " + selection);\r
+\r
+ int i = Integer.parseInt(selection.toString());\r
+ treeCanvas.setFontSize(i);\r
+ }\r
+\r
+ scrollPane.setViewportView(treeCanvas);\r
}\r
\r
protected void distanceMenu_actionPerformed(ActionEvent e)\r
}\r
\r
protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
+ {\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
}\r
\r
protected void epsTree_actionPerformed(ActionEvent e)\r
{\r
- int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();\r
+ int width = treeCanvas.getWidth();\r
+ int height = treeCanvas.getHeight();\r
+\r
try\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]{"eps"},\r
- new String[]{"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"eps"},\r
+ new String[]\r
+ {"Encapsulated Postscript"},\r
+ "Encapsulated Postscript");\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
chooser.setDialogTitle("Create EPS file from tree");\r
chooser.setToolTipText("Save");\r
\r
int value = chooser.showSaveDialog(this);\r
+\r
if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
return;\r
+ }\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
+ height);\r
\r
treeCanvas.draw(pg, width, height);\r
\r
- pg.flush();\r
- pg.close();\r
+ pg.flush();\r
+ pg.close();\r
}\r
catch (Exception ex)\r
{\r
}\r
\r
protected void pngTree_actionPerformed(ActionEvent e)\r
- {\r
- int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();\r
+ {\r
+ int width = treeCanvas.getWidth();\r
+ int height = treeCanvas.getHeight();\r
+\r
try\r
{\r
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[] {"png"},\r
- new String[] {"Portable network graphics"},\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"png"},\r
+ new String[]\r
+ {"Portable network graphics"},\r
"Portable network graphics");\r
\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
chooser.setToolTipText("Save");\r
\r
int value = chooser.showSaveDialog(this);\r
+\r
if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
return;\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
\r
- BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
+ BufferedImage bi = new BufferedImage(width, height,\r
+ BufferedImage.TYPE_INT_RGB);\r
Graphics png = bi.getGraphics();\r
\r
treeCanvas.draw(png, width, height);\r
\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
}\r
catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
}\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.GUserDefinedColours;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import javax.swing.*;\r
+import java.io.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
+import javax.swing.*;\r
import javax.swing.event.*;\r
-import jalview.schemes.*;\r
-import java.io.*;\r
-import java.util.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
\r
-public class UserDefinedColours extends GUserDefinedColours implements ChangeListener\r
+public class UserDefinedColours\r
+ extends GUserDefinedColours implements ChangeListener\r
{\r
-\r
AlignmentPanel ap;\r
SequenceGroup seqGroup;\r
JButton selectedButton;\r
ColourSchemeI oldColourScheme;\r
JInternalFrame frame;\r
\r
-\r
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
{\r
super();\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "User Defined Colours", 450,530, false );\r
- if(System.getProperty("os.name").startsWith("Mac"))\r
- frame.setSize(450,560);\r
+ Desktop.addInternalFrame(frame, "User Defined Colours", 450, 530, false);\r
\r
- if(sg!=null)\r
- frame.setTitle( frame.getTitle()+ " ("+sg.getName()+")");\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ {\r
+ frame.setSize(450, 560);\r
+ }\r
+\r
+ if (sg != null)\r
+ {\r
+ frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");\r
+ }\r
\r
colorChooser.getSelectionModel().addChangeListener(this);\r
\r
this.ap = ap;\r
seqGroup = sg;\r
\r
+ if (seqGroup != null)\r
+ {\r
+ oldColourScheme = seqGroup.cs;\r
+ }\r
+ else\r
+ {\r
+ oldColourScheme = ap.av.getGlobalColourScheme();\r
+ }\r
\r
- if (seqGroup != null)\r
- oldColourScheme = seqGroup.cs;\r
- else\r
- oldColourScheme = ap.av.getGlobalColourScheme();\r
-\r
- for (int i = 0; i < 20; i++)\r
- makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
- "", ResidueProperties.aa[i]);\r
+ for (int i = 0; i < 20; i++)\r
+ {\r
+ makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
+ "", ResidueProperties.aa[i]);\r
+ }\r
\r
- makeButton("B", "B");\r
- makeButton("Z", "Z");\r
- makeButton("X", "X");\r
- makeButton("Gap", "'.','-',' '");\r
+ makeButton("B", "B");\r
+ makeButton("Z", "Z");\r
+ makeButton("X", "X");\r
+ makeButton("Gap", "'.','-',' '");\r
\r
- if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)\r
- {\r
- loadColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));\r
- }\r
+ if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)\r
+ {\r
+ loadColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));\r
+ }\r
}\r
\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- if(selectedButton!=null)\r
- selectedButton.setBackground( colorChooser.getColor() );\r
- }\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ if (selectedButton != null)\r
+ {\r
+ selectedButton.setBackground(colorChooser.getColor());\r
+ }\r
+ }\r
\r
public void colourButtonPressed(MouseEvent e)\r
{\r
- selectedButton = (JButton)e.getSource();\r
- colorChooser.setColor(selectedButton.getBackground());\r
+ selectedButton = (JButton) e.getSource();\r
+ colorChooser.setColor(selectedButton.getBackground());\r
}\r
\r
void makeButton(String label, String aa)\r
final JButton button = new JButton();\r
Color col = Color.white;\r
\r
-\r
- try{\r
+ try\r
+ {\r
col = oldColourScheme.findColour(aa, -1);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
- button.setBackground( col );\r
- oldColours.addElement( col );\r
- button.setText( label );\r
- button.setForeground( col.darker().darker().darker() );\r
+ button.setBackground(col);\r
+ oldColours.addElement(col);\r
+ button.setText(label);\r
+ button.setForeground(col.darker().darker().darker());\r
button.setFont(new java.awt.Font("Verdana", 1, 10));\r
button.addMouseListener(new java.awt.event.MouseAdapter()\r
{\r
buttonPanel.add(button, null);\r
}\r
\r
-\r
protected void okButton_actionPerformed(ActionEvent e)\r
{\r
applyButton_actionPerformed(null);\r
- try{\r
+\r
+ try\r
+ {\r
frame.setClosed(true);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
\r
protected void applyButton_actionPerformed(ActionEvent e)\r
{\r
- Color [] newColours = new Color[24];\r
- for(int i=0; i<24; i++)\r
+ Color[] newColours = new Color[24];\r
+\r
+ for (int i = 0; i < 24; i++)\r
{\r
- JButton button = (JButton)buttonPanel.getComponent(i);\r
- newColours[i] = button.getBackground();\r
+ JButton button = (JButton) buttonPanel.getComponent(i);\r
+ newColours[i] = button.getBackground();\r
}\r
\r
UserColourScheme ucs = new UserColourScheme(newColours);\r
ucs.setThreshold(0);\r
\r
- if(seqGroup!=null)\r
+ if (seqGroup != null)\r
{\r
seqGroup.cs = ucs;\r
ap.repaint();\r
}\r
else\r
+ {\r
ap.alignFrame.changeColour(ucs);\r
-\r
+ }\r
}\r
\r
protected void loadbutton_actionPerformed(ActionEvent e)\r
{\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"jc"},\r
- new String[]{"Jalview User Colours"},\r
- "Jalview User Colours");\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"jc"},\r
+ new String[]\r
+ {"Jalview User Colours"}, "Jalview User Colours");\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
chooser.setDialogTitle("Load colour scheme");\r
chooser.setToolTipText("Load");\r
+\r
int value = chooser.showOpenDialog(this);\r
+\r
if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
File choice = chooser.getSelectedFile();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice.getPath());\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR",\r
+ choice.getPath());\r
+\r
Color[] colors = loadColours(choice.getAbsolutePath());\r
+\r
for (int i = 0; i < colors.length; i++)\r
{\r
JButton button = (JButton) buttonPanel.getComponent(i);\r
button.setBackground(colors[i]);\r
}\r
-\r
}\r
}\r
\r
public static UserColourScheme loadDefaultColours()\r
{\r
- if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)\r
- return loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));\r
+ if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)\r
+ {\r
+ return loadDefaultColours(jalview.bin.Cache.getProperty(\r
+ "USER_DEFINED_COLOUR"));\r
+ }\r
else\r
+ {\r
return null;\r
+ }\r
}\r
\r
public static UserColourScheme loadDefaultColours(String file)\r
{\r
- UserColourScheme ucs = null;\r
- Color cols[] = loadColours(file);\r
- if(cols!=null)\r
- {\r
- ucs = new UserColourScheme(cols);\r
- ucs.setThreshold(0);\r
- }\r
- return ucs;\r
+ UserColourScheme ucs = null;\r
+ Color[] cols = loadColours(file);\r
+\r
+ if (cols != null)\r
+ {\r
+ ucs = new UserColourScheme(cols);\r
+ ucs.setThreshold(0);\r
+ }\r
+\r
+ return ucs;\r
}\r
\r
- static Color [] loadColours(String file)\r
+ static Color[] loadColours(String file)\r
{\r
- Color [] newColours=null;\r
+ Color[] newColours = null;\r
+\r
try\r
{\r
- InputStreamReader in = new InputStreamReader(\r
- new FileInputStream(file), "UTF-8");\r
+ InputStreamReader in = new InputStreamReader(new FileInputStream(\r
+ file), "UTF-8");\r
\r
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
- ucs = (jalview.binding.JalviewUserColours)ucs.unmarshal(in);\r
+ jalview.binding.JalviewUserColours ucs = new jalview.binding.\r
+ JalviewUserColours();\r
+ ucs = (jalview.binding.JalviewUserColours) ucs.unmarshal(in);\r
\r
newColours = new Color[ucs.getColourCount()];\r
- for (int i = 0; i < 24; i++)\r
- newColours[i] = new Color(Integer.parseInt(ucs.getColour(i).getRGB(), 16));\r
\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ newColours[i] = new Color(Integer.parseInt(\r
+ ucs.getColour(i).getRGB(), 16));\r
+ }\r
}\r
catch (Exception ex)\r
- {System.out.println("Error loading UserColourFile "+file);}\r
+ {\r
+ System.out.println("Error loading UserColourFile " + file);\r
+ }\r
\r
return newColours;\r
}\r
\r
protected void savebutton_actionPerformed(ActionEvent e)\r
{\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"jc"},\r
- new String[]{"Jalview User Colours"},\r
- "Jalview User Colours");\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"jc"},\r
+ new String[]\r
+ {"Jalview User Colours"}, "Jalview User Colours");\r
\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
chooser.setDialogTitle("Save colour scheme");\r
chooser.setToolTipText("Save");\r
+\r
int value = chooser.showSaveDialog(this);\r
+\r
if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
String choice = chooser.getSelectedFile().getPath();\r
jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);\r
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
\r
- try{\r
+ jalview.binding.JalviewUserColours ucs = new jalview.binding.\r
+ JalviewUserColours();\r
+\r
+ try\r
+ {\r
PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
- new FileOutputStream(choice), "UTF-8"));\r
- for(int i=0; i<24; i++)\r
+ new FileOutputStream(choice), "UTF-8"));\r
+\r
+ for (int i = 0; i < 24; i++)\r
{\r
- JButton button = (JButton)buttonPanel.getComponent(i);\r
- jalview.binding.Colour col = new jalview.binding.Colour();\r
- col.setName(button.getText());\r
- col.setRGB( jalview.util.Format.getHexString( button.getBackground() ));\r
- ucs.addColour(col);\r
+ JButton button = (JButton) buttonPanel.getComponent(i);\r
+ jalview.binding.Colour col = new jalview.binding.Colour();\r
+ col.setName(button.getText());\r
+ col.setRGB(jalview.util.Format.getHexString(\r
+ button.getBackground()));\r
+ ucs.addColour(col);\r
}\r
\r
ucs.marshal(out);\r
out.close();\r
}\r
- catch(Exception ex)\r
- {ex.printStackTrace();}\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
-\r
}\r
\r
protected void cancelButton_actionPerformed(ActionEvent e)\r
{\r
+ Color[] newColours = new Color[24];\r
\r
- Color [] newColours = new Color[24];\r
- for(int i=0; i<24; i++)\r
+ for (int i = 0; i < 24; i++)\r
{\r
- newColours[i] = (Color)oldColours.elementAt(i);\r
- buttonPanel.getComponent(i).setBackground(newColours[i]);\r
+ newColours[i] = (Color) oldColours.elementAt(i);\r
+ buttonPanel.getComponent(i).setBackground(newColours[i]);\r
}\r
\r
- UserColourScheme ucs = new UserColourScheme( newColours );\r
+ UserColourScheme ucs = new UserColourScheme(newColours);\r
\r
if (seqGroup != null)\r
+ {\r
seqGroup.cs = ucs;\r
+ }\r
else\r
+ {\r
ap.av.setGlobalColourScheme(ucs);\r
+ }\r
\r
ap.repaint();\r
\r
- try{\r
+ try\r
+ {\r
frame.setClosed(true);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
-\r
-\r
}\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
-import jalview.jbgui.GWebserviceInfo;\r
\r
-public class WebserviceInfo extends GWebserviceInfo\r
-{\r
+import jalview.jbgui.*;\r
\r
+public class WebserviceInfo\r
+ extends GWebserviceInfo\r
+{\r
public static final int STATE_QUEUING = 0;\r
public static final int STATE_RUNNING = 1;\r
public static final int STATE_STOPPED_OK = 2;\r
int currentStatus = STATE_QUEUING;\r
Image image;\r
int angle = 0;\r
-\r
- String title="";\r
+ String title = "";\r
jalview.ws.WSClientI thisService;\r
boolean serviceIsCancellable;\r
- public jalview.ws.WSClientI getthisService() {\r
- return thisService;\r
- }\r
- public void setthisService(jalview.ws.WSClientI newservice) {\r
- thisService = newservice;\r
- serviceIsCancellable = newservice.isCancellable();\r
- }\r
\r
public WebserviceInfo(String title, String info)\r
{\r
init(title, info, width, height);\r
}\r
\r
+ public jalview.ws.WSClientI getthisService()\r
+ {\r
+ return thisService;\r
+ }\r
+\r
+ public void setthisService(jalview.ws.WSClientI newservice)\r
+ {\r
+ thisService = newservice;\r
+ serviceIsCancellable = newservice.isCancellable();\r
+ }\r
+\r
void init(String title, String info, int width, int height)\r
{\r
JInternalFrame frame = new JInternalFrame();\r
\r
this.title = title;\r
setInfoText(info);\r
+\r
java.net.URL url = getClass().getResource("/images/logo.gif");\r
image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+\r
MediaTracker mt = new MediaTracker(this);\r
mt.addImage(image, 0);\r
+\r
try\r
{\r
mt.waitForID(0);\r
}\r
catch (Exception ex)\r
- {}\r
-\r
+ {\r
+ }\r
\r
AnimatedPanel ap = new AnimatedPanel();\r
titlePanel.add(ap, BorderLayout.CENTER);\r
+\r
Thread thread = new Thread(ap);\r
thread.start();\r
}\r
}\r
\r
public String getInfoText()\r
- { return infoText.getText(); }\r
+ {\r
+ return infoText.getText();\r
+ }\r
\r
public void setInfoText(String text)\r
- { infoText.setText(text); }\r
+ {\r
+ infoText.setText(text);\r
+ }\r
\r
public void appendInfoText(String text)\r
- { infoText.append(text); }\r
+ {\r
+ infoText.append(text);\r
+ }\r
\r
public String getProgressText()\r
- { return progressText.getText(); }\r
+ {\r
+ return progressText.getText();\r
+ }\r
\r
public void setProgressText(String text)\r
- { progressText.setText(text); }\r
+ {\r
+ progressText.setText(text);\r
+ }\r
\r
public void appendProgressText(String text)\r
- { progressText.append(text); }\r
+ {\r
+ progressText.append(text);\r
+ }\r
\r
protected void cancel_actionPerformed(ActionEvent e)\r
{\r
if (!serviceIsCancellable)\r
+ {\r
JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "This job cannot be cancelled." ,\r
- "Cancel job"\r
- ,JOptionPane.WARNING_MESSAGE);\r
+ "This job cannot be cancelled.",\r
+ "Cancel job",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
else\r
+ {\r
thisService.cancelJob();\r
+ }\r
}\r
\r
-\r
- class AnimatedPanel extends JPanel implements Runnable\r
+ class AnimatedPanel\r
+ extends JPanel implements Runnable\r
{\r
- long startTime=0;\r
+ long startTime = 0;\r
+\r
public void run()\r
{\r
startTime = System.currentTimeMillis();\r
- while(currentStatus<STATE_STOPPED_OK)\r
- try\r
- {\r
- Thread.sleep(50);\r
\r
- int units = (int)((System.currentTimeMillis()-startTime)/10f);\r
- angle += units;\r
- angle %= 360;\r
- startTime = System.currentTimeMillis();\r
- repaint();\r
+ while (currentStatus < STATE_STOPPED_OK)\r
+ {\r
\r
+ try\r
+ {\r
+ Thread.sleep(50);\r
+\r
+ int units = (int) ( (System.currentTimeMillis() - startTime) / 10f);\r
+ angle += units;\r
+ angle %= 360;\r
+ startTime = System.currentTimeMillis();\r
+ repaint();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
- catch (Exception ex)\r
- {}\r
+\r
angle = 0;\r
cancel.setEnabled(false);\r
-\r
}\r
\r
- synchronized public void paintComponent(Graphics g1)\r
+ synchronized public void paintComponent(Graphics g1)\r
{\r
Graphics2D g = (Graphics2D) g1;\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getWidth(), getHeight());\r
+\r
if (image != null)\r
{\r
g.rotate(Math.toRadians(angle), 28, 28);\r
g.drawImage(image, 10, 10, this);\r
g.rotate( -Math.toRadians(angle), 28, 28);\r
}\r
+\r
g.setFont(new Font("Arial", Font.BOLD, 12));\r
g.setColor(Color.black);\r
- switch(currentStatus)\r
+\r
+ switch (currentStatus)\r
{\r
case STATE_QUEUING:\r
g.drawString(title.concat(" - queuing"), 60, 30);\r
+\r
break;\r
+\r
case STATE_RUNNING:\r
g.drawString(title.concat(" - running"), 60, 30);\r
+\r
break;\r
+\r
case STATE_STOPPED_OK:\r
g.drawString(title.concat(" - complete"), 60, 30);\r
+\r
break;\r
\r
case STATE_CANCELLED_OK:\r
g.drawString(title.concat(" - job cancelled!"), 60, 30);\r
+\r
break;\r
\r
case STATE_STOPPED_ERROR:\r
g.drawString(title.concat(" - job error!"), 60, 30);\r
+\r
break;\r
+\r
case STATE_STOPPED_SERVERERROR:\r
- g.drawString(title.concat(" - Server Error! (try later)"), 60, 30);\r
+ g.drawString(title.concat(" - Server Error! (try later)"), 60,\r
+ 30);\r
+\r
break;\r
}\r
-\r
}\r
}\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
+\r
public abstract class AlignFile extends FileParse {\r
- int noSeqs = 0;\r
- int maxLength = 0;\r
-\r
- Vector seqs;\r
- Vector headers;\r
-\r
- long start;\r
- long end;\r
-\r
- public AlignFile()\r
- {}\r
-\r
- public AlignFile(String inStr) {\r
- initData();\r
-System.out.println("is this ever called??");\r
- try{\r
- parse();\r
- }catch(Exception ex){}\r
- }\r
-\r
-/**\r
- * Constructor which parses the data from a file of some specified type.\r
- * @param inFile Filename to read from.\r
- * @param type What type of file to read from (File, URL)\r
- */\r
- public AlignFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
-\r
- initData();\r
-\r
- parse();\r
-\r
- }\r
-\r
-/**\r
- * Return the seqs Vector\r
- */\r
- public Vector getSeqs() {\r
- return seqs;\r
- }\r
-\r
-/**\r
- * Return the Sequences in the seqs Vector as an array of Sequences\r
- */\r
- public SequenceI [] getSeqsAsArray() {\r
- SequenceI [] s = new SequenceI[seqs.size()];\r
- for (int i=0;i < seqs.size();i++) {\r
- s[i] = (SequenceI)seqs.elementAt(i);\r
+ int noSeqs = 0;\r
+ int maxLength = 0;\r
+ Vector seqs;\r
+ Vector headers;\r
+ long start;\r
+ long end;\r
+\r
+ public AlignFile() {\r
+ }\r
+\r
+ public AlignFile(String inStr) {\r
+ initData();\r
+ System.out.println("is this ever called??");\r
+\r
+ try {\r
+ parse();\r
+ } catch (Exception ex) {\r
+ }\r
}\r
- return s;\r
- }\r
-\r
-\r
-/**\r
- * Initialise objects to store sequence data in.\r
- */\r
- protected void initData() {\r
- seqs = new Vector();\r
- headers = new Vector();\r
- }\r
-\r
- protected void setSeqs(SequenceI [] s) {\r
- seqs = new Vector();\r
- for (int i=0; i<s.length; i++) {\r
- seqs.addElement(s[i]);\r
+\r
+ /**\r
+ * Constructor which parses the data from a file of some specified type.\r
+ * @param inFile Filename to read from.\r
+ * @param type What type of file to read from (File, URL)\r
+ */\r
+ public AlignFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+\r
+ initData();\r
+\r
+ parse();\r
}\r
- }\r
\r
- // Checks whether sequence is valid aa characters\r
- protected boolean isValidProteinSequence(String sequence)\r
- {\r
- for (int i = 0; i < sequence.length(); i++)\r
- if (!jalview.schemes.ResidueProperties.aaHash.containsKey(String.valueOf(sequence.charAt(i))))\r
- return false;\r
+ /**\r
+ * Return the seqs Vector\r
+ */\r
+ public Vector getSeqs() {\r
+ return seqs;\r
+ }\r
\r
- return true;\r
- }\r
+ /**\r
+ * Return the Sequences in the seqs Vector as an array of Sequences\r
+ */\r
+ public SequenceI[] getSeqsAsArray() {\r
+ SequenceI[] s = new SequenceI[seqs.size()];\r
\r
+ for (int i = 0; i < seqs.size(); i++) {\r
+ s[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
\r
-/**\r
- * This method must be implemented to parse the contents of the file.\r
- */\r
- public abstract void parse() throws IOException;\r
+ return s;\r
+ }\r
+\r
+ /**\r
+ * Initialise objects to store sequence data in.\r
+ */\r
+ protected void initData() {\r
+ seqs = new Vector();\r
+ headers = new Vector();\r
+ }\r
+\r
+ protected void setSeqs(SequenceI[] s) {\r
+ seqs = new Vector();\r
+\r
+ for (int i = 0; i < s.length; i++) {\r
+ seqs.addElement(s[i]);\r
+ }\r
+ }\r
+\r
+ // Checks whether sequence is valid aa characters\r
+ protected boolean isValidProteinSequence(String sequence) {\r
+ for (int i = 0; i < sequence.length(); i++)\r
+ if (!jalview.schemes.ResidueProperties.aaHash.containsKey(\r
+ String.valueOf(sequence.charAt(i)))) {\r
+ return false;\r
+ }\r
+\r
+ return true;\r
+ }\r
\r
+ /**\r
+ * This method must be implemented to parse the contents of the file.\r
+ */\r
+ public abstract void parse() throws IOException;\r
\r
-/**\r
- * Print out in alignment file format the Sequences in the seqs Vector.\r
- */\r
- public abstract String print();\r
+ /**\r
+ * Print out in alignment file format the Sequences in the seqs Vector.\r
+ */\r
+ public abstract String print();\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
+\r
public class BLCFile extends AlignFile {\r
+ Vector titles;\r
\r
- Vector titles;\r
-\r
- public BLCFile()\r
- {}\r
-\r
- public BLCFile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
- public void initData() {\r
- super.initData();\r
- titles = new Vector();\r
- }\r
-\r
- public BLCFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
-\r
-\r
- public void parse()\r
- {\r
- boolean idsFound=false;\r
- Vector ids = new Vector();\r
- StringBuffer seqstrings [];\r
- Vector starts = new Vector();\r
- Vector ends = new Vector();\r
-\r
- String line=null;\r
- try{\r
- do{\r
- line = nextLine();\r
-\r
- // seek end of ids\r
- if (line.indexOf("*") > -1)\r
- {\r
- idsFound=true;\r
- break;\r
- }\r
-\r
- int abracket = line.indexOf(">");\r
-\r
- if (abracket > -1)\r
- {\r
-\r
- if(line.indexOf(" ")>-1)//\r
- {\r
- ///Colur it be this format?\r
- //>54402046 0 1 137 137:\r
- // or this??\r
- // 1 >L1H14 30539 343\r
- try{\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf(" ", abracket + 1)));\r
-\r
-\r
- // remove p Value\r
- line = line.substring(abracket + 1);\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- int value = Integer.parseInt(line.substring(0, line.indexOf(" ")));\r
- starts.addElement(value+"");\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- value = Integer.parseInt(line.substring(0, line.indexOf(" ")));\r
- ends.addElement(value+"");\r
-\r
- }catch(Exception ex)\r
- {\r
- System.err.println("Error during blockfile read.");\r
- ex.printStackTrace();\r
- starts.addElement("0");\r
- ends.addElement("0");\r
- }\r
+ public BLCFile() {\r
+ }\r
\r
- }\r
- else\r
- {\r
- ids.addElement( line.substring(abracket + 1, line.indexOf("/")));\r
- line = line.substring(line.indexOf("/") + 1);\r
- starts.addElement(line.substring(0, line.indexOf("-")));\r
- ends.addElement(line.substring(line.indexOf("-") + 1));\r
- }\r
- }\r
- }while(!idsFound);\r
-\r
- int starCol = line.indexOf("*");\r
- seqstrings = new StringBuffer[ids.size()];\r
- for(int i=0; i<ids.size(); i++)\r
- {\r
- if(seqstrings[i]==null)\r
- seqstrings[i] = new StringBuffer();\r
+ public BLCFile(String inStr) {\r
+ super(inStr);\r
+ }\r
+\r
+ public BLCFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
}\r
\r
- while ((line = nextLine()).indexOf("*")==-1)\r
- {\r
- for(int i=0; i<ids.size(); i++)\r
- {\r
- if(line.length()>i+starCol)\r
- seqstrings[i].append(line.charAt(i + starCol));\r
- }\r
+ public void initData() {\r
+ super.initData();\r
+ titles = new Vector();\r
}\r
\r
- for(int i=0; i<ids.size(); i++)\r
- {\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqstrings[i].toString(),\r
- Integer.parseInt(starts.elementAt(i).toString()),\r
- Integer.parseInt(ends.elementAt(i).toString()));\r
- seqs.addElement(newSeq);\r
+ public void parse() {\r
+ boolean idsFound = false;\r
+ Vector ids = new Vector();\r
+ StringBuffer[] seqstrings;\r
+ Vector starts = new Vector();\r
+ Vector ends = new Vector();\r
+\r
+ String line = null;\r
+\r
+ try {\r
+ do {\r
+ line = nextLine();\r
+\r
+ // seek end of ids\r
+ if (line.indexOf("*") > -1) {\r
+ idsFound = true;\r
+\r
+ break;\r
+ }\r
+\r
+ int abracket = line.indexOf(">");\r
+\r
+ if (abracket > -1) {\r
+ if (line.indexOf(" ") > -1) //\r
+ {\r
+ ///Colur it be this format?\r
+ //>54402046 0 1 137 137:\r
+ // or this??\r
+ // 1 >L1H14 30539 343\r
+ try {\r
+ ids.addElement(line.substring(abracket + 1,\r
+ line.indexOf(" ", abracket + 1)));\r
+\r
+ // remove p Value\r
+ line = line.substring(abracket + 1);\r
+ line = line.substring(line.indexOf(" ") + 1);\r
+ line = line.trim();\r
+ line = line.substring(line.indexOf(" ") + 1);\r
+ line = line.trim();\r
+\r
+ int value = Integer.parseInt(line.substring(0,\r
+ line.indexOf(" ")));\r
+ starts.addElement(value + "");\r
+ line = line.substring(line.indexOf(" ") + 1);\r
+ line = line.trim();\r
+ value = Integer.parseInt(line.substring(0,\r
+ line.indexOf(" ")));\r
+ ends.addElement(value + "");\r
+ } catch (Exception ex) {\r
+ System.err.println("Error during blockfile read.");\r
+ ex.printStackTrace();\r
+ starts.addElement("0");\r
+ ends.addElement("0");\r
+ }\r
+ } else {\r
+ ids.addElement(line.substring(abracket + 1,\r
+ line.indexOf("/")));\r
+ line = line.substring(line.indexOf("/") + 1);\r
+ starts.addElement(line.substring(0, line.indexOf("-")));\r
+ ends.addElement(line.substring(line.indexOf("-") + 1));\r
+ }\r
+ }\r
+ } while (!idsFound);\r
+\r
+ int starCol = line.indexOf("*");\r
+ seqstrings = new StringBuffer[ids.size()];\r
+\r
+ for (int i = 0; i < ids.size(); i++) {\r
+ if (seqstrings[i] == null) {\r
+ seqstrings[i] = new StringBuffer();\r
+ }\r
+ }\r
+\r
+ while ((line = nextLine()).indexOf("*") == -1) {\r
+ for (int i = 0; i < ids.size(); i++) {\r
+ if (line.length() > (i + starCol)) {\r
+ seqstrings[i].append(line.charAt(i + starCol));\r
+ }\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < ids.size(); i++) {\r
+ Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
+ seqstrings[i].toString(),\r
+ Integer.parseInt(starts.elementAt(i).toString()),\r
+ Integer.parseInt(ends.elementAt(i).toString()));\r
+ seqs.addElement(newSeq);\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
}\r
\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
- public static String print(SequenceI[] s) {\r
- StringBuffer out = new StringBuffer();\r
-\r
- int i=0;\r
- int max = -1;\r
- while (i < s.length && s[i] != null) {\r
- out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd() + "\n");\r
- if (s[i].getSequence().length() > max) { max = s[i].getSequence().length();}\r
- i++;\r
+ public String print() {\r
+ return print(getSeqsAsArray());\r
}\r
\r
- out.append("* iteration 1\n");\r
- for (int j = 0; j < max; j++) {\r
- i=0;\r
- while (i < s.length && s[i] != null) {\r
- if(s[i].getSequence().length()>j )\r
- out.append(s[i].getSequence().substring(j,j+1));\r
- else\r
- out.append("-");\r
- i++;\r
+ public static String print(SequenceI[] s) {\r
+ StringBuffer out = new StringBuffer();\r
+\r
+ int i = 0;\r
+ int max = -1;\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd() + "\n");\r
+\r
+ if (s[i].getSequence().length() > max) {\r
+ max = s[i].getSequence().length();\r
+ }\r
+\r
+ i++;\r
}\r
- out.append("\n");\r
- }\r
- out.append("*\n");\r
- return out.toString();\r
\r
- }\r
+ out.append("* iteration 1\n");\r
+\r
+ for (int j = 0; j < max; j++) {\r
+ i = 0;\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ if (s[i].getSequence().length() > j) {\r
+ out.append(s[i].getSequence().substring(j, j + 1));\r
+ } else {\r
+ out.append("-");\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ out.append("\n");\r
+ }\r
+\r
+ out.append("*\n");\r
+\r
+ return out.toString();\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+\r
import jalview.util.*;\r
\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
+\r
public class ClustalFile extends AlignFile {\r
+ Vector ids;\r
\r
- Vector ids;\r
-\r
- public ClustalFile()\r
- {}\r
-\r
- public ClustalFile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
-\r
- public void initData() {\r
- super.initData();\r
- ids = new Vector();\r
- }\r
-\r
- public ClustalFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
-\r
- public void parse() {\r
- int i = 0;\r
- boolean flag = false;\r
-\r
- Vector headers = new Vector();\r
- Hashtable seqhash = new Hashtable();\r
-\r
- String line;\r
-\r
- try {\r
- while ((line = nextLine()) != null) {\r
- if (line.indexOf(" ") != 0) {\r
- StringTokenizer str = new StringTokenizer(line," ");\r
- String id = "";\r
-\r
- if (str.hasMoreTokens()) {\r
- id = str.nextToken();\r
- if (id.equals("CLUSTAL")) {\r
- flag = true;\r
- } else {\r
- if (flag) {\r
- StringBuffer tempseq;\r
- if (seqhash.containsKey(id)) {\r
- tempseq = (StringBuffer)seqhash.get(id);\r
- } else {\r
- tempseq = new StringBuffer();\r
- seqhash.put(id,tempseq);\r
- }\r
-\r
- if (!(headers.contains(id))) {\r
- headers.addElement(id);\r
- }\r
-\r
- if(str.hasMoreTokens())\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
- }\r
- } catch (IOException e) {\r
- System.err.println("Exception parsing clustal file " + e);\r
- e.printStackTrace();\r
+ public ClustalFile() {\r
}\r
\r
- if (flag) {\r
- this.noSeqs = headers.size();\r
-\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++ ) {\r
- int start = -1;\r
- int end = -1;\r
-\r
- if ( seqhash.get(headers.elementAt(i)) != null) {\r
- if (maxLength < seqhash.get(headers.elementAt(i)).toString().length() ) {\r
- maxLength = seqhash.get(headers.elementAt(i)).toString().length();\r
- }\r
- String head = headers.elementAt(i).toString();\r
- start = 1;\r
- end = seqhash.get(headers.elementAt(i)).toString().length();\r
-\r
- if (head.indexOf("/") > 0 ) {\r
- StringTokenizer st = new StringTokenizer(head,"/");\r
- if (st.countTokens() == 2) {\r
-\r
- ids.addElement(st.nextToken());\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp,"-");\r
- if (st.countTokens() == 2) {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- } else {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
- } else {\r
- ids.addElement(headers.elementAt(i));\r
+ public ClustalFile(String inStr) {\r
+ super(inStr);\r
+ }\r
+\r
+ public ClustalFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+ }\r
\r
- }\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).toString()).toString(),start,end);\r
+ public void initData() {\r
+ super.initData();\r
+ ids = new Vector();\r
+ }\r
\r
- seqs.addElement(newSeq);\r
+ public void parse() {\r
+ int i = 0;\r
+ boolean flag = false;\r
+\r
+ Vector headers = new Vector();\r
+ Hashtable seqhash = new Hashtable();\r
+\r
+ String line;\r
+\r
+ try {\r
+ while ((line = nextLine()) != null) {\r
+ if (line.indexOf(" ") != 0) {\r
+ StringTokenizer str = new StringTokenizer(line, " ");\r
+ String id = "";\r
+\r
+ if (str.hasMoreTokens()) {\r
+ id = str.nextToken();\r
+\r
+ if (id.equals("CLUSTAL")) {\r
+ flag = true;\r
+ } else {\r
+ if (flag) {\r
+ StringBuffer tempseq;\r
+\r
+ if (seqhash.containsKey(id)) {\r
+ tempseq = (StringBuffer) seqhash.get(id);\r
+ } else {\r
+ tempseq = new StringBuffer();\r
+ seqhash.put(id, tempseq);\r
+ }\r
+\r
+ if (!(headers.contains(id))) {\r
+ headers.addElement(id);\r
+ }\r
+\r
+ if (str.hasMoreTokens()) {\r
+ tempseq.append(str.nextToken());\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ } catch (IOException e) {\r
+ System.err.println("Exception parsing clustal file " + e);\r
+ e.printStackTrace();\r
+ }\r
\r
- } else {\r
- System.err.println("Clustal File Reader: Can't find sequence for " + headers.elementAt(i));\r
+ if (flag) {\r
+ this.noSeqs = headers.size();\r
+\r
+ //Add sequences to the hash\r
+ for (i = 0; i < headers.size(); i++) {\r
+ int start = -1;\r
+ int end = -1;\r
+\r
+ if (seqhash.get(headers.elementAt(i)) != null) {\r
+ if (maxLength < seqhash.get(headers.elementAt(i)).toString()\r
+ .length()) {\r
+ maxLength = seqhash.get(headers.elementAt(i)).toString()\r
+ .length();\r
+ }\r
+\r
+ String head = headers.elementAt(i).toString();\r
+ start = 1;\r
+ end = seqhash.get(headers.elementAt(i)).toString().length();\r
+\r
+ if (head.indexOf("/") > 0) {\r
+ StringTokenizer st = new StringTokenizer(head, "/");\r
+\r
+ if (st.countTokens() == 2) {\r
+ ids.addElement(st.nextToken());\r
+\r
+ String tmp = st.nextToken();\r
+ st = new StringTokenizer(tmp, "-");\r
+\r
+ if (st.countTokens() == 2) {\r
+ start = Integer.valueOf(st.nextToken())\r
+ .intValue();\r
+ end = Integer.valueOf(st.nextToken()).intValue();\r
+ }\r
+ } else {\r
+ ids.addElement(headers.elementAt(i));\r
+ }\r
+ } else {\r
+ ids.addElement(headers.elementAt(i));\r
+ }\r
+\r
+ Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
+ seqhash.get(headers.elementAt(i).toString())\r
+ .toString(), start, end);\r
+\r
+ seqs.addElement(newSeq);\r
+ } else {\r
+ System.err.println(\r
+ "Clustal File Reader: Can't find sequence for " +\r
+ headers.elementAt(i));\r
+ }\r
+ }\r
}\r
- }\r
}\r
\r
- }\r
+ public String print() {\r
+ return print(getSeqsAsArray());\r
+ }\r
+\r
+ public static String print(SequenceI[] s) {\r
+ StringBuffer out = new StringBuffer("CLUSTAL\n\n");\r
\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
- public static String print(SequenceI[] s) {\r
+ int max = 0;\r
+ int maxid = 0;\r
\r
- StringBuffer out = new StringBuffer("CLUSTAL\n\n");\r
+ int i = 0;\r
\r
- int max = 0;\r
- int maxid = 0;\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd();\r
\r
- int i = 0;\r
+ if (s[i].getSequence().length() > max) {\r
+ max = s[i].getSequence().length();\r
+ }\r
\r
- while (i < s.length && s[i] != null) {\r
- String tmp = s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd();\r
+ if (tmp.length() > maxid) {\r
+ maxid = tmp.length();\r
+ }\r
\r
- if (s[i].getSequence().length() > max) {\r
- max = s[i].getSequence().length();\r
- }\r
- if (tmp.length() > maxid) {\r
- maxid = tmp.length();\r
- }\r
- i++;\r
- }\r
+ i++;\r
+ }\r
\r
- if (maxid < 15) {\r
- maxid = 15;\r
- }\r
- maxid++;\r
- int len = 60;\r
- int nochunks = max / len + 1;\r
-\r
- for (i = 0; i < nochunks; i++) {\r
- int j = 0;\r
- while ( j < s.length && s[j] != null) {\r
- out.append( new Format("%-" + maxid + "s").form(s[j].getName() + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
- int start = i*len;\r
- int end = start + len;\r
-\r
- if (end < s[j].getSequence().length() && start < s[j].getSequence().length() )\r
- out.append(s[j].getSequence().substring(start,end));\r
- else\r
- {\r
- if (start < s[j].getSequence().length())\r
- out.append(s[j].getSequence().substring(start));\r
+ if (maxid < 15) {\r
+ maxid = 15;\r
}\r
- out.append("\n");\r
- j++;\r
- }\r
- out.append("\n");\r
\r
- }\r
+ maxid++;\r
+\r
+ int len = 60;\r
+ int nochunks = (max / len) + 1;\r
\r
- return out.toString();\r
- }\r
+ for (i = 0; i < nochunks; i++) {\r
+ int j = 0;\r
\r
+ while ((j < s.length) && (s[j] != null)) {\r
+ out.append(new Format("%-" + maxid + "s").form(s[j].getName() +\r
+ "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
\r
+ int start = i * len;\r
+ int end = start + len;\r
+\r
+ if ((end < s[j].getSequence().length()) &&\r
+ (start < s[j].getSequence().length())) {\r
+ out.append(s[j].getSequence().substring(start, end));\r
+ } else {\r
+ if (start < s[j].getSequence().length()) {\r
+ out.append(s[j].getSequence().substring(start));\r
+ }\r
+ }\r
+\r
+ out.append("\n");\r
+ j++;\r
+ }\r
+\r
+ out.append("\n");\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
-import org.apache.axis.client.*;\r
-\r
-import java.io.*;\r
-\r
-import javax.activation.DataHandler;\r
import org.apache.axis.AxisFault;\r
+import org.apache.axis.client.*;\r
import org.apache.axis.encoding.XMLType;\r
-import javax.xml.rpc.ParameterMode;\r
-import javax.xml.namespace.QName;\r
-import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;\r
import org.apache.axis.encoding.ser.JAFDataHandlerDeserializerFactory;\r
+import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;\r
\r
+import java.io.*;\r
\r
-public class EBIFetchClient\r
-{\r
- Call call;\r
- String format = "default";\r
- String style = "raw";\r
-\r
- public EBIFetchClient()\r
- {\r
- try{\r
- call = (Call)new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/ws/services/Dbfetch"));\r
- }catch(Exception ex){}\r
- }\r
-\r
-\r
- public String [] getSupportedDBs()\r
- {\r
- try{\r
-\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
- return (String[]) call.invoke(new Object[]{});\r
-\r
- }catch(Exception ex){return null;}\r
- }\r
+import javax.activation.DataHandler;\r
\r
- public String [] getSupportedFormats()\r
- {\r
- try{\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
- return (String[]) call.invoke(new Object[] {});\r
+import javax.xml.namespace.QName;\r
+import javax.xml.rpc.ParameterMode;\r
\r
- }catch(Exception ex){ return null; }\r
- }\r
\r
- public String [] getSupportedStyles()\r
- {\r
- try{\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
- return (String[]) call.invoke(new Object[] {});\r
+public class EBIFetchClient {\r
+ Call call;\r
+ String format = "default";\r
+ String style = "raw";\r
\r
- }catch(Exception ex){return null;}\r
+ public EBIFetchClient() {\r
+ try {\r
+ call = (Call) new Service().createCall();\r
+ call.setTargetEndpointAddress(new java.net.URL(\r
+ "http://www.ebi.ac.uk/ws/services/Dbfetch"));\r
+ } catch (Exception ex) {\r
+ }\r
}\r
\r
- public String [] fetchData(String ids, String f, String s)\r
- {\r
- // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;\r
- // max 50 ids can be added at one time\r
- try{\r
- call.setOperationName(new QName("urn:Dbfetch", "fetchData"));\r
- call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- if (f != null)\r
- format = f;\r
-\r
- if (s != null)\r
- style = s;\r
-\r
- return (String[]) call.invoke(new Object[] {ids, format, style});\r
-\r
- }catch(Exception ex){return null;}\r
+ public String[] getSupportedDBs() {\r
+ try {\r
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));\r
+ call.setReturnType(XMLType.SOAP_ARRAY);\r
\r
+ return (String[]) call.invoke(new Object[] { });\r
+ } catch (Exception ex) {\r
+ return null;\r
+ }\r
}\r
\r
- public String fetchDataFile(String arg, String f, String s)\r
- {\r
-\r
- if (f != null)\r
- format = f;\r
+ public String[] getSupportedFormats() {\r
+ try {\r
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));\r
+ call.setReturnType(XMLType.SOAP_ARRAY);\r
\r
- if (s != null)\r
- style = s;\r
-\r
-\r
- call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));\r
- call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
-\r
- QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");\r
- call.registerTypeMapping(javax.activation.DataSource.class,\r
- qnameAttachment,\r
- JAFDataHandlerSerializerFactory.class,\r
- JAFDataHandlerDeserializerFactory.class);\r
+ return (String[]) call.invoke(new Object[] { });\r
+ } catch (Exception ex) {\r
+ return null;\r
+ }\r
+ }\r
\r
- call.setReturnType(qnameAttachment);\r
+ public String[] getSupportedStyles() {\r
+ try {\r
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));\r
+ call.setReturnType(XMLType.SOAP_ARRAY);\r
\r
- try{\r
- Object ret = call.invoke(new Object[]\r
- {arg, format, style});\r
+ return (String[]) call.invoke(new Object[] { });\r
+ } catch (Exception ex) {\r
+ return null;\r
+ }\r
+ }\r
\r
- if (null == ret)\r
- {\r
- System.err.println("Received null ");\r
- throw new AxisFault("", "Received null", null, null);\r
+ public String[] fetchData(String ids, String f, String s) {\r
+ // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;\r
+ // max 50 ids can be added at one time\r
+ try {\r
+ call.setOperationName(new QName("urn:Dbfetch", "fetchData"));\r
+ call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.setReturnType(XMLType.SOAP_ARRAY);\r
+\r
+ if (f != null) {\r
+ format = f;\r
+ }\r
+\r
+ if (s != null) {\r
+ style = s;\r
+ }\r
+\r
+ return (String[]) call.invoke(new Object[] { ids, format, style });\r
+ } catch (Exception ex) {\r
+ return null;\r
}\r
- if (ret instanceof String)\r
- {\r
- System.err.println("Received problem response from server: " + ret);\r
- throw new AxisFault("", (String) ret, null, null);\r
+ }\r
+\r
+ public String fetchDataFile(String arg, String f, String s) {\r
+ if (f != null) {\r
+ format = f;\r
}\r
- if (! (ret instanceof DataHandler))\r
- {\r
- //The wrong type of object that what was expected.\r
- System.err.println("Received problem response from server:" +\r
- ret.getClass().getName());\r
- throw new AxisFault("", "Received problem response from server:" +\r
- ret.getClass().getName(), null, null);\r
\r
+ if (s != null) {\r
+ style = s;\r
}\r
- //Still here, so far so good.\r
- DataHandler rdh = (DataHandler) ret;\r
\r
- //From here we'll just treat the data resource as file.\r
- String receivedfileName = rdh.getName(); //Get the filename.\r
+ call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));\r
+ call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
\r
- if (receivedfileName == null)\r
- {\r
- System.err.println("Could not get the file name.");\r
- throw new AxisFault("", "Could not get the file name.", null, null);\r
+ QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");\r
+ call.registerTypeMapping(javax.activation.DataSource.class,\r
+ qnameAttachment, JAFDataHandlerSerializerFactory.class,\r
+ JAFDataHandlerDeserializerFactory.class);\r
+\r
+ call.setReturnType(qnameAttachment);\r
+\r
+ try {\r
+ Object ret = call.invoke(new Object[] { arg, format, style });\r
+\r
+ if (null == ret) {\r
+ System.err.println("Received null ");\r
+ throw new AxisFault("", "Received null", null, null);\r
+ }\r
+\r
+ if (ret instanceof String) {\r
+ System.err.println("Received problem response from server: " +\r
+ ret);\r
+ throw new AxisFault("", (String) ret, null, null);\r
+ }\r
+\r
+ if (!(ret instanceof DataHandler)) {\r
+ //The wrong type of object that what was expected.\r
+ System.err.println("Received problem response from server:" +\r
+ ret.getClass().getName());\r
+ throw new AxisFault("",\r
+ "Received problem response from server:" +\r
+ ret.getClass().getName(), null, null);\r
+ }\r
+\r
+ //Still here, so far so good.\r
+ DataHandler rdh = (DataHandler) ret;\r
+\r
+ //From here we'll just treat the data resource as file.\r
+ String receivedfileName = rdh.getName(); //Get the filename.\r
+\r
+ if (receivedfileName == null) {\r
+ System.err.println("Could not get the file name.");\r
+ throw new AxisFault("", "Could not get the file name.", null,\r
+ null);\r
+ }\r
+\r
+ if (arg.equalsIgnoreCase("medline")) {\r
+ return receivedfileName;\r
+ } else if (arg.equalsIgnoreCase("interpro")) {\r
+ return receivedfileName;\r
+ } else {\r
+ System.err.println(receivedfileName);\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
}\r
- if (arg.equalsIgnoreCase("medline"))\r
- {\r
- return receivedfileName;\r
- }\r
- else if (arg.equalsIgnoreCase("interpro"))\r
- {\r
- return receivedfileName;\r
- }\r
- else\r
- System.err.println(receivedfileName);\r
- }catch(Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- return "ERROR";\r
- }\r
-\r
\r
+ return "ERROR";\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
-import jalview.datamodel.*;\r
import jalview.analysis.*;\r
\r
+import jalview.datamodel.*;\r
+\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
+\r
public class FastaFile extends AlignFile {\r
+ public FastaFile() {\r
+ }\r
\r
- public FastaFile()\r
- {}\r
-\r
- public FastaFile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
- public FastaFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
-\r
- public void parse() throws IOException\r
- {\r
-\r
- String id = "";\r
- StringBuffer seq = new StringBuffer();\r
- int count = 0;\r
- boolean flag = false;\r
-\r
- int sstart = 0;\r
- int send = 0;\r
-\r
- String line;\r
-\r
- while ((line = nextLine()) != null) {\r
-\r
- if (line.length() > 0) {\r
-\r
- // Do we have an id line?\r
-\r
- if (line.substring(0,1).equals(">")) {\r
-\r
- if (count != 0) {\r
- if (sstart != 0) {\r
- seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),sstart,send));\r
- } else {\r
- seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),1,seq.length()));\r
- }\r
- }\r
-\r
- count++;\r
-\r
- StringTokenizer str = new StringTokenizer(line," ");\r
-\r
- id = str.nextToken();\r
- id = id.substring(1);\r
- com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex("[A-Za-z-]+/[A-Za-z-]+\\|(\\w+)\\|(.+)");\r
- if (dbId.search(id))\r
- {\r
- String dbid = dbId.stringMatched(1);\r
- String idname = dbId.stringMatched(2);\r
- if (idname.length()>0 && idname.indexOf("_") > -1)\r
- {\r
- id = idname; // just use friendly name // JBPNote: we may lose uniprot standardised ID here.\r
- }\r
- else\r
- {\r
- id = dbid; // use dbid to ensure sensible queries\r
- }\r
-\r
- }\r
- if (id.indexOf("/") > 0 ) {\r
-\r
- StringTokenizer st = new StringTokenizer(id,"/");\r
- if (st.countTokens() == 2) {\r
- id = st.nextToken();\r
- String tmp = st.nextToken();\r
-\r
- st = new StringTokenizer(tmp,"-");\r
-\r
- if (st.countTokens() == 2) {\r
- sstart = Integer.valueOf(st.nextToken()).intValue();\r
- send = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- }\r
-\r
- seq = new StringBuffer();\r
-\r
- } else {\r
- seq = seq.append(line);\r
- }\r
- }\r
- }\r
- if (count > 0) {\r
-\r
- if(!isValidProteinSequence(seq.toString().toUpperCase()))\r
- throw new IOException("Invalid protein sequence");\r
-\r
- if (sstart != 0) {\r
- seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),sstart,send));\r
- } else {\r
- seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),1,seq.length()));\r
- }\r
- }\r
-\r
- }\r
-\r
- public static String print(SequenceI[] s) {\r
- return print(s,72);\r
- }\r
- public static String print(SequenceI[] s, int len) {\r
- return print(s,len,true);\r
- }\r
-\r
- public static String print(SequenceI[] s, int len,boolean gaps) {\r
- return print(s,len,gaps,true);\r
- }\r
-\r
- public static String print(SequenceI[] s, int len,boolean gaps, boolean displayId) {\r
- StringBuffer out = new StringBuffer();\r
- int i = 0;\r
- while (i < s.length && s[i] != null) {\r
- String seq = "";\r
- if (gaps) {\r
- seq = s[i].getSequence();\r
- } else {\r
- seq = AlignSeq.extractGaps("-. ",s[i].getSequence());\r
- }\r
- // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
- out.append(">" + ((displayId) ? s[i].getDisplayId() : s[i].getName())+"\n");\r
-\r
- int nochunks = seq.length() / len + 1;\r
-\r
- for (int j = 0; j < nochunks; j++) {\r
- int start = j*len;\r
- int end = start + len;\r
-\r
- if (end < seq.length()) {\r
- out.append(seq.substring(start,end) + "\n");\r
- } else if (start < seq.length()) {\r
- out.append(seq.substring(start) + "\n");\r
+ public FastaFile(String inStr) {\r
+ super(inStr);\r
+ }\r
+\r
+ public FastaFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public void parse() throws IOException {\r
+ String id = "";\r
+ StringBuffer seq = new StringBuffer();\r
+ int count = 0;\r
+ boolean flag = false;\r
+\r
+ int sstart = 0;\r
+ int send = 0;\r
+\r
+ String line;\r
+\r
+ while ((line = nextLine()) != null) {\r
+ if (line.length() > 0) {\r
+ // Do we have an id line?\r
+ if (line.substring(0, 1).equals(">")) {\r
+ if (count != 0) {\r
+ if (sstart != 0) {\r
+ seqs.addElement(new Sequence(id,\r
+ seq.toString().toUpperCase(), sstart, send));\r
+ } else {\r
+ seqs.addElement(new Sequence(id,\r
+ seq.toString().toUpperCase(), 1,\r
+ seq.length()));\r
+ }\r
+ }\r
+\r
+ count++;\r
+\r
+ StringTokenizer str = new StringTokenizer(line, " ");\r
+\r
+ id = str.nextToken();\r
+ id = id.substring(1);\r
+\r
+ com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(\r
+ "[A-Za-z-]+/[A-Za-z-]+\\|(\\w+)\\|(.+)");\r
+\r
+ if (dbId.search(id)) {\r
+ String dbid = dbId.stringMatched(1);\r
+ String idname = dbId.stringMatched(2);\r
+\r
+ if ((idname.length() > 0) &&\r
+ (idname.indexOf("_") > -1)) {\r
+ id = idname; // just use friendly name // JBPNote: we may lose uniprot standardised ID here.\r
+ } else {\r
+ id = dbid; // use dbid to ensure sensible queries\r
+ }\r
+ }\r
+\r
+ if (id.indexOf("/") > 0) {\r
+ StringTokenizer st = new StringTokenizer(id, "/");\r
+\r
+ if (st.countTokens() == 2) {\r
+ id = st.nextToken();\r
+\r
+ String tmp = st.nextToken();\r
+\r
+ st = new StringTokenizer(tmp, "-");\r
+\r
+ if (st.countTokens() == 2) {\r
+ sstart = Integer.valueOf(st.nextToken())\r
+ .intValue();\r
+ send = Integer.valueOf(st.nextToken()).intValue();\r
+ }\r
+ }\r
+ }\r
+\r
+ seq = new StringBuffer();\r
+ } else {\r
+ seq = seq.append(line);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (count > 0) {\r
+ if (!isValidProteinSequence(seq.toString().toUpperCase())) {\r
+ throw new IOException("Invalid protein sequence");\r
+ }\r
+\r
+ if (sstart != 0) {\r
+ seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),\r
+ sstart, send));\r
+ } else {\r
+ seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),\r
+ 1, seq.length()));\r
+ }\r
}\r
- }\r
- i++;\r
}\r
- return out.toString();\r
- }\r
\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
-}\r
+ public static String print(SequenceI[] s) {\r
+ return print(s, 72);\r
+ }\r
\r
+ public static String print(SequenceI[] s, int len) {\r
+ return print(s, len, true);\r
+ }\r
+\r
+ public static String print(SequenceI[] s, int len, boolean gaps) {\r
+ return print(s, len, gaps, true);\r
+ }\r
+\r
+ public static String print(SequenceI[] s, int len, boolean gaps,\r
+ boolean displayId) {\r
+ StringBuffer out = new StringBuffer();\r
+ int i = 0;\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String seq = "";\r
+\r
+ if (gaps) {\r
+ seq = s[i].getSequence();\r
+ } else {\r
+ seq = AlignSeq.extractGaps("-. ", s[i].getSequence());\r
+ }\r
+\r
+ // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
+ out.append(">" +\r
+ ((displayId) ? s[i].getDisplayId() : s[i].getName()) + "\n");\r
+\r
+ int nochunks = (seq.length() / len) + 1;\r
\r
+ for (int j = 0; j < nochunks; j++) {\r
+ int start = j * len;\r
+ int end = start + len;\r
\r
+ if (end < seq.length()) {\r
+ out.append(seq.substring(start, end) + "\n");\r
+ } else if (start < seq.length()) {\r
+ out.append(seq.substring(start) + "\n");\r
+ }\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ public String print() {\r
+ return print(getSeqsAsArray());\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import java.io.*;\r
-import java.net.*;\r
-\r
-public class FileParse {\r
-\r
- public File inFile;\r
- public int fileSize;\r
- public int noLines;\r
\r
- protected String type;\r
- protected BufferedReader dataIn;\r
+import java.net.*;\r
\r
- public FileParse() {}\r
\r
- public FileParse(String fileStr, String type) throws MalformedURLException, IOException\r
- {\r
+public class FileParse {\r
+ public File inFile;\r
+ public int fileSize;\r
+ public int noLines;\r
+ protected String type;\r
+ protected BufferedReader dataIn;\r
\r
- this.type = type;\r
+ public FileParse() {\r
+ }\r
\r
- if (type.equals("File")) {\r
- this.inFile = new File(fileStr);\r
- this.fileSize = (int)inFile.length();\r
+ public FileParse(String fileStr, String type)\r
+ throws MalformedURLException, IOException {\r
+ this.type = type;\r
+\r
+ if (type.equals("File")) {\r
+ this.inFile = new File(fileStr);\r
+ this.fileSize = (int) inFile.length();\r
+\r
+ dataIn = new BufferedReader(new FileReader(fileStr));\r
+ } else if (type.equals("URL")) {\r
+ URL url = new URL(fileStr);\r
+ this.fileSize = 0;\r
+ dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ } else if (type.equals("Paste")) {\r
+ dataIn = new BufferedReader(new StringReader(fileStr));\r
+ }\r
+ }\r
\r
- dataIn = new BufferedReader(new FileReader( fileStr ));\r
+ public String nextLine() throws IOException {\r
+ String next = dataIn.readLine();\r
\r
- } else if (type.equals("URL")) {\r
- URL url = new URL(fileStr);\r
- this.fileSize = 0;\r
- dataIn = new BufferedReader(new InputStreamReader( url.openStream() ));\r
- } else if(type.equals("Paste"))\r
- {\r
- dataIn = new BufferedReader(new StringReader(fileStr));\r
- }\r
- }\r
+ if (next != null) {\r
+ noLines++;\r
+ }\r
\r
- public String nextLine() throws IOException {\r
- String next = dataIn.readLine();\r
- if (next != null) {\r
- noLines++;\r
+ return next;\r
}\r
- return next;\r
- }\r
-\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+\r
import java.util.Vector;\r
-public class FormatAdapter\r
-{\r
-\r
- public static Vector formats = new Vector();\r
- static{\r
- formats.addElement("FASTA");\r
- formats.addElement("MSF");\r
- formats.addElement("PileUp");\r
- formats.addElement("CLUSTAL");\r
- formats.addElement("BLC");\r
- formats.addElement("PIR");\r
- formats.addElement("PFAM");\r
- }\r
-\r
- public static SequenceI[] readFile(String inFile, String type, String format)\r
- {\r
-\r
- try\r
- {\r
- AlignFile afile = null;\r
- if (format.equals("FASTA"))\r
- afile = new FastaFile(inFile, type);\r
- else if (format.equals("MSF"))\r
- afile = new MSFfile(inFile, type);\r
- else if (format.equals("PileUp"))\r
- afile = new PileUpfile(inFile, type);\r
- else if (format.equals("CLUSTAL"))\r
- afile = new ClustalFile(inFile, type);\r
- else if (format.equals("BLC"))\r
- afile = new BLCFile(inFile, type);\r
- else if (format.equals("PIR"))\r
- afile = new PIRFile(inFile, type);\r
- else if (format.equals("PFAM"))\r
- afile = new PfamFile(inFile, type);\r
-\r
- return afile.getSeqsAsArray();\r
- }\r
- catch (Exception e) {\r
- System.err.println("Failed to read alignment using the '"+format+"' reader.");\r
- e.printStackTrace();\r
- }\r
\r
- return null;\r
- }\r
-\r
-\r
- public static String formatSequences(String format, Vector seqs)\r
- {\r
- SequenceI [] s = new SequenceI[seqs.size()];\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- s[i] = (SequenceI) seqs.elementAt(i);\r
-\r
- try\r
- {\r
- AlignFile afile = null;\r
- if (format.equals("FASTA"))\r
- afile = new FastaFile();\r
- else if (format.equals("MSF"))\r
- afile = new MSFfile();\r
- else if (format.equals("PileUp"))\r
- afile = new PileUpfile();\r
- else if (format.equals("CLUSTAL"))\r
- afile = new ClustalFile();\r
- else if (format.equals("BLC"))\r
- afile = new BLCFile();\r
- else if (format.equals("PIR"))\r
- afile = new PIRFile();\r
- else if (format.equals("PFAM"))\r
- afile = new PfamFile();\r
-\r
- afile.setSeqs(s);\r
- return afile.print();\r
+\r
+public class FormatAdapter {\r
+ public static Vector formats = new Vector();\r
+\r
+ static {\r
+ formats.addElement("FASTA");\r
+ formats.addElement("MSF");\r
+ formats.addElement("PileUp");\r
+ formats.addElement("CLUSTAL");\r
+ formats.addElement("BLC");\r
+ formats.addElement("PIR");\r
+ formats.addElement("PFAM");\r
}\r
- catch (Exception e) {\r
- System.err.println("Failed to write alignment as a '"+format+"' file\n");\r
- e.printStackTrace();\r
+\r
+ public static SequenceI[] readFile(String inFile, String type, String format) {\r
+ try {\r
+ AlignFile afile = null;\r
+\r
+ if (format.equals("FASTA")) {\r
+ afile = new FastaFile(inFile, type);\r
+ } else if (format.equals("MSF")) {\r
+ afile = new MSFfile(inFile, type);\r
+ } else if (format.equals("PileUp")) {\r
+ afile = new PileUpfile(inFile, type);\r
+ } else if (format.equals("CLUSTAL")) {\r
+ afile = new ClustalFile(inFile, type);\r
+ } else if (format.equals("BLC")) {\r
+ afile = new BLCFile(inFile, type);\r
+ } else if (format.equals("PIR")) {\r
+ afile = new PIRFile(inFile, type);\r
+ } else if (format.equals("PFAM")) {\r
+ afile = new PfamFile(inFile, type);\r
+ }\r
+\r
+ return afile.getSeqsAsArray();\r
+ } catch (Exception e) {\r
+ System.err.println("Failed to read alignment using the '" + format +\r
+ "' reader.");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ return null;\r
}\r
\r
- return null;\r
- }\r
+ public static String formatSequences(String format, Vector seqs) {\r
+ SequenceI[] s = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ s[i] = (SequenceI) seqs.elementAt(i);\r
+\r
+ try {\r
+ AlignFile afile = null;\r
+\r
+ if (format.equals("FASTA")) {\r
+ afile = new FastaFile();\r
+ } else if (format.equals("MSF")) {\r
+ afile = new MSFfile();\r
+ } else if (format.equals("PileUp")) {\r
+ afile = new PileUpfile();\r
+ } else if (format.equals("CLUSTAL")) {\r
+ afile = new ClustalFile();\r
+ } else if (format.equals("BLC")) {\r
+ afile = new BLCFile();\r
+ } else if (format.equals("PIR")) {\r
+ afile = new PIRFile();\r
+ } else if (format.equals("PFAM")) {\r
+ afile = new PfamFile();\r
+ }\r
+\r
+ afile.setSeqs(s);\r
+\r
+ return afile.print();\r
+ } catch (Exception e) {\r
+ System.err.println("Failed to write alignment as a '" + format +\r
+ "' file\n");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ return null;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
-import jalview.gui.*;\r
import jalview.datamodel.*;\r
+\r
+import jalview.gui.*;\r
+\r
import jalview.schemes.*;\r
+\r
import java.awt.*;\r
-import javax.swing.*;\r
+\r
import java.io.*;\r
-import java.util.*;\r
\r
+import java.util.*;\r
\r
-public class HTMLOutput\r
-{\r
- AlignViewport av;\r
- SequenceRenderer sr;\r
- Color color;\r
-\r
- public HTMLOutput(AlignViewport av)\r
- {\r
- this.av = av;\r
- sr = new SequenceRenderer(av);\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"html"},\r
- new String[]{"HTML files"},\r
- "HTML files");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save as HTML");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(null);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- try{\r
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));\r
- out.println("<HTML>");\r
- out.println("<style type=\"text/css\">");\r
- out.println("<!--");\r
- out.print("td {font-family: \""+av.getFont().getFamily()+"\", \""+av.getFont().getName()+ "\", mono; "\r
- +"font-size: "+av.getFont().getSize()+"px; ");\r
-\r
-\r
- if (av.getFont().getStyle() == Font.BOLD)\r
- out.print("font-weight: BOLD; ");\r
-\r
- if (av.getFont().getStyle() == Font.ITALIC)\r
- out.print("font-style: italic; ");\r
-\r
- out.println("text-align: center; }");\r
-\r
- out.println("-->");\r
- out.println("</style>");\r
- out.println("<BODY>");\r
-\r
-\r
- if(av.getWrapAlignment())\r
- drawWrappedAlignment(out);\r
- else\r
- drawUnwrappedAlignment(out);\r
-\r
- out.println("\n</body>\n</html>");\r
- out.close();\r
- jalview.util.BrowserLauncher.openURL( "file:///"+choice );\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\r
- }\r
- }\r
+import javax.swing.*;\r
\r
- void drawUnwrappedAlignment(PrintWriter out)\r
- {\r
\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
+public class HTMLOutput {\r
+ AlignViewport av;\r
+ SequenceRenderer sr;\r
+ Color color;\r
\r
+ public HTMLOutput(AlignViewport av) {\r
+ this.av = av;\r
+ sr = new SequenceRenderer(av);\r
\r
- //////////////\r
- SequenceGroup [] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- AlignmentI alignment = av.getAlignment();\r
- String r,g,b;\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[] { "html" },\r
+ new String[] { "HTML files" }, "HTML files");\r
\r
- // draws the top row, the measure rule\r
- out.println("<tr><td colspan=\"6\"></td>");\r
- int i=0;\r
- for(i=10; i<alignment.getWidth()-10; i+=10)\r
- out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save as HTML");\r
+ chooser.setToolTipText("Save");\r
\r
- out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");\r
- out.println("</tr>");\r
+ int value = chooser.showSaveDialog(null);\r
\r
- for (i = 0; i < alignment.getHeight(); i++)\r
- {\r
- seq = alignment.getSequenceAt(i);\r
- groups = alignment.findAllGroups( seq );\r
- if(av.getShowFullId())\r
- out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");\r
- else\r
- out.println("<tr><td nowrap>"+seq.getName()+" </td>");\r
+ if (value == JalviewFileChooser.APPROVE_OPTION) {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
+ try {\r
+ PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
+ choice));\r
+ out.println("<HTML>");\r
+ out.println("<style type=\"text/css\">");\r
+ out.println("<!--");\r
+ out.print("td {font-family: \"" + av.getFont().getFamily() +\r
+ "\", \"" + av.getFont().getName() + "\", mono; " +\r
+ "font-size: " + av.getFont().getSize() + "px; ");\r
\r
+ if (av.getFont().getStyle() == Font.BOLD) {\r
+ out.print("font-weight: BOLD; ");\r
+ }\r
\r
- for (int res = 0; res < seq.getLength(); res++)\r
- {\r
- cs = av.getGlobalColourScheme();\r
+ if (av.getFont().getStyle() == Font.ITALIC) {\r
+ out.print("font-style: italic; ");\r
+ }\r
\r
- if(groups!=null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
- {\r
- cs = groups[k].cs;\r
- break;\r
- }\r
- }\r
+ out.println("text-align: center; }");\r
\r
+ out.println("-->");\r
+ out.println("</style>");\r
+ out.println("<BODY>");\r
\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
+ if (av.getWrapAlignment()) {\r
+ drawWrappedAlignment(out);\r
+ } else {\r
+ drawUnwrappedAlignment(out);\r
+ }\r
\r
- if(color.getRGB()<-1)\r
- {\r
- out.println("<td bgcolor=\"#"\r
- + jalview.util.Format.getHexString(color)\r
- + "\">"+seq.getCharAt(res)+"</td>");\r
+ out.println("\n</body>\n</html>");\r
+ out.close();\r
+ jalview.util.BrowserLauncher.openURL("file:///" + choice);\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
}\r
- else\r
- out.println("<td>"+seq.getCharAt(res)+"</td>");\r
-\r
- }\r
-\r
- out.println("</tr>");\r
}\r
- //////////////\r
- out.println("</table>");\r
- out.println("</td></tr></table>");\r
-\r
- }\r
-\r
- void drawWrappedAlignment(PrintWriter out)\r
- {\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- AlignmentI al = av.getAlignment();\r
- SequenceGroup [] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- String r,g,b;\r
-\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
- for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())\r
- {\r
-\r
- int endRes = startRes+av.getChunkWidth();\r
- if(endRes>al.getWidth())\r
- endRes = al.getWidth();\r
-\r
- out.println("<tr>");\r
- out.println("<td colspan=\"6\"> </td>");\r
- for (int i = startRes+10; i < endRes; i += 10)\r
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-\r
- // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
- // "<br>|</td>");\r
- out.println("</tr>");\r
-\r
-\r
-\r
- for (int s = 0; s < al.getHeight(); s++)\r
- {\r
- out.println("<tr>");\r
- seq = al.getSequenceAt(s);\r
- groups = al.findAllGroups( seq );\r
- if(av.getShowFullId())\r
- out.println("<td nowrap>"+seq.getDisplayId()+" </td>");\r
- else\r
- out.println("<td nowrap>"+seq.getName()+" </td>");\r
-\r
- for (int res = startRes; res < endRes; res++)\r
- {\r
+\r
+ void drawUnwrappedAlignment(PrintWriter out) {\r
+ out.println("<table border=\"1\"><tr><td>\n");\r
+ out.println(\r
+ "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
+\r
+ //////////////\r
+ SequenceGroup[] groups;\r
+ SequenceI seq;\r
+ ColourSchemeI cs = null;\r
+ AlignmentI alignment = av.getAlignment();\r
+ String r;\r
+ String g;\r
+ String b;\r
+\r
+ // draws the top row, the measure rule\r
+ out.println("<tr><td colspan=\"6\"></td>");\r
+\r
+ int i = 0;\r
+\r
+ for (i = 10; i < (alignment.getWidth() - 10); i += 10)\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
+\r
+ out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
+ "<br>|</td>");\r
+ out.println("</tr>");\r
+\r
+ for (i = 0; i < alignment.getHeight(); i++) {\r
+ seq = alignment.getSequenceAt(i);\r
+ groups = alignment.findAllGroups(seq);\r
+\r
+ if (av.getShowFullId()) {\r
+ out.println("<tr><td nowrap>" + seq.getDisplayId() +\r
+ " </td>");\r
+ } else {\r
+ out.println("<tr><td nowrap>" + seq.getName() +\r
+ " </td>");\r
+ }\r
+\r
+ for (int res = 0; res < seq.getLength(); res++) {\r
cs = av.getGlobalColourScheme();\r
- if(groups!=null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
- {\r
- cs = groups[k].cs;\r
- break;\r
- }\r
- }\r
+\r
+ if (groups != null) {\r
+ for (int k = 0; k < groups.length; k++)\r
+ if ((groups[k].getStartRes() <= res) &&\r
+ (groups[k].getEndRes() >= res)) {\r
+ cs = groups[k].cs;\r
+\r
+ break;\r
+ }\r
+ }\r
\r
color = sr.getResidueBoxColour(cs, seq, res);\r
\r
- if(color.getRGB()<-1)\r
- {\r
- r = Integer.toHexString(color.getRed());\r
- if(r.length()<2)\r
- r = "0"+r;\r
- g = Integer.toHexString(color.getGreen());\r
- if(g.length()<2)\r
- g = "0"+g;\r
- b = Integer.toHexString(color.getBlue());\r
- if(b.length()<2)\r
- b = "0"+b;\r
- out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
+ if (color.getRGB() < -1) {\r
+ out.println("<td bgcolor=\"#" +\r
+ jalview.util.Format.getHexString(color) + "\">" +\r
+ seq.getCharAt(res) + "</td>");\r
+ } else {\r
+ out.println("<td>" + seq.getCharAt(res) + "</td>");\r
+ }\r
+ }\r
+\r
+ out.println("</tr>");\r
+ }\r
+\r
+ //////////////\r
+ out.println("</table>");\r
+ out.println("</td></tr></table>");\r
+ }\r
+\r
+ void drawWrappedAlignment(PrintWriter out) {\r
+ ////////////////////////////////////\r
+ /// How many sequences and residues can we fit on a printable page?\r
+ AlignmentI al = av.getAlignment();\r
+ SequenceGroup[] groups;\r
+ SequenceI seq;\r
+ ColourSchemeI cs = null;\r
+ String r;\r
+ String g;\r
+ String b;\r
+\r
+ out.println("<table border=\"1\"><tr><td>\n");\r
+ out.println(\r
+ "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
+\r
+ for (int startRes = 0; startRes < al.getWidth();\r
+ startRes += av.getChunkWidth()) {\r
+ int endRes = startRes + av.getChunkWidth();\r
+\r
+ if (endRes > al.getWidth()) {\r
+ endRes = al.getWidth();\r
+ }\r
+\r
+ out.println("<tr>");\r
+ out.println("<td colspan=\"6\"> </td>");\r
+\r
+ for (int i = startRes + 10; i < endRes; i += 10)\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
+\r
+ // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
+ // "<br>|</td>");\r
+ out.println("</tr>");\r
+\r
+ for (int s = 0; s < al.getHeight(); s++) {\r
+ out.println("<tr>");\r
+ seq = al.getSequenceAt(s);\r
+ groups = al.findAllGroups(seq);\r
+\r
+ if (av.getShowFullId()) {\r
+ out.println("<td nowrap>" + seq.getDisplayId() +\r
+ " </td>");\r
+ } else {\r
+ out.println("<td nowrap>" + seq.getName() +\r
+ " </td>");\r
}\r
- else\r
- out.println("<td>"+seq.getCharAt(res)+"</td>");\r
\r
- }\r
+ for (int res = startRes; res < endRes; res++) {\r
+ cs = av.getGlobalColourScheme();\r
+\r
+ if (groups != null) {\r
+ for (int k = 0; k < groups.length; k++)\r
+ if ((groups[k].getStartRes() <= res) &&\r
+ (groups[k].getEndRes() >= res)) {\r
+ cs = groups[k].cs;\r
\r
- out.println("</tr>");\r
+ break;\r
+ }\r
+ }\r
\r
- }\r
- if(endRes<al.getWidth())\r
- out.println("<tr><td height=\"5\"></td></tr>");\r
+ color = sr.getResidueBoxColour(cs, seq, res);\r
\r
+ if (color.getRGB() < -1) {\r
+ r = Integer.toHexString(color.getRed());\r
\r
+ if (r.length() < 2) {\r
+ r = "0" + r;\r
+ }\r
\r
- }\r
+ g = Integer.toHexString(color.getGreen());\r
\r
- out.println("</table>");\r
- out.println("</table>");\r
+ if (g.length() < 2) {\r
+ g = "0" + g;\r
+ }\r
\r
+ b = Integer.toHexString(color.getBlue());\r
\r
+ if (b.length() < 2) {\r
+ b = "0" + b;\r
+ }\r
\r
- }\r
+ out.println("<td bgcolor=\"#" + r + g + b + "\">" +\r
+ seq.getCharAt(res) + "</td>");\r
+ } else {\r
+ out.println("<td>" + seq.getCharAt(res) + "</td>");\r
+ }\r
+ }\r
+\r
+ out.println("</tr>");\r
+ }\r
\r
+ if (endRes < al.getWidth()) {\r
+ out.println("<tr><td height=\"5\"></td></tr>");\r
+ }\r
+ }\r
\r
+ out.println("</table>");\r
+ out.println("</table>");\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import java.io.*;\r
+\r
import java.net.*;\r
\r
-public class IdentifyFile\r
-{\r
- public static String Identify(String file, String protocol)\r
- {\r
- String reply = "PFAM";\r
- try{\r
-\r
- BufferedReader reader = null;\r
-\r
- if(protocol.equals("File"))\r
- reader = new BufferedReader(new FileReader(file));\r
-\r
- else if (protocol.equals("URL"))\r
- {\r
- reply = "URL NOT FOUND";\r
- URL url = new URL(file);\r
- reader = new BufferedReader(new InputStreamReader( url.openStream() ) );\r
- reply = "error";\r
- }\r
- else if( protocol.equals("Paste"))\r
- reader = new BufferedReader( new StringReader(file) );\r
-\r
-\r
- String data;\r
- while( (data=reader.readLine())!=null)\r
- {\r
- data = data.toUpperCase();\r
- if(data.indexOf("#")==0 || data.length()<1)\r
- continue;\r
-\r
- if(data.indexOf("PILEUP")>-1)\r
- {\r
- reply = "PileUp";\r
- break;\r
- }\r
- if((data.indexOf("//")==0)\r
- || ((data.indexOf("!!")>-1)\r
- && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT "))))\r
- {\r
- reply = "MSF";\r
- break;\r
- }\r
- else if(data.indexOf("CLUSTAL")>-1)\r
- {\r
- reply = "CLUSTAL";\r
- break;\r
- }\r
- else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)\r
- {\r
- reply = "PIR";\r
- break;\r
- }\r
- else if(data.indexOf(">")>-1)\r
- {\r
- // could be BLC file, read next line to confirm\r
- data = reader.readLine();\r
- if(data.indexOf(">")>-1)\r
- reply = "BLC";\r
- else\r
- reply = "FASTA";\r
-\r
- break;\r
- }\r
- }\r
- reader.close();\r
- }\r
- catch(Exception ex){\r
- System.err.println("File Identification failed!\n"+ex);}\r
\r
- return reply;\r
- }\r
+public class IdentifyFile {\r
+ public static String Identify(String file, String protocol) {\r
+ String reply = "PFAM";\r
+\r
+ try {\r
+ BufferedReader reader = null;\r
+\r
+ if (protocol.equals("File")) {\r
+ reader = new BufferedReader(new FileReader(file));\r
+ }\r
+ else if (protocol.equals("URL")) {\r
+ reply = "URL NOT FOUND";\r
+\r
+ URL url = new URL(file);\r
+ reader = new BufferedReader(new InputStreamReader(\r
+ url.openStream()));\r
+ reply = "error";\r
+ } else if (protocol.equals("Paste")) {\r
+ reader = new BufferedReader(new StringReader(file));\r
+ }\r
+\r
+ String data;\r
\r
+ while ((data = reader.readLine()) != null) {\r
+ data = data.toUpperCase();\r
\r
+ if ((data.indexOf("#") == 0) || (data.length() < 1)) {\r
+ continue;\r
+ }\r
+\r
+ if (data.indexOf("PILEUP") > -1) {\r
+ reply = "PileUp";\r
+\r
+ break;\r
+ }\r
+\r
+ if ((data.indexOf("//") == 0) ||\r
+ ((data.indexOf("!!") > -1) &&\r
+ (data.indexOf("!!") < data.indexOf(\r
+ "_MULTIPLE_ALIGNMENT ")))) {\r
+ reply = "MSF";\r
+\r
+ break;\r
+ } else if (data.indexOf("CLUSTAL") > -1) {\r
+ reply = "CLUSTAL";\r
+\r
+ break;\r
+ } else if ((data.indexOf(">P1;") > -1) ||\r
+ (data.indexOf(">DL;") > -1)) {\r
+ reply = "PIR";\r
+\r
+ break;\r
+ } else if (data.indexOf(">") > -1) {\r
+ // could be BLC file, read next line to confirm\r
+ data = reader.readLine();\r
+\r
+ if (data.indexOf(">") > -1) {\r
+ reply = "BLC";\r
+ } else {\r
+ reply = "FASTA";\r
+ }\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ reader.close();\r
+ } catch (Exception ex) {\r
+ System.err.println("File Identification failed!\n" + ex);\r
+ }\r
+\r
+ return reply;\r
+ }\r
}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
+*/\r
+\r
/**
* PredFile.java
* JalviewX / Vamsas Project
* JPred.seq.concise reader
- */
-
-package jalview.io;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-import java.io.*;
-import java.util.*;
-
-public class JPredFile
- extends AlignFile
-{
- Vector ids;
- Vector conf;
- Hashtable Scores; // Hash of names and score vectors
- Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
- private int QuerySeqPosition;
- public void setQuerySeqPosition(int QuerySeqPosition)
- {
- this.QuerySeqPosition = QuerySeqPosition;
- }
-
- public int getQuerySeqPosition()
- {
- return QuerySeqPosition;
- }
- public Hashtable getScores() {
- return Scores;
- }
- public Hashtable getSymscores() {
- return Symscores;
- }
-
- public JPredFile(String inStr)
- {
- super(inStr);
- }
-
- public void initData()
- {
-
- super.initData();
- Scores = new Hashtable();
- ids = null;
- conf = null;
- }
-
- public JPredFile(String inFile, String type)
- throws IOException
- {
-
- super(inFile, type);
- }
+ */\r
+package jalview.io;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import jalview.util.*;\r
+\r
+import java.io.*;\r
+\r
+import java.util.*;\r
+\r
+\r
+public class JPredFile extends AlignFile {\r
+ Vector ids;\r
+ Vector conf;\r
+ Hashtable Scores; // Hash of names and score vectors\r
+ Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector\r
+ private int QuerySeqPosition;\r
+\r
+ public JPredFile(String inStr) {\r
+ super(inStr);\r
+ }\r
+\r
+ public JPredFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public void setQuerySeqPosition(int QuerySeqPosition) {\r
+ this.QuerySeqPosition = QuerySeqPosition;\r
+ }\r
+\r
+ public int getQuerySeqPosition() {\r
+ return QuerySeqPosition;\r
+ }\r
+\r
+ public Hashtable getScores() {\r
+ return Scores;\r
+ }\r
+\r
+ public Hashtable getSymscores() {\r
+ return Symscores;\r
+ }\r
+\r
+ public void initData() {\r
+ super.initData();\r
+ Scores = new Hashtable();\r
+ ids = null;\r
+ conf = null;\r
+ }\r
+\r
+ /**
+ * parse a JPred concise file into a sequence-alignment like object.
+ */\r
+ public void parse() throws IOException {\r
+ // JBPNote log.System.out.println("all read in ");\r
+ String line;\r
+ QuerySeqPosition = -1;\r
+ noSeqs = 0;\r
+\r
+ Vector seq_entries = new Vector();\r
+ Vector ids = new Vector();\r
+ Hashtable Symscores = new Hashtable();\r
+\r
+ while ((line = nextLine()) != null) {\r
+ // Concise format allows no comments or non comma-formatted data\r
+ StringTokenizer str = new StringTokenizer(line, ":");\r
+ String id = "";\r
+\r
+ if (!str.hasMoreTokens()) {\r
+ continue;\r
+ }\r
+\r
+ id = str.nextToken();\r
+\r
+ String seqsym = str.nextToken();\r
+ StringTokenizer symbols = new StringTokenizer(seqsym, ",");\r
+\r
+ // decide if we have more than just alphanumeric symbols\r
+ int numSymbols = symbols.countTokens();\r
+\r
+ if (numSymbols == 0) {\r
+ continue;\r
+ }\r
+\r
+ if (seqsym.length() != (2 * numSymbols)) {\r
+ // Set of scalars for some property\r
+ if (Scores.containsKey(id)) {\r
+ int i = 1;\r
+\r
+ while (Scores.containsKey(id + "_" + i)) {\r
+ i++;\r
+ }\r
+\r
+ id = id + "_" + i;\r
+ }\r
+\r
+ Vector scores = new Vector();\r
+\r
+ // Typecheck from first entry\r
+ int i = 0;\r
+ String ascore = "dead";\r
+\r
+ try {\r
+ // store elements as floats...\r
+ while (symbols.hasMoreTokens()) {\r
+ ascore = symbols.nextToken();\r
+\r
+ Float score = new Float(ascore);\r
+ scores.addElement((Object) score);\r
+ }\r
+\r
+ Scores.put(id, scores);\r
+ } catch (Exception e) {\r
+ // or just keep them as strings\r
+ i = scores.size();\r
+\r
+ for (int j = 0; j < i; j++) {\r
+ scores.set(j,\r
+ (Object) ((Float) scores.get(j)).toString());\r
+ }\r
+\r
+ scores.addElement((Object) ascore);\r
+\r
+ while (symbols.hasMoreTokens()) {\r
+ ascore = symbols.nextToken();\r
+ scores.addElement((Object) ascore);\r
+ }\r
+\r
+ Scores.put(id, scores);\r
+ }\r
+ } else if (id.equals("jnetconf")) {\r
+ // log.debug System.out.println("here");\r
+ id = "Prediction Confidence";\r
+ this.conf = new Vector(numSymbols);\r
+\r
+ for (int i = 0; i < numSymbols; i++) {\r
+ conf.set(i, (Object) symbols.nextToken());\r
+ }\r
+ } else {\r
+ // Sequence or a prediction string (rendered as sequence)\r
+ StringBuffer newseq = new StringBuffer();\r
+\r
+ for (int i = 0; i < numSymbols; i++) {\r
+ newseq.append(symbols.nextToken());\r
+ }\r
+\r
+ if (id.indexOf(";") > -1) {\r
+ seq_entries.addElement(newseq);\r
+\r
+ int i = 1;\r
+ String name = id.substring(id.indexOf(";") + 1);\r
+\r
+ while (ids.lastIndexOf(name) > -1) {\r
+ name = id.substring(id.indexOf(";") + 1) + "_" + 1;\r
+ }\r
+\r
+ ids.addElement(name);\r
+\r
+ noSeqs++;\r
+ } else {\r
+ if (id.equals("JNETPRED")) {\r
+ id = "Predicted Secondary Structure";\r
+ }\r
+\r
+ seq_entries.addElement(newseq.toString());\r
+ ids.addElement(id);\r
+ Symscores.put((Object) id,\r
+ (Object) new Integer(ids.size() - 1));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (noSeqs < 1) {\r
+ throw new IOException(\r
+ "JpredFile Parser: No sequence in the prediction!");\r
+ }\r
+\r
+ maxLength = seq_entries.elementAt(0).toString().length();\r
+\r
+ for (int i = 0; i < ids.size(); i++) {\r
+ // Add all sequence like objects\r
+ Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
+ seq_entries.elementAt(i).toString(), 1,\r
+ seq_entries.elementAt(i).toString().length());\r
+\r
+ if (!Symscores.containsKey(ids.elementAt(i)) &&\r
+ !isValidProteinSequence(newSeq.getSequence())) {\r
+ throw new IOException(\r
+ "JPredConcise: Not a valid protein sequence - (" +\r
+ ids.elementAt(i).toString() + ")");\r
+ }\r
+\r
+ if (maxLength != seq_entries.elementAt(i).toString().length()) {\r
+ throw new IOException("JPredConcise: Entry (" +\r
+ ids.elementAt(i).toString() +\r
+ ") has an unexpected number of columns");\r
+ }\r
+\r
+ if (newSeq.getName().startsWith("QUERY") &&\r
+ (QuerySeqPosition == -1)) {\r
+ QuerySeqPosition = seqs.size();\r
+ }\r
+\r
+ seqs.addElement(newSeq);\r
+ }\r
+ }\r
+\r
+ /**
+ * print
+ *
+ * @return String
+ */\r
+ public String print() {\r
+ return "Not Supported";\r
+ }\r
+\r
+ public static void main(String[] args) {\r
+ try {\r
+ JPredFile blc = new JPredFile(args[0], "File");\r
+\r
+ for (int i = 0; i < blc.seqs.size(); i++) {\r
+ System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() +\r
+ "\n" + ((Sequence) blc.seqs.elementAt(i)).getSequence() +\r
+ "\n");\r
+ }\r
+ } catch (java.io.IOException e) {\r
+ System.err.println("Exception " + e);\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+}\r
+\r
+\r
+/*
+ StringBuffer out = new StringBuffer();
+
+ out.append("START PRED\n");
+ for (int i = 0; i < s[0].sequence.length(); i++)
+ {
+ out.append(s[0].sequence.substring(i, i + 1) + " ");
+ out.append(s[1].sequence.substring(i, i + 1) + " ");
+ out.append(s[1].score[0].elementAt(i) + " ");
+ out.append(s[1].score[1].elementAt(i) + " ");
+ out.append(s[1].score[2].elementAt(i) + " ");
+ out.append(s[1].score[3].elementAt(i) + " ");
+
+ out.append("\n");
+ }
+ out.append("END PRED\n");
+ return out.toString();
+ }
- /**
- * parse a JPred concise file into a sequence-alignment like object.
- */
- public void parse()
- throws IOException
+ public static void main(String[] args)
+ {
+ try
{
- // JBPNote log.System.out.println("all read in ");
- String line;
- QuerySeqPosition = -1;
- noSeqs = 0;
- Vector seq_entries = new Vector();
- Vector ids = new Vector();
- Hashtable Symscores = new Hashtable();
- while ( (line = nextLine()) != null)
+ BLCFile blc = new BLCFile(args[0], "File");
+ DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
+ for (int i = 0; i < blc.seqs.size(); i++)
{
- // Concise format allows no comments or non comma-formatted data
- StringTokenizer str = new StringTokenizer(line, ":");
- String id = "";
- if (!str.hasMoreTokens())
- {
- continue;
- }
-
- id = str.nextToken();
- String seqsym = str.nextToken();
- StringTokenizer symbols = new StringTokenizer(seqsym, ",");
- // decide if we have more than just alphanumeric symbols
- int numSymbols = symbols.countTokens();
-
- if (numSymbols==0) {
- continue;
- }
-
- if (seqsym.length() != (2 * numSymbols))
- {
- // Set of scalars for some property
- if (Scores.containsKey(id))
- {
- int i = 1;
- while (Scores.containsKey(id + "_" + i))
- {
- i++;
- }
- id = id + "_" + i;
- }
- Vector scores = new Vector();
- // Typecheck from first entry
- int i = 0;
- String ascore="dead";
- try
- {
- // store elements as floats...
- while (symbols.hasMoreTokens()) {
- ascore = symbols.nextToken();
- Float score = new Float(ascore);
- scores.addElement( (Object) score);
- }
- Scores.put(id, scores);
- }
- catch (Exception e)
- {
- // or just keep them as strings
- i = scores.size();
- for (int j = 0; j < i; j++)
- {
- scores.set(j,
- (Object) ( (Float) scores.get(j)).toString());
- }
- scores.addElement((Object) ascore);
- while (symbols.hasMoreTokens()) {
- {
- ascore = symbols.nextToken();
- scores.addElement( (Object) ascore);
- }
- }
- Scores.put(id, scores);
- }
- }
- else if (id.equals("jnetconf"))
- {
- // log.debug System.out.println("here");
- id = "Prediction Confidence";
- this.conf = new Vector(numSymbols);
- for (int i = 0; i < numSymbols; i++)
- {
- conf.set(i, (Object) symbols.nextToken());
- }
- }
- else
- {
- // Sequence or a prediction string (rendered as sequence)
-
- StringBuffer newseq = new StringBuffer();
-
- for (int i = 0; i < numSymbols; i++) {
- newseq.append(symbols.nextToken());
- }
-
- if (id.indexOf(";") > -1) {
- seq_entries.addElement(newseq);
- int i=1;
- String name = id.substring(id.indexOf(";")+1);
- while (ids.lastIndexOf(name)>-1) {
- name = id.substring(id.indexOf(";")+1)+"_"+1;
- }
- ids.addElement(name);
-
- noSeqs++;
- }
- else
- {
- if (id.equals("JNETPRED")) {
- id = "Predicted Secondary Structure";
- }
- seq_entries.addElement( newseq.toString() );
- ids.addElement(id);
- Symscores.put((Object) id, (Object) new Integer(ids.size()-1));
- }
- }
- }
-
-
- if (noSeqs < 1)
- {
- throw new IOException(
- "JpredFile Parser: No sequence in the prediction!");
+ s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
}
- maxLength = seq_entries.elementAt(0).toString().length();
- for (int i = 0; i < ids.size(); i++)
- {
- // Add all sequence like objects
-
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
- seq_entries.elementAt(i).toString(), 1,
- seq_entries.elementAt(i).toString().
- length());
- if (!Symscores.containsKey(ids.elementAt(i))
- && !isValidProteinSequence(newSeq.getSequence()))
- {
- throw new IOException(
- "JPredConcise: Not a valid protein sequence - ("
- + ids.elementAt(i).toString() + ")");
- }
+ String out = BLCFile.print(s);
- if (maxLength != seq_entries.elementAt(i).toString().length())
- {
- throw new IOException("JPredConcise: Entry (" +
- ids.elementAt(i).toString()
- + ") has an unexpected number of columns");
- }
- if (newSeq.getName().startsWith("QUERY") && QuerySeqPosition==-1) {
- QuerySeqPosition = seqs.size();
- }
-
- seqs.addElement(newSeq);
-
- }
+ AlignFrame af = new AlignFrame(null, s);
+ af.resize(700, 500);
+ af.show();
+ System.out.println(out);
}
-
- /**
- * print
- *
- * @return String
- */
-
- public String print()
- {
- return "Not Supported";
- }
-
- public static void main(String[] args)
- {
- try
- {
- JPredFile blc = new JPredFile(args[0], "File");
- for (int i = 0; i < blc.seqs.size(); i++)
- {
- System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName()
- + "\n" +
- ( (Sequence) blc.seqs.elementAt(i)).getSequence()
- + "\n");
- }
- }
- catch (java.io.IOException e)
- {
- System.err.println("Exception " + e);
- e.printStackTrace();
- }
- }
+ catch (java.io.IOException e)
+ {
+ System.out.println("Exception " + e);
}
+ }
- /*
- StringBuffer out = new StringBuffer();
-
- out.append("START PRED\n");
- for (int i = 0; i < s[0].sequence.length(); i++)
- {
- out.append(s[0].sequence.substring(i, i + 1) + " ");
- out.append(s[1].sequence.substring(i, i + 1) + " ");
- out.append(s[1].score[0].elementAt(i) + " ");
- out.append(s[1].score[1].elementAt(i) + " ");
- out.append(s[1].score[2].elementAt(i) + " ");
- out.append(s[1].score[3].elementAt(i) + " ");
-
- out.append("\n");
- }
- out.append("END PRED\n");
- return out.toString();
- }
-
- public static void main(String[] args)
- {
- try
- {
- BLCFile blc = new BLCFile(args[0], "File");
- DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
- for (int i = 0; i < blc.seqs.size(); i++)
- {
- s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
- }
- String out = BLCFile.print(s);
-
- AlignFrame af = new AlignFrame(null, s);
- af.resize(700, 500);
- af.show();
- System.out.println(out);
- }
- catch (java.io.IOException e)
- {
- System.out.println("Exception " + e);
- }
- }
-
- }
- */
+ }
+ */\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
-\r
/*///////////////////////////////////////////////////////////////////\r
// This file was taken from java forum\r
// Re: JFileChooser functioning like normal Windows Apps FileChooser\r
// Author: ddanimal\r
// http://forum.java.sun.com/thread.jspa?forumID=57&threadID=327712\r
-*///////////////////////////////////////////////////////////////////\r
+*/\r
\r
+//////////////////////////////////////////////////////////////////\r
package jalview.io;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
+\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
import javax.swing.*;\r
import javax.swing.plaf.metal.*;\r
import javax.swing.table.*;\r
\r
-public class JalviewFileChooser extends JFileChooser\r
-{\r
-\r
- private static final int COLUMN_FILENAME = 0;\r
- private static final int COLUMN_FILESIZE = 1;\r
- private static final int COLUMN_FILETYPE = 2;\r
- private static final int COLUMN_FILEDATE = 3;\r
- private static final int COLUMN_FILEATTR = 4;\r
- private static final int COLUMN_COLCOUNT = 5;\r
- private static String[] COLUMNS = null;\r
-\r
-\r
- public JalviewFileChooser(String dir, String [] suffix, String [] desc, String selected)\r
- {\r
- super(dir);\r
-\r
- JalviewFileFilter chosen = null;\r
- for(int i=0; i<suffix.length; i++)\r
- {\r
- JalviewFileFilter jvf = new JalviewFileFilter(suffix[i], desc[i]);\r
- addChoosableFileFilter(jvf);\r
- if(selected!=null && selected.equalsIgnoreCase(desc[i]))\r
- chosen = jvf;\r
+\r
+public class JalviewFileChooser extends JFileChooser {\r
+ private static final int COLUMN_FILENAME = 0;\r
+ private static final int COLUMN_FILESIZE = 1;\r
+ private static final int COLUMN_FILETYPE = 2;\r
+ private static final int COLUMN_FILEDATE = 3;\r
+ private static final int COLUMN_FILEATTR = 4;\r
+ private static final int COLUMN_COLCOUNT = 5;\r
+ private static String[] COLUMNS = null;\r
+\r
+ public JalviewFileChooser(String dir, String[] suffix, String[] desc,\r
+ String selected) {\r
+ super(dir);\r
+\r
+ JalviewFileFilter chosen = null;\r
+\r
+ for (int i = 0; i < suffix.length; i++) {\r
+ JalviewFileFilter jvf = new JalviewFileFilter(suffix[i], desc[i]);\r
+ addChoosableFileFilter(jvf);\r
+\r
+ if ((selected != null) && selected.equalsIgnoreCase(desc[i])) {\r
+ chosen = jvf;\r
+ }\r
+ }\r
+\r
+ if (chosen != null) {\r
+ setFileFilter(chosen);\r
+ }\r
+\r
+ initColumns();\r
}\r
- if(chosen!=null)\r
- setFileFilter(chosen);\r
- initColumns();\r
- }\r
-\r
- public String getSelectedFormat()\r
- {\r
-\r
- String format = getFileFilter().getDescription();\r
-\r
- if (format.toUpperCase().startsWith("JALVIEW"))\r
- format = "Jalview";\r
- else if (format.toUpperCase().startsWith("FASTA"))\r
- format = "FASTA";\r
- else if (format.toUpperCase().startsWith("MSF"))\r
- format = "MSF";\r
- else if (format.toUpperCase().startsWith("CLUSTAL"))\r
- format = "CLUSTAL";\r
- else if (format.toUpperCase().startsWith("BLC"))\r
- format = "BLC";\r
- else if (format.toUpperCase().startsWith("PIR"))\r
- format = "PIR";\r
- else if (format.toUpperCase().startsWith("PFAM"))\r
- format = "PFAM";\r
-\r
- return format;\r
- }\r
- public JalviewFileChooser(String dir)\r
- {\r
- super(dir);\r
- initColumns();\r
- }\r
-\r
- public int showSaveDialog(Component parent) throws HeadlessException {\r
- setDialogType(SAVE_DIALOG);\r
- int ret = showDialog(parent, null);\r
-\r
- if(getFileFilter() instanceof JalviewFileFilter)\r
- {\r
- JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();\r
- if (!jvf.accept(getSelectedFile()))\r
- {\r
- String withExtension = getSelectedFile() + "." + jvf.getAcceptableExtension();\r
- setSelectedFile(new File(withExtension));\r
+\r
+ public JalviewFileChooser(String dir) {\r
+ super(dir);\r
+ initColumns();\r
+ }\r
+\r
+ public String getSelectedFormat() {\r
+ String format = getFileFilter().getDescription();\r
+\r
+ if (format.toUpperCase().startsWith("JALVIEW")) {\r
+ format = "Jalview";\r
+ } else if (format.toUpperCase().startsWith("FASTA")) {\r
+ format = "FASTA";\r
+ } else if (format.toUpperCase().startsWith("MSF")) {\r
+ format = "MSF";\r
+ } else if (format.toUpperCase().startsWith("CLUSTAL")) {\r
+ format = "CLUSTAL";\r
+ } else if (format.toUpperCase().startsWith("BLC")) {\r
+ format = "BLC";\r
+ } else if (format.toUpperCase().startsWith("PIR")) {\r
+ format = "PIR";\r
+ } else if (format.toUpperCase().startsWith("PFAM")) {\r
+ format = "PFAM";\r
}\r
- }\r
-\r
- if(ret == JalviewFileChooser.APPROVE_OPTION && getSelectedFile().exists() )\r
- {\r
- int confirm = JOptionPane.showConfirmDialog(parent,\r
- "Overwrite existing file?",\r
- "File exists",\r
- JOptionPane.YES_NO_OPTION);\r
- if(confirm!=JOptionPane.YES_OPTION)\r
- ret = this.CANCEL_OPTION;\r
- }\r
- return ret;\r
- }\r
-\r
-\r
- void initColumns()\r
- {\r
- if (COLUMNS == null)\r
- {\r
- Locale l = getLocale();\r
- COLUMNS = new String[]{\r
- UIManager.getString("FileChooser.fileNameHeaderText",l),\r
- UIManager.getString("FileChooser.fileSizeHeaderText",l),\r
- UIManager.getString("FileChooser.fileTypeHeaderText",l),\r
- UIManager.getString("FileChooser.fileDateHeaderText",l),\r
- UIManager.getString("FileChooser.fileAttrHeaderText",l)\r
- };\r
+\r
+ return format;\r
}\r
- }\r
-\r
- /**************************************************************************\r
- * Always create the local UI\r
- * @param comp\r
- *************************************************************************/\r
- public final void setUI(ComponentUI comp)\r
- {\r
- super.setUI(new UI(this));\r
- }\r
-\r
- /**************************************************************************\r
- * Internal implementation of Metal LookAndFeel to create the table sorting\r
- * ability.\r
- *************************************************************************/\r
- private final static class UI extends MetalFileChooserUI\r
- {\r
- private DirectoryModel model;\r
-\r
- /**************************************************************************\r
- * Must be overridden to extend\r
- * @param e\r
- *************************************************************************/\r
- public UI(JFileChooser e)\r
- {\r
- super(e);\r
- }\r
-\r
- /**************************************************************************\r
- * Overridden to create our own model\r
- *************************************************************************/\r
- protected final void createModel()\r
- {\r
- model = new DirectoryModel(getFileChooser());\r
- }\r
-\r
- /**************************************************************************\r
- * Overridden to get our own model\r
- * @return\r
- *************************************************************************/\r
- public final BasicDirectoryModel getModel() { return model; }\r
-\r
- /**************************************************************************\r
- * Calls the default method then adds a MouseListener to the JTable\r
- * @param chooser\r
- * @return\r
- *************************************************************************/\r
- protected final JPanel createDetailsView(JFileChooser chooser)\r
- {\r
- final JPanel panel = super.createDetailsView(chooser);\r
-\r
- //Since we can't access MetalFileChooserUI's private member detailsTable\r
- //directly, we have to find it in the JPanel\r
- final JTable tbl = findJTable(panel.getComponents());\r
- if (tbl != null)\r
- {\r
- //Fix the columns so they can't be rearranged, if we don't do this\r
- //we would need to keep track when each column is moved\r
- tbl.getTableHeader().setReorderingAllowed(false);\r
-\r
- //Add a mouselistener to listen for clicks on column headers\r
- tbl.getTableHeader().addMouseListener(new MouseAdapter(){\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- //Only process single clicks\r
- if (e.getClickCount() > 1) return;\r
- e.consume();\r
- final int col = tbl.getTableHeader().columnAtPoint(e.getPoint());\r
- if (col == COLUMN_FILENAME || col == COLUMN_FILESIZE ||\r
- col == COLUMN_FILEDATE)\r
- model.sort(col,tbl);\r
- }\r
- });\r
- }\r
- return panel;\r
- }\r
-\r
- /**************************************************************************\r
- * Finds the JTable in the panel so we can add MouseListener\r
- * @param comp\r
- * @return\r
- *************************************************************************/\r
- private final static JTable findJTable(Component[] comp)\r
- {\r
- for (int i=0;i<comp.length;i++)\r
- {\r
- if (comp[i] instanceof JTable)\r
- {\r
- return (JTable)comp[i];\r
- }\r
- if (comp[i] instanceof Container)\r
- {\r
- JTable tbl = findJTable(((Container)comp[i]).getComponents());\r
- if (tbl != null) return tbl;\r
- }\r
- }\r
- return null;\r
- }\r
- }\r
-\r
- /***************************************************************************\r
- * Implementation of BasicDirectoryModel that sorts the Files by column\r
- **************************************************************************/\r
- private final static class DirectoryModel extends BasicDirectoryModel\r
- {\r
- int col = 0;\r
- boolean ascending;\r
-\r
- /**************************************************************************\r
- * Must be overridden to extend BasicDirectoryModel\r
- * @param chooser\r
- *************************************************************************/\r
- DirectoryModel(JFileChooser chooser)\r
- {\r
- super(chooser);\r
- }\r
-\r
-\r
- /**************************************************************************\r
- * Supposedly this is not used anymore, hopefully not. We implemented\r
- * some basic attempt at sorting just in case\r
- * @param a\r
- * @param b\r
- * @return\r
- *************************************************************************/\r
- protected final boolean lt(File a, File b)\r
- {\r
- System.out.println("DEBUG:LT called?");\r
- boolean less = false;\r
- switch (col)\r
- {\r
- case COLUMN_FILEDATE:\r
- less = a.lastModified() > b.lastModified();\r
- break;\r
- case COLUMN_FILESIZE:\r
- less = a.length() > b.length();\r
- break;\r
- default:\r
- less = a.getName().compareToIgnoreCase(b.getName()) > 0;\r
- break;\r
- }\r
- if (ascending) return less = !less;\r
- return less;\r
- }\r
-\r
- /**************************************************************************\r
- * Resorts the JFileChooser table based on new column\r
- * @param c\r
- *************************************************************************/\r
- protected final void sort(int c, JTable tbl)\r
- {\r
- //Set column and order\r
- col = c;\r
- ascending = !ascending;\r
- String indicator = " (^)";\r
- if (ascending)\r
- indicator = " (v)";\r
-\r
- final JTableHeader th = tbl.getTableHeader();\r
- final TableColumnModel tcm = th.getColumnModel();\r
-\r
- for (int i=0;i<JalviewFileChooser.COLUMN_COLCOUNT;i++)\r
- {\r
- final TableColumn tc = tcm.getColumn( i ); // the column to change\r
- tc.setHeaderValue( COLUMNS[i] );\r
- }\r
-\r
- final TableColumn tc = tcm.getColumn( col ); // the column to change\r
- tc.setHeaderValue( COLUMNS[col] + indicator );\r
-\r
- th.repaint();\r
-\r
- //Requery the file listing\r
- validateFileCache();\r
- }\r
-\r
- /**************************************************************************\r
- * Sorts the data based on current column setting\r
- * @param data\r
- *************************************************************************/\r
- protected final void sort(Vector data)\r
- {\r
- switch (col)\r
- {\r
- case COLUMN_FILEDATE:\r
- Collections.sort(data,new Comparator(){\r
- public int compare(Object o1,Object o2)\r
- {\r
- int ret = 1;\r
- final File a = (File)o1;\r
- final File b = (File)o2;\r
- if (a.lastModified() > b.lastModified())\r
- ret = -1;\r
- else if (a.lastModified() == b.lastModified())\r
- ret = 0;\r
-\r
- if (ascending)\r
- ret *= -1;\r
- return ret;\r
- }\r
-\r
- });\r
- break;\r
- case COLUMN_FILESIZE:\r
- Collections.sort(data,new Comparator(){\r
- public int compare(Object o1,Object o2)\r
- {\r
- int ret = 1;\r
- final File a = (File)o1;\r
- final File b = (File)o2;\r
- if (a.length() > b.length())\r
- ret = -1;\r
- else if (a.length() == b.length())\r
- ret = 0;\r
-\r
- if (ascending)\r
- ret *= -1;\r
- return ret;\r
- }\r
-\r
- });\r
- break;\r
- case COLUMN_FILENAME:\r
- Collections.sort(data,new Comparator(){\r
- public int compare(Object o1,Object o2)\r
- {\r
- final File a = (File)o1;\r
- final File b = (File)o2;\r
- if (ascending)\r
- return a.getName().compareToIgnoreCase(b.getName());\r
- else\r
- return -1 * a.getName().compareToIgnoreCase(b.getName());\r
- }\r
-\r
- });\r
- break;\r
- }\r
- }\r
- }\r
-}\r
\r
+ public int showSaveDialog(Component parent) throws HeadlessException {\r
+ setDialogType(SAVE_DIALOG);\r
+\r
+ int ret = showDialog(parent, null);\r
+\r
+ if (getFileFilter() instanceof JalviewFileFilter) {\r
+ JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();\r
+\r
+ if (!jvf.accept(getSelectedFile())) {\r
+ String withExtension = getSelectedFile() + "." +\r
+ jvf.getAcceptableExtension();\r
+ setSelectedFile(new File(withExtension));\r
+ }\r
+ }\r
+\r
+ if ((ret == JalviewFileChooser.APPROVE_OPTION) &&\r
+ getSelectedFile().exists()) {\r
+ int confirm = JOptionPane.showConfirmDialog(parent,\r
+ "Overwrite existing file?", "File exists",\r
+ JOptionPane.YES_NO_OPTION);\r
+\r
+ if (confirm != JOptionPane.YES_OPTION) {\r
+ ret = this.CANCEL_OPTION;\r
+ }\r
+ }\r
+\r
+ return ret;\r
+ }\r
+\r
+ void initColumns() {\r
+ if (COLUMNS == null) {\r
+ Locale l = getLocale();\r
+ COLUMNS = new String[] {\r
+ UIManager.getString("FileChooser.fileNameHeaderText", l),\r
+ UIManager.getString("FileChooser.fileSizeHeaderText", l),\r
+ UIManager.getString("FileChooser.fileTypeHeaderText", l),\r
+ UIManager.getString("FileChooser.fileDateHeaderText", l),\r
+ UIManager.getString("FileChooser.fileAttrHeaderText", l)\r
+ };\r
+ }\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Always create the local UI\r
+ * @param comp\r
+ *************************************************************************/\r
+ public final void setUI(ComponentUI comp) {\r
+ super.setUI(new UI(this));\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Internal implementation of Metal LookAndFeel to create the table sorting\r
+ * ability.\r
+ *************************************************************************/\r
+ private final static class UI extends MetalFileChooserUI {\r
+ private DirectoryModel model;\r
+\r
+ /**************************************************************************\r
+ * Must be overridden to extend\r
+ * @param e\r
+ *************************************************************************/\r
+ public UI(JFileChooser e) {\r
+ super(e);\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Overridden to create our own model\r
+ *************************************************************************/\r
+ protected final void createModel() {\r
+ model = new DirectoryModel(getFileChooser());\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Overridden to get our own model\r
+ * @return\r
+ *************************************************************************/\r
+ public final BasicDirectoryModel getModel() {\r
+ return model;\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Calls the default method then adds a MouseListener to the JTable\r
+ * @param chooser\r
+ * @return\r
+ *************************************************************************/\r
+ protected final JPanel createDetailsView(JFileChooser chooser) {\r
+ final JPanel panel = super.createDetailsView(chooser);\r
+\r
+ //Since we can't access MetalFileChooserUI's private member detailsTable\r
+ //directly, we have to find it in the JPanel\r
+ final JTable tbl = findJTable(panel.getComponents());\r
+\r
+ if (tbl != null) {\r
+ //Fix the columns so they can't be rearranged, if we don't do this\r
+ //we would need to keep track when each column is moved\r
+ tbl.getTableHeader().setReorderingAllowed(false);\r
+\r
+ //Add a mouselistener to listen for clicks on column headers\r
+ tbl.getTableHeader().addMouseListener(new MouseAdapter() {\r
+ public void mouseClicked(MouseEvent e) {\r
+ //Only process single clicks\r
+ if (e.getClickCount() > 1) {\r
+ return;\r
+ }\r
+\r
+ e.consume();\r
+\r
+ final int col = tbl.getTableHeader().columnAtPoint(e.getPoint());\r
+\r
+ if ((col == COLUMN_FILENAME) ||\r
+ (col == COLUMN_FILESIZE) ||\r
+ (col == COLUMN_FILEDATE)) {\r
+ model.sort(col, tbl);\r
+ }\r
+ }\r
+ });\r
+ }\r
+\r
+ return panel;\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Finds the JTable in the panel so we can add MouseListener\r
+ * @param comp\r
+ * @return\r
+ *************************************************************************/\r
+ private final static JTable findJTable(Component[] comp) {\r
+ for (int i = 0; i < comp.length; i++) {\r
+ if (comp[i] instanceof JTable) {\r
+ return (JTable) comp[i];\r
+ }\r
+\r
+ if (comp[i] instanceof Container) {\r
+ JTable tbl = findJTable(((Container) comp[i]).getComponents());\r
+\r
+ if (tbl != null) {\r
+ return tbl;\r
+ }\r
+ }\r
+ }\r
+\r
+ return null;\r
+ }\r
+ }\r
+\r
+ /***************************************************************************\r
+ * Implementation of BasicDirectoryModel that sorts the Files by column\r
+ **************************************************************************/\r
+ private final static class DirectoryModel extends BasicDirectoryModel {\r
+ int col = 0;\r
+ boolean ascending;\r
+\r
+ /**************************************************************************\r
+ * Must be overridden to extend BasicDirectoryModel\r
+ * @param chooser\r
+ *************************************************************************/\r
+ DirectoryModel(JFileChooser chooser) {\r
+ super(chooser);\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Supposedly this is not used anymore, hopefully not. We implemented\r
+ * some basic attempt at sorting just in case\r
+ * @param a\r
+ * @param b\r
+ * @return\r
+ *************************************************************************/\r
+ protected final boolean lt(File a, File b) {\r
+ System.out.println("DEBUG:LT called?");\r
+\r
+ boolean less = false;\r
+\r
+ switch (col) {\r
+ case COLUMN_FILEDATE:\r
+ less = a.lastModified() > b.lastModified();\r
+\r
+ break;\r
+\r
+ case COLUMN_FILESIZE:\r
+ less = a.length() > b.length();\r
+\r
+ break;\r
+\r
+ default:\r
+ less = a.getName().compareToIgnoreCase(b.getName()) > 0;\r
+\r
+ break;\r
+ }\r
+\r
+ if (ascending) {\r
+ return less = !less;\r
+ }\r
+\r
+ return less;\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Resorts the JFileChooser table based on new column\r
+ * @param c\r
+ *************************************************************************/\r
+ protected final void sort(int c, JTable tbl) {\r
+ //Set column and order\r
+ col = c;\r
+ ascending = !ascending;\r
+\r
+ String indicator = " (^)";\r
+\r
+ if (ascending) {\r
+ indicator = " (v)";\r
+ }\r
+\r
+ final JTableHeader th = tbl.getTableHeader();\r
+ final TableColumnModel tcm = th.getColumnModel();\r
+\r
+ for (int i = 0; i < JalviewFileChooser.COLUMN_COLCOUNT; i++) {\r
+ final TableColumn tc = tcm.getColumn(i); // the column to change\r
+ tc.setHeaderValue(COLUMNS[i]);\r
+ }\r
+\r
+ final TableColumn tc = tcm.getColumn(col); // the column to change\r
+ tc.setHeaderValue(COLUMNS[col] + indicator);\r
+\r
+ th.repaint();\r
+\r
+ //Requery the file listing\r
+ validateFileCache();\r
+ }\r
+\r
+ /**************************************************************************\r
+ * Sorts the data based on current column setting\r
+ * @param data\r
+ *************************************************************************/\r
+ protected final void sort(Vector data) {\r
+ switch (col) {\r
+ case COLUMN_FILEDATE:\r
+ Collections.sort(data,\r
+ new Comparator() {\r
+ public int compare(Object o1, Object o2) {\r
+ int ret = 1;\r
+ final File a = (File) o1;\r
+ final File b = (File) o2;\r
+\r
+ if (a.lastModified() > b.lastModified()) {\r
+ ret = -1;\r
+ } else if (a.lastModified() == b.lastModified()) {\r
+ ret = 0;\r
+ }\r
+\r
+ if (ascending) {\r
+ ret *= -1;\r
+ }\r
+\r
+ return ret;\r
+ }\r
+ });\r
+\r
+\r
+ break;\r
+\r
+ case COLUMN_FILESIZE:\r
+ Collections.sort(data,\r
+ new Comparator() {\r
+ public int compare(Object o1, Object o2) {\r
+ int ret = 1;\r
+ final File a = (File) o1;\r
+ final File b = (File) o2;\r
+\r
+ if (a.length() > b.length()) {\r
+ ret = -1;\r
+ } else if (a.length() == b.length()) {\r
+ ret = 0;\r
+ }\r
+\r
+ if (ascending) {\r
+ ret *= -1;\r
+ }\r
+\r
+ return ret;\r
+ }\r
+ });\r
+\r
+\r
+ break;\r
+\r
+ case COLUMN_FILENAME:\r
+ Collections.sort(data,\r
+ new Comparator() {\r
+ public int compare(Object o1, Object o2) {\r
+ final File a = (File) o1;\r
+ final File b = (File) o2;\r
+\r
+ if (ascending) {\r
+ return a.getName().compareToIgnoreCase(b.getName());\r
+ } else {\r
+ return -1 * a.getName().compareToIgnoreCase(b.getName());\r
+ }\r
+ }\r
+ });\r
+\r
+\r
+ break;\r
+ }\r
+ }\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
-import javax.swing.filechooser.*;\r
import java.io.File;\r
+\r
import java.util.*;\r
\r
-public class JalviewFileFilter extends FileFilter\r
-{\r
- private static String TYPE_UNKNOWN = "Type Unknown";\r
- private static String HIDDEN_FILE = "Hidden File";\r
- public static Hashtable suffixHash = new Hashtable();\r
+import javax.swing.filechooser.*;\r
+\r
+\r
+public class JalviewFileFilter extends FileFilter {\r
+ private static String TYPE_UNKNOWN = "Type Unknown";\r
+ private static String HIDDEN_FILE = "Hidden File";\r
+ public static Hashtable suffixHash = new Hashtable();\r
+ private Hashtable filters = null;\r
+ private String description = "no description";\r
+ private String fullDescription = "full description";\r
+ private boolean useExtensionsInDescription = true;\r
\r
- private Hashtable filters = null;\r
- private String description = "no description";\r
- private String fullDescription = "full description";\r
- private boolean useExtensionsInDescription = true;\r
+ public JalviewFileFilter(String extension, String description) {\r
+ StringTokenizer st = new StringTokenizer(extension, ",");\r
\r
+ while (st.hasMoreElements()) {\r
+ addExtension(st.nextToken().trim());\r
+ }\r
\r
- public JalviewFileFilter(String extension, String description) {\r
+ setDescription(description);\r
+ }\r
\r
- StringTokenizer st = new StringTokenizer(extension, ",");\r
- while(st.hasMoreElements())\r
- {\r
- addExtension(st.nextToken().trim());\r
- }\r
- setDescription(description);\r
- }\r
+ public JalviewFileFilter(String[] filts) {\r
+ this(filts, null);\r
+ }\r
\r
- public JalviewFileFilter(String[] filts) {\r
- this(filts, null);\r
- }\r
+ public JalviewFileFilter(String[] filts, String description) {\r
+ for (int i = 0; i < filts.length; i++) {\r
+ // add filters one by one\r
+ addExtension(filts[i]);\r
+ }\r
\r
- public String getAcceptableExtension()\r
- {\r
+ if (description != null) {\r
+ setDescription(description);\r
+ }\r
+ }\r
+\r
+ public String getAcceptableExtension() {\r
return filters.keys().nextElement().toString();\r
- }\r
-\r
- public JalviewFileFilter(String[] filts, String description) {\r
- for (int i = 0; i < filts.length; i++) {\r
- // add filters one by one\r
- addExtension(filts[i]);\r
- }\r
- if(description!=null) setDescription(description);\r
- }\r
-\r
- // takes account of the fact that database is a directory\r
- public boolean accept(File f) {\r
- if(f != null) {\r
- String extension = getExtension(f);\r
- if(f.isDirectory()) {\r
- if(extension == null || extension.equals("")) {\r
+ }\r
+\r
+ // takes account of the fact that database is a directory\r
+ public boolean accept(File f) {\r
+ if (f != null) {\r
+ String extension = getExtension(f);\r
+\r
+ if (f.isDirectory()) {\r
+ if ((extension == null) || extension.equals("")) {\r
return true;\r
- } else {\r
- if(filters.get(getExtension(f)) != null) {\r
- return true;\r
+ } else {\r
+ if (filters.get(getExtension(f)) != null) {\r
+ return true;\r
+ }\r
+ }\r
+ }\r
+\r
+ if ((extension != null) && (filters.get(getExtension(f)) != null)) {\r
+ return true;\r
+ }\r
+ }\r
+\r
+ return false;\r
+ }\r
+\r
+ public String getExtension(File f) {\r
+ if (f != null) {\r
+ String filename = f.getName();\r
+ int i = filename.lastIndexOf('.');\r
+\r
+ if ((i > 0) && (i < (filename.length() - 1))) {\r
+ return filename.substring(i + 1).toLowerCase();\r
+ }\r
+\r
+ ;\r
+ }\r
+\r
+ return "";\r
+ }\r
+\r
+ public void addExtension(String extension) {\r
+ if (filters == null) {\r
+ filters = new Hashtable(5);\r
+ }\r
+\r
+ filters.put(extension.toLowerCase(), this);\r
+ fullDescription = null;\r
+ }\r
+\r
+ public String getDescription() {\r
+ if (fullDescription == null) {\r
+ if ((description == null) || isExtensionListInDescription()) {\r
+ fullDescription = (description == null) ? "(" : (description +\r
+ " (");\r
+\r
+ // build the description from the extension list\r
+ Enumeration extensions = filters.keys();\r
+\r
+ if (extensions != null) {\r
+ fullDescription += ("." +\r
+ (String) extensions.nextElement());\r
+\r
+ while (extensions.hasMoreElements()) {\r
+ fullDescription += (", " +\r
+ (String) extensions.nextElement());\r
}\r
- }\r
- }\r
- if(extension != null && filters.get(getExtension(f)) != null) {\r
- return true;\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- public String getExtension(File f) {\r
- if(f != null) {\r
- String filename = f.getName();\r
- int i = filename.lastIndexOf('.');\r
- if(i>0 && i<filename.length()-1) {\r
- return filename.substring(i+1).toLowerCase();\r
- };\r
- }\r
- return "";\r
- }\r
-\r
- public void addExtension(String extension) {\r
- if(filters == null) {\r
- filters = new Hashtable(5);\r
- }\r
- filters.put(extension.toLowerCase(), this);\r
- fullDescription = null;\r
- }\r
-\r
-\r
- public String getDescription() {\r
- if(fullDescription == null) {\r
- if(description == null || isExtensionListInDescription()) {\r
- fullDescription = description==null ? "(" : description + " (";\r
- // build the description from the extension list\r
- Enumeration extensions = filters.keys();\r
- if(extensions != null) {\r
- fullDescription += "." + (String) extensions.nextElement();\r
- while (extensions.hasMoreElements()) {\r
- fullDescription += ", " + (String) extensions.nextElement();\r
- }\r
- }\r
- fullDescription += ")";\r
- } else {\r
- fullDescription = description;\r
- }\r
- }\r
- return fullDescription;\r
- }\r
-\r
- public void setDescription(String description) {\r
- this.description = description;\r
- fullDescription = null;\r
- }\r
-\r
- public void setExtensionListInDescription(boolean b) {\r
- useExtensionsInDescription = b;\r
- fullDescription = null;\r
- }\r
-\r
- public boolean isExtensionListInDescription() {\r
- return useExtensionsInDescription;\r
- }\r
- }\r
+ }\r
+\r
+ fullDescription += ")";\r
+ } else {\r
+ fullDescription = description;\r
+ }\r
+ }\r
+\r
+ return fullDescription;\r
+ }\r
+\r
+ public void setDescription(String description) {\r
+ this.description = description;\r
+ fullDescription = null;\r
+ }\r
+\r
+ public void setExtensionListInDescription(boolean b) {\r
+ useExtensionsInDescription = b;\r
+ fullDescription = null;\r
+ }\r
+\r
+ public boolean isExtensionListInDescription() {\r
+ return useExtensionsInDescription;\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
-import javax.swing.filechooser.FileView;\r
-import javax.swing.*;\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
-public class JalviewFileView extends FileView\r
-{\r
- static Hashtable alignSuffix = new Hashtable();\r
- static{\r
- alignSuffix.put("fasta", "Fasta file");\r
- alignSuffix.put("fa", "Fasta file");\r
- alignSuffix.put("fastq", "Fasta file");\r
- alignSuffix.put("blc", "BLC file");\r
- alignSuffix.put("msf", "MSF file");\r
- alignSuffix.put("pfam", "PFAM file");\r
- alignSuffix.put("aln", "Clustal file");\r
- alignSuffix.put("pir", "PIR file");\r
- }\r
- public String getTypeDescription(File f)\r
- {\r
- String extension = getExtension(f);\r
- String type = null;\r
-\r
- if (extension != null)\r
- {\r
- if (alignSuffix.containsKey(extension))\r
- {\r
- type = alignSuffix.get(extension).toString();\r
- }\r
+import javax.swing.*;\r
+import javax.swing.filechooser.FileView;\r
+\r
+\r
+public class JalviewFileView extends FileView {\r
+ static Hashtable alignSuffix = new Hashtable();\r
+\r
+ static {\r
+ alignSuffix.put("fasta", "Fasta file");\r
+ alignSuffix.put("fa", "Fasta file");\r
+ alignSuffix.put("fastq", "Fasta file");\r
+ alignSuffix.put("blc", "BLC file");\r
+ alignSuffix.put("msf", "MSF file");\r
+ alignSuffix.put("pfam", "PFAM file");\r
+ alignSuffix.put("aln", "Clustal file");\r
+ alignSuffix.put("pir", "PIR file");\r
}\r
- return type;\r
- }\r
-\r
- public Icon getIcon(File f)\r
- {\r
- String extension = getExtension(f);\r
- Icon icon = null;\r
-\r
- if (extension != null)\r
- {\r
- if (alignSuffix.containsKey(extension))\r
- {\r
- icon = createImageIcon("/images/file.png");\r
- }\r
+\r
+ public String getTypeDescription(File f) {\r
+ String extension = getExtension(f);\r
+ String type = null;\r
+\r
+ if (extension != null) {\r
+ if (alignSuffix.containsKey(extension)) {\r
+ type = alignSuffix.get(extension).toString();\r
+ }\r
+ }\r
+\r
+ return type;\r
}\r
- return icon;\r
- }\r
-\r
-\r
- /*\r
- * Get the extension of a file.\r
- */\r
- public static String getExtension(File f) {\r
- String ext = null;\r
- String s = f.getName();\r
- int i = s.lastIndexOf('.');\r
-\r
- if (i > 0 && i < s.length() - 1) {\r
- ext = s.substring(i+1).toLowerCase();\r
- }\r
- return ext;\r
- }\r
-\r
- /** Returns an ImageIcon, or null if the path was invalid. */\r
- protected static ImageIcon createImageIcon(String path) {\r
- java.net.URL imgURL = JalviewFileView.class.getResource(path);\r
- if (imgURL != null) {\r
- return new ImageIcon(imgURL);\r
- } else {\r
- System.err.println("JalviewFileView.createImageIcon: Couldn't find file: " + path);\r
- return null;\r
- }\r
- }\r
\r
-}\r
+ public Icon getIcon(File f) {\r
+ String extension = getExtension(f);\r
+ Icon icon = null;\r
+\r
+ if (extension != null) {\r
+ if (alignSuffix.containsKey(extension)) {\r
+ icon = createImageIcon("/images/file.png");\r
+ }\r
+ }\r
+\r
+ return icon;\r
+ }\r
+\r
+ /*\r
+ * Get the extension of a file.\r
+ */\r
+ public static String getExtension(File f) {\r
+ String ext = null;\r
+ String s = f.getName();\r
+ int i = s.lastIndexOf('.');\r
\r
+ if ((i > 0) && (i < (s.length() - 1))) {\r
+ ext = s.substring(i + 1).toLowerCase();\r
+ }\r
\r
+ return ext;\r
+ }\r
+\r
+ /** Returns an ImageIcon, or null if the path was invalid. */\r
+ protected static ImageIcon createImageIcon(String path) {\r
+ java.net.URL imgURL = JalviewFileView.class.getResource(path);\r
+\r
+ if (imgURL != null) {\r
+ return new ImageIcon(imgURL);\r
+ } else {\r
+ System.err.println(\r
+ "JalviewFileView.createImageIcon: Couldn't find file: " + path);\r
+\r
+ return null;\r
+ }\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+\r
import jalview.util.*;\r
\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
+\r
public class MSFfile extends AlignFile {\r
+ private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",\r
+ "-");\r
+ private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(\r
+ "[" + jalview.util.Comparison.GapChars + "]", "\\~");\r
\r
- public MSFfile()\r
- {}\r
+ public MSFfile() {\r
+ }\r
\r
- public MSFfile(String inStr) {\r
- super(inStr);\r
- }\r
+ public MSFfile(String inStr) {\r
+ super(inStr);\r
+ }\r
\r
- public MSFfile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
+ public MSFfile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+ }\r
\r
- private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~","-");\r
- private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex("["+jalview.util.Comparison.GapChars+"]","\\~");\r
+ public void parse() {\r
+ int i = 0;\r
+ boolean seqFlag = false;\r
+ String key = new String();\r
+ Vector headers = new Vector();\r
+ Hashtable seqhash = new Hashtable();\r
+ String line;\r
+\r
+ try {\r
+ while ((line = nextLine()) != null) {\r
+ StringTokenizer str = new StringTokenizer(line);\r
+\r
+ while (str.hasMoreTokens()) {\r
+ String inStr = str.nextToken();\r
+\r
+ //If line has header information add to the headers vector\r
+ if (inStr.indexOf("Name:") != -1) {\r
+ key = str.nextToken();\r
+ headers.addElement(key);\r
+ }\r
+\r
+ //if line has // set SeqFlag to 1 so we know sequences are coming\r
+ if (inStr.indexOf("//") != -1) {\r
+ seqFlag = true;\r
+ }\r
+\r
+ //Process lines as sequence lines if seqFlag is set\r
+ if ((inStr.indexOf("//") == -1) && (seqFlag == true)) {\r
+ //seqeunce id is the first field\r
+ key = inStr;\r
+\r
+ StringBuffer tempseq;\r
+\r
+ //Get sequence from hash if it exists\r
+ if (seqhash.containsKey(key)) {\r
+ tempseq = (StringBuffer) seqhash.get(key);\r
+ } else {\r
+ tempseq = new StringBuffer();\r
+ seqhash.put(key, tempseq);\r
+ }\r
+\r
+ //loop through the rest of the words\r
+ while (str.hasMoreTokens()) {\r
+ //append the word to the sequence\r
+ tempseq.append(str.nextToken());\r
+ }\r
+ }\r
+ }\r
+ }\r
+ } catch (IOException e) {\r
+ System.err.println("Exception parsing MSFFile " + e);\r
+ e.printStackTrace();\r
+ }\r
\r
- public void parse() {\r
- int i = 0;\r
- boolean seqFlag = false;\r
- String key = new String();\r
- Vector headers = new Vector();\r
- Hashtable seqhash = new Hashtable();\r
- String line;\r
+ this.noSeqs = headers.size();\r
\r
- try {\r
- while ((line = nextLine()) != null) {\r
+ //Add sequences to the hash\r
+ for (i = 0; i < headers.size(); i++) {\r
+ if (seqhash.get(headers.elementAt(i)) != null) {\r
+ String head = headers.elementAt(i).toString();\r
+ String seq = seqhash.get(head).toString();\r
\r
- StringTokenizer str = new StringTokenizer(line);\r
+ int start = 1;\r
+ int end = seq.length();\r
\r
- while (str.hasMoreTokens()) {\r
+ if (maxLength < head.length()) {\r
+ maxLength = head.length();\r
+ }\r
\r
- String inStr = str.nextToken();\r
+ if (head.indexOf("/") > 0) {\r
+ StringTokenizer st = new StringTokenizer(head, "/");\r
\r
- //If line has header information add to the headers vector\r
- if (inStr.indexOf("Name:") != -1) {\r
- key = str.nextToken();\r
- headers.addElement(key);\r
- }\r
+ if (st.countTokens() == 2) {\r
+ head = st.nextToken();\r
\r
- //if line has // set SeqFlag to 1 so we know sequences are coming\r
- if (inStr.indexOf("//") != -1) {\r
- seqFlag = true;\r
- }\r
+ String tmp = st.nextToken();\r
+ st = new StringTokenizer(tmp, "-");\r
\r
- //Process lines as sequence lines if seqFlag is set\r
- if (( inStr.indexOf("//") == -1) && (seqFlag == true)) {\r
- //seqeunce id is the first field\r
- key = inStr;\r
- StringBuffer tempseq;\r
-\r
- //Get sequence from hash if it exists\r
- if (seqhash.containsKey(key)) {\r
- tempseq = (StringBuffer)seqhash.get(key);\r
- } else {\r
- tempseq = new StringBuffer();\r
- seqhash.put(key,tempseq);\r
- }\r
-\r
- //loop through the rest of the words\r
- while (str.hasMoreTokens()) {\r
- //append the word to the sequence\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
- } catch (IOException e) {\r
- System.err.println("Exception parsing MSFFile " + e);\r
- e.printStackTrace();\r
- }\r
-\r
- this.noSeqs = headers.size();\r
+ if (st.countTokens() == 2) {\r
+ start = Integer.valueOf(st.nextToken()).intValue();\r
+ end = Integer.valueOf(st.nextToken()).intValue();\r
+ }\r
+ }\r
+ }\r
\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++ ) {\r
+ // Replace ~ with a sensible gap character\r
+ seq = gapre.replaceAll(seq);\r
\r
- if ( seqhash.get(headers.elementAt(i)) != null) {\r
- String head = headers.elementAt(i).toString();\r
- String seq = seqhash.get(head).toString();\r
+ Sequence newSeq = new Sequence(head, seq, start, end);\r
\r
- int start = 1;\r
- int end = seq.length();\r
+ seqs.addElement(newSeq);\r
+ } else {\r
+ System.err.println("MSFFile Parser: Can't find sequence for " +\r
+ headers.elementAt(i));\r
+ }\r
+ }\r
+ }\r
\r
- if (maxLength < head.length() ) {\r
- maxLength = head.length();\r
+ public static int checkSum(String seq) {\r
+ //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";\r
+ int check = 0;\r
+\r
+ String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";\r
+ index += "--------------------------------------------------------------------------------------------------------------------------------";\r
+\r
+ for (int i = 0; i < seq.length(); i++) {\r
+ try {\r
+ if (i < seq.length()) {\r
+ int pos = index.indexOf(seq.substring(i, i + 1));\r
+\r
+ if (!index.substring(pos, pos + 1).equals("_")) {\r
+ check += (((i % 57) + 1) * pos);\r
+ }\r
+ }\r
+ } catch (Exception e) {\r
+ System.err.println("Exception during MSF Checksum calculation");\r
+ e.printStackTrace();\r
+ }\r
}\r
\r
- if (head.indexOf("/") > 0 ) {\r
+ return check % 10000;\r
+ }\r
+\r
+ public static String print(SequenceI[] s) {\r
+ return print(s, false);\r
+ }\r
+\r
+ public static String print(SequenceI[] s, boolean is_NA) {\r
+ StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
+ "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
\r
- StringTokenizer st = new StringTokenizer(head,"/");\r
+ int max = 0;\r
+ int maxid = 0;\r
+ int i = 0;\r
+ String big = "";\r
\r
- if (st.countTokens() == 2) {\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String sq;\r
+ big += (sq = s[i].getSequence());\r
\r
- head = st.nextToken();\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp,"-");\r
- if (st.countTokens() == 2) {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
+ if (sq.length() > max) {\r
+ max = sq.length();\r
}\r
- }\r
- }\r
- // Replace ~ with a sensible gap character\r
- seq = gapre.replaceAll(seq);\r
- Sequence newSeq = new Sequence(head,seq,start,end);\r
\r
- seqs.addElement(newSeq);\r
+ i++;\r
+ }\r
\r
- } else {\r
- System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i));\r
- }\r
- }\r
+ Format maxLenpad = new Format("%" + (new String("" + max)).length() +\r
+ "d");\r
+ Format maxChkpad = new Format("%" + (new String("1" + max)).length() +\r
+ "d");\r
+ i = 0;\r
+\r
+ long bigcheck = checkSum(big);\r
+ long maxNB = 0;\r
+ out.append(" MSF: " + s[0].getSequence().length() + " Type: " +\r
+ (is_NA ? "N" : "P") + " Check: " + bigcheck + " ..\n\n\n");\r
+\r
+ String[] nameBlock = new String[s.length];\r
+ String[] idBlock = new String[s.length];\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String seq = s[i].getSequence();\r
+ String name = s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd();\r
+ int check = checkSum(s[i].getSequence());\r
+ nameBlock[i] = new String(" Name: " + name + " ");\r
+ idBlock[i] = new String("Len: " +\r
+ maxLenpad.form(s[i].getSequence().length()) + " Check:" +\r
+ maxChkpad.form(check) + " Weight: 1.00\n");\r
+\r
+ if (name.length() > maxid) {\r
+ maxid = name.length();\r
+ }\r
\r
- }\r
+ if (nameBlock[i].length() > maxNB) {\r
+ maxNB = nameBlock[i].length();\r
+ }\r
\r
- public static int checkSum(String seq) {\r
- //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";\r
- int check = 0;\r
+ i++;\r
+ }\r
\r
- String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";\r
- index += "--------------------------------------------------------------------------------------------------------------------------------";\r
+ if (maxid < 10) {\r
+ maxid = 10;\r
+ }\r
\r
- for(int i = 0; i < seq.length(); i++) {\r
- try {\r
- if (i <seq.length()) {\r
- int pos = index.indexOf(seq.substring(i,i+1));\r
- if (!index.substring(pos,pos+1).equals("_")) {\r
- check += ((i % 57) + 1) * pos;\r
- }\r
+ if (maxNB < 15) {\r
+ maxNB = 15;\r
}\r
- } catch (Exception e) {\r
- System.err.println("Exception during MSF Checksum calculation");\r
- e.printStackTrace();\r
- }\r
- }\r
- return check % 10000;\r
- }\r
-\r
- public static String print(SequenceI[] s) {\r
- return print(s, false);\r
- }\r
- public static String print(SequenceI[] s, boolean is_NA) {\r
- StringBuffer out = new StringBuffer("!!"+(is_NA ? "NA":"AA")+"_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
-\r
- int max = 0;\r
- int maxid = 0;\r
- int i = 0;\r
- String big = "";\r
-\r
- while (i < s.length && s[i] != null) {\r
- String sq;\r
- big += (sq=s[i].getSequence());\r
- if (sq.length() > max) {\r
- max = sq.length();\r
- }\r
- i++;\r
- }\r
- Format maxLenpad = new Format("%"+(new String(""+max)).length()+"d");\r
- Format maxChkpad = new Format("%"+(new String("1"+max)).length()+"d");\r
- i = 0;\r
- long bigcheck = checkSum(big);\r
- long maxNB=0;\r
- out.append(" MSF: " + s[0].getSequence().length() + " Type: "+(is_NA?"N":"P")+" Check: " + bigcheck + " ..\n\n\n");\r
- String nameBlock[] = new String[s.length];\r
- String idBlock[] = new String[s.length];\r
- while (i < s.length && s[i] != null) {\r
- String seq = s[i].getSequence();\r
- String name = s[i].getName()+ "/" + s[i].getStart() + "-" + s[i].getEnd();\r
- int check = checkSum(s[i].getSequence());\r
- nameBlock[i]=new String(" Name: "+name+" ");\r
- idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getSequence().length()) + " Check:" + maxChkpad.form(check) + " Weight: 1.00\n");\r
-\r
- if (name.length() > maxid) {\r
- maxid = name.length();\r
- }\r
- if (nameBlock[i].length()>maxNB) {\r
- maxNB=nameBlock[i].length();\r
- }\r
-\r
- i++;\r
- }\r
- if (maxid < 10) {\r
- maxid = 10;\r
- }\r
- if (maxNB<15) {\r
- maxNB=15;\r
- }\r
- Format nbFormat = new Format("%-"+maxNB+"s");\r
- for (i=0;i<s.length && s[i]!=null;i++) {\r
- out.append(nbFormat.form(nameBlock[i])+idBlock[i]);\r
- }\r
- maxid++;\r
- out.append( "\n\n//\n\n");\r
\r
- int len = 50;\r
+ Format nbFormat = new Format("%-" + maxNB + "s");\r
\r
- int nochunks = max / len + 1;\r
- if (max%len == 0) {\r
- nochunks--;\r
- }\r
- for (i = 0; i < nochunks; i++) {\r
- int j = 0;\r
- while (j < s.length && s[j] != null) {\r
- String name = s[j].getName();\r
- out.append( new Format("%-" + maxid + "s").form(name + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
- for (int k = 0; k < 5; k++) {\r
-\r
- int start = i*50 + k*10;\r
- int end = start + 10;\r
-\r
- if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {\r
- out.append(re2gap.replaceAll(s[j].getSequence().substring(start,end)));\r
- if (k < 4) {\r
- // out.append(" ");\r
- } else {\r
- out.append("\n");\r
- }\r
- } else {\r
- if (start < s[j].getSequence().length()) {\r
- out.append(re2gap.replaceAll(s[j].getSequence().substring(start)));\r
- out.append("\n");\r
- } else {\r
- if (k == 0) {\r
- out.append("\n");\r
- }\r
- }\r
- }\r
+ for (i = 0; (i < s.length) && (s[i] != null); i++) {\r
+ out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);\r
}\r
- j++;\r
- }\r
- out.append("\n");\r
\r
- }\r
- return out.toString();\r
- }\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
-}\r
+ maxid++;\r
+ out.append("\n\n//\n\n");\r
\r
+ int len = 50;\r
\r
+ int nochunks = (max / len) + 1;\r
\r
+ if ((max % len) == 0) {\r
+ nochunks--;\r
+ }\r
\r
+ for (i = 0; i < nochunks; i++) {\r
+ int j = 0;\r
+\r
+ while ((j < s.length) && (s[j] != null)) {\r
+ String name = s[j].getName();\r
+ out.append(new Format("%-" + maxid + "s").form(name + "/" +\r
+ s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+\r
+ for (int k = 0; k < 5; k++) {\r
+ int start = (i * 50) + (k * 10);\r
+ int end = start + 10;\r
+\r
+ if ((end < s[j].getSequence().length()) &&\r
+ (start < s[j].getSequence().length())) {\r
+ out.append(re2gap.replaceAll(s[j].getSequence()\r
+ .substring(start, end)));\r
+\r
+ if (k < 4) {\r
+ // out.append(" ");\r
+ } else {\r
+ out.append("\n");\r
+ }\r
+ } else {\r
+ if (start < s[j].getSequence().length()) {\r
+ out.append(re2gap.replaceAll(\r
+ s[j].getSequence().substring(start)));\r
+ out.append("\n");\r
+ } else {\r
+ if (k == 0) {\r
+ out.append("\n");\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ j++;\r
+ }\r
\r
+ out.append("\n");\r
+ }\r
\r
+ return out.toString();\r
+ }\r
\r
+ public String print() {\r
+ return print(getSeqsAsArray());\r
+ }\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-// NewickFile.java
-// Tree I/O
-// http://evolution.genetics.washington.edu/phylip/newick_doc.html
-
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-import jalview.datamodel.*;
-
-public class NewickFile extends FileParse
-{
- SequenceNode root;
-
- private boolean HasBootstrap = false;
- private boolean HasDistances = false;
- private boolean RootHasDistance = false;
-
- private String ErrorStringrange(String Error, String Er, int r, int p, String s) {
- return ((Error==null) ? "" : Error)
- + Er +
- " at position "+p+" ( "
- + s.substring((p-r)<0 ? 0 : (p-r),
- (p+r)>s.length() ? s.length() : (p+r))
- + " )\n";
- }
-
- // @tree annotations
- // These are set automatically by the reader
- public boolean HasBootstrap() {
- return HasBootstrap;
- }
-
- public boolean HasDistances() {
- return HasDistances;
- }
- public NewickFile(String inStr) throws IOException
- {
- super(inStr, "Paste");
- }
-
- public NewickFile(String inFile, String type)
- throws IOException
- {
-
- super(inFile, type);
- }
- // File IO Flags
- boolean ReplaceUnderscores = false;
-
- public void parse() throws IOException
- {
- String nf;
-
- { // fill nf with complete tree file
- StringBuffer file = new StringBuffer();
- while ( (nf = nextLine()) != null)
- {
- file.append(nf);
- }
- nf = file.toString();
- }
-
- root = new SequenceNode();
- SequenceNode realroot = null;
- SequenceNode c = root;
-
- int d = -1;
- int cp = 0;
- int flen = nf.length();
-
- String Error = null;
- String nodename = null;
-
- float DefDistance = (float) 0.00001; // @param Default distance for a node - very very small
- int DefBootstrap = 0; // @param Default bootstrap for a node
-
- float distance=DefDistance;
- int bootstrap=DefBootstrap;
-
- boolean ascending = false; // flag indicating that we are leaving the current node
-
- com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex("[(\\['),;]");
-
- while (majorsyms.searchFrom(nf, cp) && Error==null) {
- int fcp = majorsyms.matchedFrom();
- switch (nf.charAt(fcp)) {
-
- case '[': // Comment or structured/extended NH format info
- com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]");
- if (comment.searchFrom(nf, fcp))
- {
- // Skip the comment field
- cp = 1 + comment.matchedFrom();
- }
- else
- {
- Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf);
- }
- ;
- break;
-
- case '(':
-
- // ascending should not be set
- // New Internal node
- if (ascending)
- {
- Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
- continue;
- }
- ;
- d++;
- if (c.right() == null)
- {
- c.setRight(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false));
- c = (SequenceNode) c.right();
- }
- else
- {
- if (c.left() != null)
- {
- // Dummy node for polytomy - keeps c.left free for new node
- SequenceNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
- tmpn.SetChildren(c.left(), c.right());
- c.setRight(tmpn);
- }
- c.setLeft(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false));
- c = (SequenceNode) c.left();
- }
- if (realroot==null) {
- realroot = c;
- }
- nodename = null;
- distance = DefDistance;
- bootstrap = DefBootstrap;
- cp = fcp + 1;
- break;
-
- // Deal with quoted fields
- case '\'':
- com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
- "([^']|'')+'");
- if (qnodename.searchFrom(nf, fcp))
- {
- int nl = qnodename.stringMatched().length();
- nodename = new String(qnodename.stringMatched().substring(0, nl - 1));
- cp = fcp + nl + 1;
- }
- else
- {
- Error = ErrorStringrange(Error, "Unterminated quotes for nodename",
- 7, fcp, nf);
- }
- break;
-
- case ';':
- if (d != -1)
- {
- Error = ErrorStringrange(Error,
- "Wayward semicolon (depth=" + d + ")", 7,
- fcp, nf);
- }
- // cp advanced at the end of default
-
- default:
-
- // Parse simpler field strings
- String fstring = nf.substring(cp, fcp);
- com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
- "\\b([^' :;\\](),]+)");
- com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
- "\\S+([0-9+]+)\\S*:");
- com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
- ":([-0-9.+]+)");
- if (uqnodename.search(fstring)
- && (uqnodename.matchedFrom(1) == 0
- || fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':')) // JBPNote HACK!
-
- {
- if (nodename == null)
- {
- if (ReplaceUnderscores) {
- nodename = uqnodename.stringMatched(1).replace('_', ' ');
- } else {
- nodename = uqnodename.stringMatched(1);
- }
- }
- else
- {
- Error = ErrorStringrange(Error,
- "File has broken algorithm - overwritten nodename",
- 10, fcp,
- nf);
- }
- }
- if (nbootstrap.search(fstring)
- &&
- nbootstrap.matchedFrom(1)
- > uqnodename.matchedFrom(1) + uqnodename.stringMatched().length())
- {
- try
- {
- bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
- HasBootstrap = true;
- }
- catch (Exception e)
- {
- Error = ErrorStringrange(Error, "Can't parse bootstrap value", 4,
- cp + nbootstrap.matchedFrom(), nf);
- }
- }
- boolean nodehasdistance=false;
- if (ndist.search(fstring))
- {
- try
- {
- distance = (new Float(ndist.stringMatched(1))).floatValue();
- HasDistances = true;
- nodehasdistance = true;
- }
- catch (Exception e)
- {
- Error = ErrorStringrange(Error, "Can't parse node distance value",
- 7, cp + ndist.matchedFrom(), nf);
- }
- }
-
- if (ascending)
- {
- // Write node info here
- c.setName(nodename);
- c.dist = (HasDistances) ? distance : 0;
- c.setBootstrap((HasBootstrap) ? bootstrap : 0);
- if (c==realroot) {
- RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!
- }
- }
- else
- {
- // Find a place to put the leaf
- SequenceNode newnode =
- new SequenceNode(null, c,
- nodename,
- (HasDistances) ? distance : DefDistance,
- (HasBootstrap) ? bootstrap : DefBootstrap,
- false);
-
- if (c.right() == null)
- {
- c.setRight(newnode);
- }
- else
- {
- if (c.left() == null)
- {
- c.setLeft(newnode);
- }
- else
- {
- // Insert a dummy node for polytomy
- SequenceNode newdummy = new SequenceNode(null, c, null, 0, 0, true);
- newdummy.SetChildren(c.left(), newnode);
- c.setLeft(newdummy);
- }
- }
- }
- if (ascending)
- {
- // move back up the tree from preceding closure
- c = c.AscendTree();
- if (d > -1 && c == null)
- {
- Error = ErrorStringrange(Error,
- "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
- 7, fcp, nf);
- }
- }
-
- if (nf.charAt(fcp) == ')') {
- d--;
- ascending = true;
- } else {
- if (nf.charAt(fcp) == ',') {
- if (ascending) {
- ascending = false;
- } else {
- // Just advance focus, if we need to
- if (c.left()!=null && (!c.left().isLeaf())) {
- c = (SequenceNode) c.left();
- }
- }
- } // else : We do nothing if ';' is encountered.
- }
- // Reset new node properties to obvious fakes
- nodename = null;
- distance = DefDistance;
- bootstrap = DefBootstrap;
-
- cp=fcp+1;
- }
- }
-
- if (Error!=null) {
- throw(new IOException("NewickFile: "+Error+"\n"));
- }
-
- root = (SequenceNode) root.right().detach(); // remove the imaginary root.
- if (!RootHasDistance) {
- root.dist = 0;
- }
-
- }
-
- public NewickFile(SequenceNode newtree) {
- root = newtree;
- }
-
- public NewickFile(SequenceNode newtree, boolean bootstrap) {
- HasBootstrap = bootstrap;
- root=newtree;
- }
- public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances) {
- root = newtree;
- HasBootstrap = bootstrap;
- HasDistances = distances;
- }
-
- public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances, boolean rootdistance) {
- root = newtree;
- HasBootstrap = bootstrap;
- HasDistances = distances;
- RootHasDistance = rootdistance;
- }
-
- public SequenceNode getTree() {
- return root;
- }
-
- public String print() {
- synchronized (this) {
- StringBuffer tf = new StringBuffer();
- print(tf, root);
- return (tf.append(";").toString());
- }
- }
-
- public String print(boolean withbootstraps) {
- synchronized(this) {
- boolean boots = this.HasBootstrap;
- this.HasBootstrap = withbootstraps;
- String rv = print();
- this.HasBootstrap = boots;
- return rv;
- }
- }
-
- public String print(boolean withbootstraps, boolean withdists) {
- synchronized(this) {
- boolean dists = this.HasDistances;
- this.HasDistances = withdists;
- String rv = print(withbootstraps);
- this.HasDistances = dists;
- return rv;
- }
- }
- boolean printRootInfo = false;
-
-
- public String print(boolean withbootstraps, boolean withdists, boolean printRootInfo) {
- synchronized(this) {
- boolean rootinfo = printRootInfo;
- this.printRootInfo = printRootInfo;
- String rv = print(withbootstraps, withdists);
- this.printRootInfo = rootinfo;
- return rv;
- }
- }
- private com.stevesoft.pat.Regex[] NodeSafeName =
- new com.stevesoft.pat.Regex[]
- { new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes
- new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters
- new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation
- };
- char QuoteChar='\'';
- char getQuoteChar() {
- return QuoteChar;
- }
-
- char setQuoteChar(char c) {
- char old = QuoteChar;
- QuoteChar = c;
- return old;
- }
-
- private String nodeName(String name) {
- if (NodeSafeName[0].search(name)) {
- return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
- } else {
- return NodeSafeName[2].replaceAll(name);
- }
- }
- private String printNodeField(SequenceNode c) {
-
- return ( (c.getName() == null) ? ""
- : nodeName(c.getName()))
- + ( (HasBootstrap)
- ? ( (c.getBootstrap() > -1)
- ? " " + c.getBootstrap()
- : "")
- : "")
- + ( (HasDistances)
- ? ":" + c.dist : "");
- }
- private String printRootField(SequenceNode root) {
-
- return (printRootInfo)
- ? (( (root.getName() == null) ? ""
- : nodeName(root.getName()))
- + ( (HasBootstrap)
- ? ( (root.getBootstrap() > -1)
- ? " " + root.getBootstrap()
- : "")
- : "")
- + ( (RootHasDistance)
- ? ":" + root.dist : ""))
- : "";
- }
-
-// Non recursive call deals with root node properties
- public void print(StringBuffer tf, SequenceNode root) {
- if (root!=null) {
- if (root.isLeaf() && printRootInfo) {
- tf.append(printRootField(root));
- } else {
- if (root.isDummy()) {
- _print(tf, (SequenceNode) root.right());
- _print(tf, (SequenceNode) root.left());
- } else {
- tf.append("(");
- _print(tf, (SequenceNode) root.right());
- if (root.left() != null) {
- tf.append(",");
- }
- _print(tf, (SequenceNode) root.left());
- tf.append(")" + printRootField(root));
- }
- }
- }
- }
-
- // Recursive call for non-root nodes
- public void _print(StringBuffer tf, SequenceNode c) {
- if (c!=null) {
- if (c.isLeaf()) {
- tf.append(printNodeField(c));
- } else {
- if (c.isDummy()) {
- _print(tf, (SequenceNode) c.right());
- _print(tf, (SequenceNode) c.left());
- } else {
- tf.append("(");
- _print(tf, (SequenceNode) c.right());
- if (c.left() != null) {
- tf.append(",");
- }
- _print(tf, (SequenceNode) c.left());
- tf.append(")" + printNodeField(c));
- }
- }
- }
- }
-
-// Test
- public static void main(String[] args)
-{
- try
- {
- File fn = new File(args[0]);
-
- StringBuffer newickfile = new StringBuffer();
- BufferedReader treefile =
- new BufferedReader(new FileReader(fn));
- String l;
- while ((l = treefile.readLine())!=null) {
- newickfile.append(l);
- }
- treefile.close();
- System.out.println("Read file :\n");
- NewickFile trf = new NewickFile(args[0], "File");
- trf.parse();
- System.out.println("Original file :\n");
- com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
- System.out.println(nonl.replaceAll(newickfile.toString())+"\n");
-
- System.out.println("Parsed file.\n");
- System.out.println("Default output type for original input.\n");
- System.out.println(trf.print());
- System.out.println("Without bootstraps.\n");
- System.out.println(trf.print(false));
- System.out.println("Without distances.\n");
- System.out.println(trf.print(true,false));
- System.out.println("Without bootstraps but with distanecs.\n");
- System.out.println(trf.print(false, true));
- System.out.println("Without bootstraps or distanecs.\n");
- System.out.println(trf.print(false, false));
- System.out.println("With bootstraps and with distances.\n");
- System.out.println(trf.print(true, true));
- }
- catch (java.io.IOException e)
- {
- System.err.println("Exception\n" + e);
- e.printStackTrace();
- }
-}
-
-}
+*/\r
+\r
+// NewickFile.java\r
+// Tree I/O\r
+// http://evolution.genetics.washington.edu/phylip/newick_doc.html\r
+package jalview.io;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import java.io.*;\r
+\r
+import java.util.*;\r
+\r
+\r
+public class NewickFile extends FileParse {\r
+ SequenceNode root;\r
+ private boolean HasBootstrap = false;\r
+ private boolean HasDistances = false;\r
+ private boolean RootHasDistance = false;\r
+\r
+ // File IO Flags\r
+ boolean ReplaceUnderscores = false;\r
+ boolean printRootInfo = false;\r
+ private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] {\r
+ new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes\r
+ new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters\r
+ new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation\r
+ };\r
+ char QuoteChar = '\'';\r
+\r
+ public NewickFile(String inStr) throws IOException {\r
+ super(inStr, "Paste");\r
+ }\r
+\r
+ public NewickFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public NewickFile(SequenceNode newtree) {\r
+ root = newtree;\r
+ }\r
+\r
+ public NewickFile(SequenceNode newtree, boolean bootstrap) {\r
+ HasBootstrap = bootstrap;\r
+ root = newtree;\r
+ }\r
+\r
+ public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances) {\r
+ root = newtree;\r
+ HasBootstrap = bootstrap;\r
+ HasDistances = distances;\r
+ }\r
+\r
+ public NewickFile(SequenceNode newtree, boolean bootstrap,\r
+ boolean distances, boolean rootdistance) {\r
+ root = newtree;\r
+ HasBootstrap = bootstrap;\r
+ HasDistances = distances;\r
+ RootHasDistance = rootdistance;\r
+ }\r
+\r
+ private String ErrorStringrange(String Error, String Er, int r, int p,\r
+ String s) {\r
+ return ((Error == null) ? "" : Error) + Er + " at position " + p +\r
+ " ( " +\r
+ s.substring(((p - r) < 0) ? 0 : (p - r),\r
+ ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";\r
+ }\r
+\r
+ // @tree annotations\r
+ // These are set automatically by the reader\r
+ public boolean HasBootstrap() {\r
+ return HasBootstrap;\r
+ }\r
+\r
+ public boolean HasDistances() {\r
+ return HasDistances;\r
+ }\r
+\r
+ public void parse() throws IOException {\r
+ String nf;\r
+\r
+ { // fill nf with complete tree file\r
+\r
+ StringBuffer file = new StringBuffer();\r
+\r
+ while ((nf = nextLine()) != null) {\r
+ file.append(nf);\r
+ }\r
+\r
+ nf = file.toString();\r
+ }\r
+\r
+ root = new SequenceNode();\r
+\r
+ SequenceNode realroot = null;\r
+ SequenceNode c = root;\r
+\r
+ int d = -1;\r
+ int cp = 0;\r
+ int flen = nf.length();\r
+\r
+ String Error = null;\r
+ String nodename = null;\r
+\r
+ float DefDistance = (float) 0.00001; // @param Default distance for a node - very very small\r
+ int DefBootstrap = 0; // @param Default bootstrap for a node\r
+\r
+ float distance = DefDistance;\r
+ int bootstrap = DefBootstrap;\r
+\r
+ boolean ascending = false; // flag indicating that we are leaving the current node\r
+\r
+ com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(\r
+ "[(\\['),;]");\r
+\r
+ while (majorsyms.searchFrom(nf, cp) && (Error == null)) {\r
+ int fcp = majorsyms.matchedFrom();\r
+\r
+ switch (nf.charAt(fcp)) {\r
+ case '[': // Comment or structured/extended NH format info\r
+\r
+ com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(\r
+ "]");\r
+\r
+ if (comment.searchFrom(nf, fcp)) {\r
+ // Skip the comment field\r
+ cp = 1 + comment.matchedFrom();\r
+ } else {\r
+ Error = ErrorStringrange(Error, "Unterminated comment", 3,\r
+ fcp, nf);\r
+ }\r
+\r
+ ;\r
+\r
+ break;\r
+\r
+ case '(':\r
+\r
+ // ascending should not be set\r
+ // New Internal node\r
+ if (ascending) {\r
+ Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);\r
+\r
+ continue;\r
+ }\r
+\r
+ ;\r
+ d++;\r
+\r
+ if (c.right() == null) {\r
+ c.setRight(new SequenceNode(null, c, null, DefDistance,\r
+ DefBootstrap, false));\r
+ c = (SequenceNode) c.right();\r
+ } else {\r
+ if (c.left() != null) {\r
+ // Dummy node for polytomy - keeps c.left free for new node\r
+ SequenceNode tmpn = new SequenceNode(null, c, null, 0,\r
+ 0, true);\r
+ tmpn.SetChildren(c.left(), c.right());\r
+ c.setRight(tmpn);\r
+ }\r
+\r
+ c.setLeft(new SequenceNode(null, c, null, DefDistance,\r
+ DefBootstrap, false));\r
+ c = (SequenceNode) c.left();\r
+ }\r
+\r
+ if (realroot == null) {\r
+ realroot = c;\r
+ }\r
+\r
+ nodename = null;\r
+ distance = DefDistance;\r
+ bootstrap = DefBootstrap;\r
+ cp = fcp + 1;\r
+\r
+ break;\r
+\r
+ // Deal with quoted fields\r
+ case '\'':\r
+\r
+ com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(\r
+ "([^']|'')+'");\r
+\r
+ if (qnodename.searchFrom(nf, fcp)) {\r
+ int nl = qnodename.stringMatched().length();\r
+ nodename = new String(qnodename.stringMatched().substring(0,\r
+ nl - 1));\r
+ cp = fcp + nl + 1;\r
+ } else {\r
+ Error = ErrorStringrange(Error,\r
+ "Unterminated quotes for nodename", 7, fcp, nf);\r
+ }\r
+\r
+ break;\r
+\r
+ case ';':\r
+\r
+ if (d != -1) {\r
+ Error = ErrorStringrange(Error,\r
+ "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);\r
+ }\r
+\r
+ // cp advanced at the end of default\r
+ default:\r
+\r
+ // Parse simpler field strings\r
+ String fstring = nf.substring(cp, fcp);\r
+ com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(\r
+ "\\b([^' :;\\](),]+)");\r
+ com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(\r
+ "\\S+([0-9+]+)\\S*:");\r
+ com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(\r
+ ":([-0-9.+]+)");\r
+\r
+ if (uqnodename.search(fstring) &&\r
+ ((uqnodename.matchedFrom(1) == 0) ||\r
+ (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!\r
+ {\r
+ if (nodename == null) {\r
+ if (ReplaceUnderscores) {\r
+ nodename = uqnodename.stringMatched(1).replace('_',\r
+ ' ');\r
+ } else {\r
+ nodename = uqnodename.stringMatched(1);\r
+ }\r
+ } else {\r
+ Error = ErrorStringrange(Error,\r
+ "File has broken algorithm - overwritten nodename",\r
+ 10, fcp, nf);\r
+ }\r
+ }\r
+\r
+ if (nbootstrap.search(fstring) &&\r
+ (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +\r
+ uqnodename.stringMatched().length()))) {\r
+ try {\r
+ bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();\r
+ HasBootstrap = true;\r
+ } catch (Exception e) {\r
+ Error = ErrorStringrange(Error,\r
+ "Can't parse bootstrap value", 4,\r
+ cp + nbootstrap.matchedFrom(), nf);\r
+ }\r
+ }\r
+\r
+ boolean nodehasdistance = false;\r
+\r
+ if (ndist.search(fstring)) {\r
+ try {\r
+ distance = (new Float(ndist.stringMatched(1))).floatValue();\r
+ HasDistances = true;\r
+ nodehasdistance = true;\r
+ } catch (Exception e) {\r
+ Error = ErrorStringrange(Error,\r
+ "Can't parse node distance value", 7,\r
+ cp + ndist.matchedFrom(), nf);\r
+ }\r
+ }\r
+\r
+ if (ascending) {\r
+ // Write node info here\r
+ c.setName(nodename);\r
+ c.dist = (HasDistances) ? distance : 0;\r
+ c.setBootstrap((HasBootstrap) ? bootstrap : 0);\r
+\r
+ if (c == realroot) {\r
+ RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!\r
+ }\r
+ } else {\r
+ // Find a place to put the leaf\r
+ SequenceNode newnode = new SequenceNode(null, c, nodename,\r
+ (HasDistances) ? distance : DefDistance,\r
+ (HasBootstrap) ? bootstrap : DefBootstrap, false);\r
+\r
+ if (c.right() == null) {\r
+ c.setRight(newnode);\r
+ } else {\r
+ if (c.left() == null) {\r
+ c.setLeft(newnode);\r
+ } else {\r
+ // Insert a dummy node for polytomy\r
+ SequenceNode newdummy = new SequenceNode(null, c,\r
+ null, 0, 0, true);\r
+ newdummy.SetChildren(c.left(), newnode);\r
+ c.setLeft(newdummy);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (ascending) {\r
+ // move back up the tree from preceding closure\r
+ c = c.AscendTree();\r
+\r
+ if ((d > -1) && (c == null)) {\r
+ Error = ErrorStringrange(Error,\r
+ "File broke algorithm: Lost place in tree (is there an extra ')' ?)",\r
+ 7, fcp, nf);\r
+ }\r
+ }\r
+\r
+ if (nf.charAt(fcp) == ')') {\r
+ d--;\r
+ ascending = true;\r
+ } else {\r
+ if (nf.charAt(fcp) == ',') {\r
+ if (ascending) {\r
+ ascending = false;\r
+ } else {\r
+ // Just advance focus, if we need to\r
+ if ((c.left() != null) && (!c.left().isLeaf())) {\r
+ c = (SequenceNode) c.left();\r
+ }\r
+ }\r
+ }\r
+ // else : We do nothing if ';' is encountered.\r
+ }\r
+\r
+ // Reset new node properties to obvious fakes\r
+ nodename = null;\r
+ distance = DefDistance;\r
+ bootstrap = DefBootstrap;\r
+\r
+ cp = fcp + 1;\r
+ }\r
+ }\r
+\r
+ if (Error != null) {\r
+ throw (new IOException("NewickFile: " + Error + "\n"));\r
+ }\r
+\r
+ root = (SequenceNode) root.right().detach(); // remove the imaginary root.\r
+\r
+ if (!RootHasDistance) {\r
+ root.dist = 0;\r
+ }\r
+ }\r
+\r
+ public SequenceNode getTree() {\r
+ return root;\r
+ }\r
+\r
+ public String print() {\r
+ synchronized (this) {\r
+ StringBuffer tf = new StringBuffer();\r
+ print(tf, root);\r
+\r
+ return (tf.append(";").toString());\r
+ }\r
+ }\r
+\r
+ public String print(boolean withbootstraps) {\r
+ synchronized (this) {\r
+ boolean boots = this.HasBootstrap;\r
+ this.HasBootstrap = withbootstraps;\r
+\r
+ String rv = print();\r
+ this.HasBootstrap = boots;\r
+\r
+ return rv;\r
+ }\r
+ }\r
+\r
+ public String print(boolean withbootstraps, boolean withdists) {\r
+ synchronized (this) {\r
+ boolean dists = this.HasDistances;\r
+ this.HasDistances = withdists;\r
+\r
+ String rv = print(withbootstraps);\r
+ this.HasDistances = dists;\r
+\r
+ return rv;\r
+ }\r
+ }\r
+\r
+ public String print(boolean withbootstraps, boolean withdists,\r
+ boolean printRootInfo) {\r
+ synchronized (this) {\r
+ boolean rootinfo = printRootInfo;\r
+ this.printRootInfo = printRootInfo;\r
+\r
+ String rv = print(withbootstraps, withdists);\r
+ this.printRootInfo = rootinfo;\r
+\r
+ return rv;\r
+ }\r
+ }\r
+\r
+ char getQuoteChar() {\r
+ return QuoteChar;\r
+ }\r
+\r
+ char setQuoteChar(char c) {\r
+ char old = QuoteChar;\r
+ QuoteChar = c;\r
+\r
+ return old;\r
+ }\r
+\r
+ private String nodeName(String name) {\r
+ if (NodeSafeName[0].search(name)) {\r
+ return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;\r
+ } else {\r
+ return NodeSafeName[2].replaceAll(name);\r
+ }\r
+ }\r
+\r
+ private String printNodeField(SequenceNode c) {\r
+ return ((c.getName() == null) ? "" : nodeName(c.getName())) +\r
+ ((HasBootstrap)\r
+ ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +\r
+ ((HasDistances) ? (":" + c.dist) : "");\r
+ }\r
+\r
+ private String printRootField(SequenceNode root) {\r
+ return (printRootInfo)\r
+ ? (((root.getName() == null) ? "" : nodeName(root.getName())) +\r
+ ((HasBootstrap)\r
+ ? ((root.getBootstrap() > -1) ? (" " + root.getBootstrap()) : "") : "") +\r
+ ((RootHasDistance) ? (":" + root.dist) : "")) : "";\r
+ }\r
+\r
+ // Non recursive call deals with root node properties\r
+ public void print(StringBuffer tf, SequenceNode root) {\r
+ if (root != null) {\r
+ if (root.isLeaf() && printRootInfo) {\r
+ tf.append(printRootField(root));\r
+ } else {\r
+ if (root.isDummy()) {\r
+ _print(tf, (SequenceNode) root.right());\r
+ _print(tf, (SequenceNode) root.left());\r
+ } else {\r
+ tf.append("(");\r
+ _print(tf, (SequenceNode) root.right());\r
+\r
+ if (root.left() != null) {\r
+ tf.append(",");\r
+ }\r
+\r
+ _print(tf, (SequenceNode) root.left());\r
+ tf.append(")" + printRootField(root));\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ // Recursive call for non-root nodes\r
+ public void _print(StringBuffer tf, SequenceNode c) {\r
+ if (c != null) {\r
+ if (c.isLeaf()) {\r
+ tf.append(printNodeField(c));\r
+ } else {\r
+ if (c.isDummy()) {\r
+ _print(tf, (SequenceNode) c.right());\r
+ _print(tf, (SequenceNode) c.left());\r
+ } else {\r
+ tf.append("(");\r
+ _print(tf, (SequenceNode) c.right());\r
+\r
+ if (c.left() != null) {\r
+ tf.append(",");\r
+ }\r
+\r
+ _print(tf, (SequenceNode) c.left());\r
+ tf.append(")" + printNodeField(c));\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ // Test\r
+ public static void main(String[] args) {\r
+ try {\r
+ File fn = new File(args[0]);\r
+\r
+ StringBuffer newickfile = new StringBuffer();\r
+ BufferedReader treefile = new BufferedReader(new FileReader(fn));\r
+ String l;\r
+\r
+ while ((l = treefile.readLine()) != null) {\r
+ newickfile.append(l);\r
+ }\r
+\r
+ treefile.close();\r
+ System.out.println("Read file :\n");\r
+\r
+ NewickFile trf = new NewickFile(args[0], "File");\r
+ trf.parse();\r
+ System.out.println("Original file :\n");\r
+\r
+ com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");\r
+ System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");\r
+\r
+ System.out.println("Parsed file.\n");\r
+ System.out.println("Default output type for original input.\n");\r
+ System.out.println(trf.print());\r
+ System.out.println("Without bootstraps.\n");\r
+ System.out.println(trf.print(false));\r
+ System.out.println("Without distances.\n");\r
+ System.out.println(trf.print(true, false));\r
+ System.out.println("Without bootstraps but with distanecs.\n");\r
+ System.out.println(trf.print(false, true));\r
+ System.out.println("Without bootstraps or distanecs.\n");\r
+ System.out.println(trf.print(false, false));\r
+ System.out.println("With bootstraps and with distances.\n");\r
+ System.out.println(trf.print(true, true));\r
+ } catch (java.io.IOException e) {\r
+ System.err.println("Exception\n" + e);\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
-import jalview.datamodel.*;\r
import jalview.analysis.*;\r
\r
+import jalview.datamodel.*;\r
+\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
+\r
public class PIRFile extends AlignFile {\r
+ Vector words = new Vector(); //Stores the words in a line after splitting\r
+\r
+ public PIRFile() {\r
+ }\r
\r
- Vector words = new Vector(); //Stores the words in a line after splitting\r
-\r
- public PIRFile()\r
- {}\r
-\r
- public PIRFile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
- public PIRFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
-\r
- public void parse() {\r
- try{\r
- String id, start, end;\r
- StringBuffer sequence;\r
- String line = null;\r
- while( (line = nextLine())!=null)\r
- {\r
- try{\r
- id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
- line = line.substring(line.indexOf("/") + 1);\r
- start = line.substring(0, line.indexOf("-"));\r
- end = line.substring(line.indexOf("-") + 1);\r
- }catch(Exception ex)\r
- { id="No id"; start="0"; end="0"; }\r
-\r
- sequence = new StringBuffer();\r
-\r
- line = nextLine(); // this is the title line\r
-\r
- boolean starFound = false;\r
- do\r
- {\r
- line = nextLine();\r
- sequence.append( line );\r
- if(line.indexOf("*")>-1)\r
- starFound = true;\r
-\r
- }while(!starFound);\r
-\r
- sequence.setLength( sequence.length()-1);\r
-\r
- Sequence newSeq = new Sequence(id,\r
- sequence.toString(),\r
- Integer.parseInt(start),\r
- Integer.parseInt(end));\r
- seqs.addElement(newSeq);\r
- }\r
+ public PIRFile(String inStr) {\r
+ super(inStr);\r
+ }\r
\r
+ public PIRFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
}\r
- catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
- public static String print(SequenceI[] s) {\r
- return print(s,72,true);\r
- }\r
- public static String print(SequenceI[] s, int len) {\r
- return print(s,len,true);\r
- }\r
- public static String print(SequenceI[] s, int len,boolean gaps) {\r
- StringBuffer out = new StringBuffer();\r
- int i = 0;\r
-\r
- while (i < s.length && s[i] != null) {\r
- String seq = "";\r
- if (gaps) {\r
- seq = s[i].getSequence() + "*";\r
- } else {\r
- seq = AlignSeq.extractGaps(s[i].getSequence(),"-");\r
- seq = AlignSeq.extractGaps(seq,".");\r
- seq = AlignSeq.extractGaps(seq," ");\r
- seq = seq + "*";\r
- }\r
-\r
- out.append(">P1;" + s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd() + "\n");\r
- out.append(" Dummy title\n");\r
- int nochunks = seq.length() / len + 1;\r
-\r
- for (int j = 0; j < nochunks; j++) {\r
- int start = j*len;\r
- int end = start + len;\r
-\r
- if (end < seq.length()) {\r
- out.append(seq.substring(start,end) + "\n");\r
- } else if (start < seq.length()) {\r
- out.append(seq.substring(start) + "\n");\r
+\r
+ public void parse() {\r
+ try {\r
+ String id;\r
+ String start;\r
+ String end;\r
+ StringBuffer sequence;\r
+ String line = null;\r
+\r
+ while ((line = nextLine()) != null) {\r
+ try {\r
+ id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
+ line = line.substring(line.indexOf("/") + 1);\r
+ start = line.substring(0, line.indexOf("-"));\r
+ end = line.substring(line.indexOf("-") + 1);\r
+ } catch (Exception ex) {\r
+ id = "No id";\r
+ start = "0";\r
+ end = "0";\r
+ }\r
+\r
+ sequence = new StringBuffer();\r
+\r
+ line = nextLine(); // this is the title line\r
+\r
+ boolean starFound = false;\r
+\r
+ do {\r
+ line = nextLine();\r
+ sequence.append(line);\r
+\r
+ if (line.indexOf("*") > -1) {\r
+ starFound = true;\r
+ }\r
+ } while (!starFound);\r
+\r
+ sequence.setLength(sequence.length() - 1);\r
+\r
+ Sequence newSeq = new Sequence(id, sequence.toString(),\r
+ Integer.parseInt(start), Integer.parseInt(end));\r
+ seqs.addElement(newSeq);\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
}\r
- }\r
- i++;\r
}\r
- return out.toString();\r
- }\r
\r
- public static void main(String[] args) {\r
- String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";\r
- PIRFile fa = new PIRFile(inStr);\r
- }\r
-}\r
+ public String print() {\r
+ return print(getSeqsAsArray());\r
+ }\r
\r
+ public static String print(SequenceI[] s) {\r
+ return print(s, 72, true);\r
+ }\r
\r
+ public static String print(SequenceI[] s, int len) {\r
+ return print(s, len, true);\r
+ }\r
\r
+ public static String print(SequenceI[] s, int len, boolean gaps) {\r
+ StringBuffer out = new StringBuffer();\r
+ int i = 0;\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String seq = "";\r
+\r
+ if (gaps) {\r
+ seq = s[i].getSequence() + "*";\r
+ } else {\r
+ seq = AlignSeq.extractGaps(s[i].getSequence(), "-");\r
+ seq = AlignSeq.extractGaps(seq, ".");\r
+ seq = AlignSeq.extractGaps(seq, " ");\r
+ seq = seq + "*";\r
+ }\r
+\r
+ out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd() + "\n");\r
+ out.append(" Dummy title\n");\r
+\r
+ int nochunks = (seq.length() / len) + 1;\r
+\r
+ for (int j = 0; j < nochunks; j++) {\r
+ int start = j * len;\r
+ int end = start + len;\r
+\r
+ if (end < seq.length()) {\r
+ out.append(seq.substring(start, end) + "\n");\r
+ } else if (start < seq.length()) {\r
+ out.append(seq.substring(start) + "\n");\r
+ }\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ public static void main(String[] args) {\r
+ String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";\r
+ PIRFile fa = new PIRFile(inStr);\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+\r
import jalview.util.*;\r
\r
import java.io.*;\r
-import java.util.*;\r
-\r
-public class PfamFile extends AlignFile {\r
-\r
- Vector ids;\r
\r
- public PfamFile()\r
- {}\r
+import java.util.*;\r
\r
- public PfamFile(String inStr) {\r
- super(inStr);\r
- }\r
\r
- public void initData() {\r
- super.initData();\r
- ids = new Vector();\r
- }\r
+public class PfamFile extends AlignFile {\r
+ Vector ids;\r
\r
- public PfamFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
+ public PfamFile() {\r
+ }\r
\r
- public void parse() throws IOException{\r
- int i = 0;\r
- String line;\r
+ public PfamFile(String inStr) {\r
+ super(inStr);\r
+ }\r
\r
+ public PfamFile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+ }\r
\r
- Hashtable seqhash = new Hashtable();\r
- Vector headers = new Vector();\r
+ public void initData() {\r
+ super.initData();\r
+ ids = new Vector();\r
+ }\r
\r
+ public void parse() throws IOException {\r
+ int i = 0;\r
+ String line;\r
\r
- while ((line = nextLine()) != null)\r
- {\r
+ Hashtable seqhash = new Hashtable();\r
+ Vector headers = new Vector();\r
\r
- if (line.indexOf(" ") != 0)\r
- {\r
- if (line.indexOf("#") != 0)\r
- {\r
+ while ((line = nextLine()) != null) {\r
+ if (line.indexOf(" ") != 0) {\r
+ if (line.indexOf("#") != 0) {\r
+ StringTokenizer str = new StringTokenizer(line, " ");\r
+ String id = "";\r
\r
- StringTokenizer str = new StringTokenizer(line," ");\r
- String id = "";\r
+ if (str.hasMoreTokens()) {\r
+ id = str.nextToken();\r
\r
- if (str.hasMoreTokens())\r
- {\r
- id = str.nextToken();\r
+ StringBuffer tempseq;\r
\r
- StringBuffer tempseq;\r
+ if (seqhash.containsKey(id)) {\r
+ tempseq = (StringBuffer) seqhash.get(id);\r
+ } else {\r
+ tempseq = new StringBuffer();\r
+ seqhash.put(id, tempseq);\r
+ }\r
\r
- if (seqhash.containsKey(id))\r
- tempseq = (StringBuffer)seqhash.get(id);\r
- else\r
- {\r
- tempseq = new StringBuffer();\r
- seqhash.put(id,tempseq);\r
- }\r
+ if (!(headers.contains(id))) {\r
+ headers.addElement(id);\r
+ }\r
\r
- if (!(headers.contains(id)))\r
- headers.addElement(id);\r
+ tempseq.append(str.nextToken());\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
+ this.noSeqs = headers.size();\r
\r
- tempseq.append(str.nextToken());\r
- }\r
+ if (noSeqs < 1) {\r
+ throw new IOException("No sequences found (PFAM input)");\r
}\r
- }\r
- }\r
\r
- this.noSeqs = headers.size();\r
- if(noSeqs<1)\r
- throw new IOException("No sequences found (PFAM input)");\r
-\r
- for (i = 0; i < headers.size(); i++ ) {\r
-\r
- if ( seqhash.get(headers.elementAt(i)) != null) {\r
- if (maxLength < seqhash.get(headers.elementAt(i)).toString().length() )\r
- maxLength = seqhash.get(headers.elementAt(i)).toString().length();\r
-\r
- String head = headers.elementAt(i).toString();\r
- int start = 1;\r
- int end = seqhash.get(headers.elementAt(i)).toString().length();\r
-\r
- if (head.indexOf("/") > 0 ) {\r
- StringTokenizer st = new StringTokenizer(head,"/");\r
- if (st.countTokens() == 2) {\r
- ids.addElement(st.nextToken());\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp,"-");\r
- if (st.countTokens() == 2) {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- } else\r
- {\r
- start = -1;\r
- end = -1;\r
+ for (i = 0; i < headers.size(); i++) {\r
+ if (seqhash.get(headers.elementAt(i)) != null) {\r
+ if (maxLength < seqhash.get(headers.elementAt(i)).toString()\r
+ .length()) {\r
+ maxLength = seqhash.get(headers.elementAt(i)).toString()\r
+ .length();\r
+ }\r
+\r
+ String head = headers.elementAt(i).toString();\r
+ int start = 1;\r
+ int end = seqhash.get(headers.elementAt(i)).toString().length();\r
+\r
+ if (head.indexOf("/") > 0) {\r
+ StringTokenizer st = new StringTokenizer(head, "/");\r
+\r
+ if (st.countTokens() == 2) {\r
+ ids.addElement(st.nextToken());\r
+\r
+ String tmp = st.nextToken();\r
+ st = new StringTokenizer(tmp, "-");\r
+\r
+ if (st.countTokens() == 2) {\r
+ start = Integer.valueOf(st.nextToken()).intValue();\r
+ end = Integer.valueOf(st.nextToken()).intValue();\r
+ } else {\r
+ start = -1;\r
+ end = -1;\r
+ }\r
+ } else {\r
+ ids.addElement(headers.elementAt(i));\r
+ }\r
+ } else {\r
+ ids.addElement(headers.elementAt(i));\r
+ }\r
+\r
+ Sequence newSeq = null;\r
+\r
+ if ((start != -1) && (end != -1)) {\r
+ newSeq = new Sequence(ids.elementAt(i).toString(),\r
+ seqhash.get(headers.elementAt(i).toString())\r
+ .toString(), start, end);\r
+ seqs.addElement(newSeq);\r
+ } else {\r
+ newSeq = new Sequence(ids.elementAt(i).toString(),\r
+ seqhash.get(headers.elementAt(i).toString())\r
+ .toString(), 1,\r
+ seqhash.get(headers.elementAt(i).toString())\r
+ .toString().length());\r
+ seqs.addElement(newSeq);\r
+ }\r
+\r
+ if (!isValidProteinSequence(newSeq.getSequence())) {\r
+ throw new IOException(\r
+ "Not a valid protein sequence - (PFAM input)");\r
+ }\r
+ } else {\r
+ System.err.println("PFAM File reader: Can't find sequence for " +\r
+ headers.elementAt(i));\r
}\r
- } else\r
- ids.addElement(headers.elementAt(i));\r
-\r
}\r
- else\r
- ids.addElement(headers.elementAt(i));\r
+ }\r
\r
+ public static String print(SequenceI[] s) {\r
+ StringBuffer out = new StringBuffer("");\r
\r
- Sequence newSeq = null;\r
- if (start != -1 && end != -1)\r
- {\r
- newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).toString()).toString(),start,end);\r
- seqs.addElement(newSeq);\r
- }\r
- else\r
- {\r
- newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).toString()).toString(),1,\r
- seqhash.get(headers.elementAt(i).toString()).toString().length());\r
- seqs.addElement(newSeq);\r
- }\r
+ int max = 0;\r
+ int maxid = 0;\r
\r
- if(!isValidProteinSequence(newSeq.getSequence()))\r
- throw new IOException("Not a valid protein sequence - (PFAM input)");\r
- }\r
- else\r
- System.err.println("PFAM File reader: Can't find sequence for " + headers.elementAt(i));\r
+ int i = 0;\r
\r
- }\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd();\r
\r
- }\r
+ if (s[i].getSequence().length() > max) {\r
+ max = s[i].getSequence().length();\r
+ }\r
\r
- public static String print(SequenceI[] s) {\r
- StringBuffer out = new StringBuffer("");\r
+ if (tmp.length() > maxid) {\r
+ maxid = tmp.length();\r
+ }\r
\r
- int max = 0;\r
- int maxid = 0;\r
+ i++;\r
+ }\r
\r
- int i = 0;\r
+ if (maxid < 15) {\r
+ maxid = 15;\r
+ }\r
\r
- while (i < s.length && s[i] != null) {\r
- String tmp = s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd();\r
+ int j = 0;\r
\r
- if (s[i].getSequence().length() > max) {\r
- max = s[i].getSequence().length();\r
- }\r
- if (tmp.length() > maxid) {\r
- maxid = tmp.length();\r
- }\r
- i++;\r
- }\r
+ while ((j < s.length) && (s[j] != null)) {\r
+ out.append(new Format("%-" + maxid + "s").form(s[j].getName() +\r
+ "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
\r
- if (maxid < 15) {\r
- maxid = 15;\r
- }\r
+ out.append(s[j].getSequence() + "\n");\r
+ j++;\r
+ }\r
\r
- int j = 0;\r
- while ( j < s.length && s[j] != null) {\r
- out.append( new Format("%-" + maxid + "s").form(s[j].getName() + "/" + s[j].getStart() + "-" + s[j].getEnd() ) + " ");\r
+ out.append("\n");\r
\r
- out.append(s[j].getSequence() + "\n");\r
- j++;\r
+ return out.toString();\r
}\r
- out.append("\n");\r
-\r
- return out.toString();\r
- }\r
\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
+ public String print() {\r
+ return print(getSeqsAsArray());\r
+ }\r
}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.io;
-
+*/\r
+package jalview.io;\r
+\r
+\r
/**
* <p>Title: </p>
* PileUpfile
* of a subset of the MSF alignment format. But, that was updated to reflect current
* GCG style IO fashion, as found in Emboss (thanks David Martin!)
*
- **/
-
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-import java.io.*;
-import java.util.*;
-
-
-public class PileUpfile
- extends AlignFile
-{
-
-public PileUpfile()
-{}
-
-public PileUpfile(String inStr) {
- super(inStr);
-}
-
-public PileUpfile(String inFile, String type) throws IOException {
- super(inFile,type);
-}
-
-public void parse() {
-
- int i = 0;
- boolean seqFlag = false;
- String key = new String();
- Vector headers = new Vector();
- Hashtable seqhash = new Hashtable();
- String line;
-
- try {
- while ((line = nextLine()) != null) {
-
- StringTokenizer str = new StringTokenizer(line);
-
- while (str.hasMoreTokens()) {
-
- String inStr = str.nextToken();
-
- //If line has header information add to the headers vector
- if (inStr.indexOf("Name:") != -1) {
- key = str.nextToken();
- headers.addElement(key);
- }
-
- //if line has // set SeqFlag to 1 so we know sequences are coming
- if (inStr.indexOf("//") != -1) {
- seqFlag = true;
- }
-
- //Process lines as sequence lines if seqFlag is set
- if (( inStr.indexOf("//") == -1) && (seqFlag == true)) {
- //seqeunce id is the first field
- key = inStr;
- StringBuffer tempseq;
-
- //Get sequence from hash if it exists
- if (seqhash.containsKey(key)) {
- tempseq = (StringBuffer)seqhash.get(key);
- } else {
- tempseq = new StringBuffer();
- seqhash.put(key,tempseq);
- }
-
- //loop through the rest of the words
- while (str.hasMoreTokens()) {
- //append the word to the sequence
- tempseq.append(str.nextToken());
- }
- }
- }
- }
- } catch (IOException e) {
- System.err.println("Exception parsing PileUpfile " + e);
- e.printStackTrace();
- }
-
- this.noSeqs = headers.size();
-
- //Add sequences to the hash
- for (i = 0; i < headers.size(); i++ ) {
-
- if ( seqhash.get(headers.elementAt(i)) != null) {
- String head = headers.elementAt(i).toString();
- String seq = seqhash.get(head).toString();
-
- int start = 1;
- int end = seq.length();
-
- if (maxLength < head.length() ) {
- maxLength = head.length();
- }
-
- if (head.indexOf("/") > 0 ) {
-
- StringTokenizer st = new StringTokenizer(head,"/");
-
- if (st.countTokens() == 2) {
-
- head = st.nextToken();
- String tmp = st.nextToken();
- st = new StringTokenizer(tmp,"-");
- if (st.countTokens() == 2) {
- start = Integer.valueOf(st.nextToken()).intValue();
- end = Integer.valueOf(st.nextToken()).intValue();
- }
- }
- }
-
- Sequence newSeq = new Sequence(head,seq,start,end);
-
- seqs.addElement(newSeq);
-
- } else {
- System.err.println("PileUpfile Parser: Can't find sequence for " + headers.elementAt(i));
- }
- }
-
-}
-
-public static int checkSum(String seq) {
- //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
- int check = 0;
-
- String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
- index += "--------------------------------------------------------------------------------------------------------------------------------";
-
- for(int i = 0; i < seq.length(); i++) {
- try {
- if (i <seq.length()) {
- int pos = index.indexOf(seq.substring(i,i+1));
- if (!index.substring(pos,pos+1).equals("_")) {
- check += ((i % 57) + 1) * pos;
- }
- }
- } catch (Exception e) {
- System.err.println("Exception during MSF Checksum calculation");
- e.printStackTrace();
- }
- }
- return check % 10000;
-}
-
-public static String print(SequenceI[] s) {
- StringBuffer out = new StringBuffer("PileUp\n\n");
-
- int max = 0;
- int maxid = 0;
-
- int i = 0;
- String big = "";
- while (i < s.length && s[i] != null) {
- big += s[i].getSequence();
- i++;
- }
- i = 0;
- int bigcheck = checkSum(big);
-
- out.append(" MSF: " + s[0].getSequence().length() + " Type: P Check: " + bigcheck + " ..\n\n\n");
-
- while (i < s.length && s[i] != null) {
- String seq = s[i].getSequence();
- String name = s[i].getName()+ "/" + s[i].getStart() + "-" + s[i].getEnd();
- int check = checkSum(s[i].getSequence());
- out.append(" Name: " + name + " oo Len: " + s[i].getSequence().length() + " Check: " + check + " Weight: 1.00\n");
- if (seq.length() > max) {
- max = seq.length();
- }
- if (name.length() > maxid) {
- maxid = name.length();
- }
- i++;
- }
-
- if (maxid < 10) {
- maxid = 10;
- }
- maxid++;
- out.append( "\n\n//\n\n");
-
- int len = 50;
-
- int nochunks = max / len + 1;
- if (max%len == 0) {
- nochunks--;
- }
- for (i = 0; i < nochunks; i++) {
- int j = 0;
- while (j < s.length && s[j] != null) {
- String name = s[j].getName();
- out.append( new Format("%-" + maxid + "s").form(name + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
- for (int k = 0; k < 5; k++) {
-
- int start = i*50 + k*10;
- int end = start + 10;
-
- if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
- out.append(s[j].getSequence().substring(start,end));
- if (k < 4) {
- out.append(" ");
- } else {
- out.append("\n");
- }
- } else {
- if (start < s[j].getSequence().length()) {
- out.append(s[j].getSequence().substring(start));
- out.append("\n");
- } else {
- if (k == 0) {
- out.append("\n");
- }
- }
- }
- }
- j++;
- }
- out.append("\n");
-
- }
- return out.toString();
-}
-public String print() {
- return print(getSeqsAsArray());
-}
-}
-
-
-
-
-
-
-
+ **/\r
+import jalview.datamodel.*;\r
+\r
+import jalview.util.*;\r
+\r
+import java.io.*;\r
+\r
+import java.util.*;\r
+\r
+\r
+public class PileUpfile extends AlignFile {\r
+ public PileUpfile() {\r
+ }\r
+\r
+ public PileUpfile(String inStr) {\r
+ super(inStr);\r
+ }\r
+\r
+ public PileUpfile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public void parse() {\r
+ int i = 0;\r
+ boolean seqFlag = false;\r
+ String key = new String();\r
+ Vector headers = new Vector();\r
+ Hashtable seqhash = new Hashtable();\r
+ String line;\r
+\r
+ try {\r
+ while ((line = nextLine()) != null) {\r
+ StringTokenizer str = new StringTokenizer(line);\r
+\r
+ while (str.hasMoreTokens()) {\r
+ String inStr = str.nextToken();\r
+\r
+ //If line has header information add to the headers vector\r
+ if (inStr.indexOf("Name:") != -1) {\r
+ key = str.nextToken();\r
+ headers.addElement(key);\r
+ }\r
+\r
+ //if line has // set SeqFlag to 1 so we know sequences are coming\r
+ if (inStr.indexOf("//") != -1) {\r
+ seqFlag = true;\r
+ }\r
+\r
+ //Process lines as sequence lines if seqFlag is set\r
+ if ((inStr.indexOf("//") == -1) && (seqFlag == true)) {\r
+ //seqeunce id is the first field\r
+ key = inStr;\r
+\r
+ StringBuffer tempseq;\r
+\r
+ //Get sequence from hash if it exists\r
+ if (seqhash.containsKey(key)) {\r
+ tempseq = (StringBuffer) seqhash.get(key);\r
+ } else {\r
+ tempseq = new StringBuffer();\r
+ seqhash.put(key, tempseq);\r
+ }\r
+\r
+ //loop through the rest of the words\r
+ while (str.hasMoreTokens()) {\r
+ //append the word to the sequence\r
+ tempseq.append(str.nextToken());\r
+ }\r
+ }\r
+ }\r
+ }\r
+ } catch (IOException e) {\r
+ System.err.println("Exception parsing PileUpfile " + e);\r
+ e.printStackTrace();\r
+ }\r
+\r
+ this.noSeqs = headers.size();\r
+\r
+ //Add sequences to the hash\r
+ for (i = 0; i < headers.size(); i++) {\r
+ if (seqhash.get(headers.elementAt(i)) != null) {\r
+ String head = headers.elementAt(i).toString();\r
+ String seq = seqhash.get(head).toString();\r
+\r
+ int start = 1;\r
+ int end = seq.length();\r
+\r
+ if (maxLength < head.length()) {\r
+ maxLength = head.length();\r
+ }\r
+\r
+ if (head.indexOf("/") > 0) {\r
+ StringTokenizer st = new StringTokenizer(head, "/");\r
+\r
+ if (st.countTokens() == 2) {\r
+ head = st.nextToken();\r
+\r
+ String tmp = st.nextToken();\r
+ st = new StringTokenizer(tmp, "-");\r
+\r
+ if (st.countTokens() == 2) {\r
+ start = Integer.valueOf(st.nextToken()).intValue();\r
+ end = Integer.valueOf(st.nextToken()).intValue();\r
+ }\r
+ }\r
+ }\r
+\r
+ Sequence newSeq = new Sequence(head, seq, start, end);\r
+\r
+ seqs.addElement(newSeq);\r
+ } else {\r
+ System.err.println(\r
+ "PileUpfile Parser: Can't find sequence for " +\r
+ headers.elementAt(i));\r
+ }\r
+ }\r
+ }\r
+\r
+ public static int checkSum(String seq) {\r
+ //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";\r
+ int check = 0;\r
+\r
+ String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";\r
+ index += "--------------------------------------------------------------------------------------------------------------------------------";\r
+\r
+ for (int i = 0; i < seq.length(); i++) {\r
+ try {\r
+ if (i < seq.length()) {\r
+ int pos = index.indexOf(seq.substring(i, i + 1));\r
+\r
+ if (!index.substring(pos, pos + 1).equals("_")) {\r
+ check += (((i % 57) + 1) * pos);\r
+ }\r
+ }\r
+ } catch (Exception e) {\r
+ System.err.println("Exception during MSF Checksum calculation");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ return check % 10000;\r
+ }\r
+\r
+ public static String print(SequenceI[] s) {\r
+ StringBuffer out = new StringBuffer("PileUp\n\n");\r
+\r
+ int max = 0;\r
+ int maxid = 0;\r
+\r
+ int i = 0;\r
+ String big = "";\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ big += s[i].getSequence();\r
+ i++;\r
+ }\r
+\r
+ i = 0;\r
+\r
+ int bigcheck = checkSum(big);\r
+\r
+ out.append(" MSF: " + s[0].getSequence().length() +\r
+ " Type: P Check: " + bigcheck + " ..\n\n\n");\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String seq = s[i].getSequence();\r
+ String name = s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd();\r
+ int check = checkSum(s[i].getSequence());\r
+ out.append(" Name: " + name + " oo Len: " +\r
+ s[i].getSequence().length() + " Check: " + check +\r
+ " Weight: 1.00\n");\r
+\r
+ if (seq.length() > max) {\r
+ max = seq.length();\r
+ }\r
+\r
+ if (name.length() > maxid) {\r
+ maxid = name.length();\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ if (maxid < 10) {\r
+ maxid = 10;\r
+ }\r
+\r
+ maxid++;\r
+ out.append("\n\n//\n\n");\r
+\r
+ int len = 50;\r
+\r
+ int nochunks = (max / len) + 1;\r
+\r
+ if ((max % len) == 0) {\r
+ nochunks--;\r
+ }\r
+\r
+ for (i = 0; i < nochunks; i++) {\r
+ int j = 0;\r
+\r
+ while ((j < s.length) && (s[j] != null)) {\r
+ String name = s[j].getName();\r
+ out.append(new Format("%-" + maxid + "s").form(name + "/" +\r
+ s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+\r
+ for (int k = 0; k < 5; k++) {\r
+ int start = (i * 50) + (k * 10);\r
+ int end = start + 10;\r
+\r
+ if ((end < s[j].getSequence().length()) &&\r
+ (start < s[j].getSequence().length())) {\r
+ out.append(s[j].getSequence().substring(start, end));\r
+\r
+ if (k < 4) {\r
+ out.append(" ");\r
+ } else {\r
+ out.append("\n");\r
+ }\r
+ } else {\r
+ if (start < s[j].getSequence().length()) {\r
+ out.append(s[j].getSequence().substring(start));\r
+ out.append("\n");\r
+ } else {\r
+ if (k == 0) {\r
+ out.append("\n");\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ j++;\r
+ }\r
+\r
+ out.append("\n");\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ public String print() {\r
+ return print(getSeqsAsArray());\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
+import jalview.datamodel.*;\r
+\r
+import jalview.gui.*;\r
+\r
+import jalview.io.*;\r
+\r
import java.io.*;\r
+\r
import java.util.*;\r
+\r
import javax.swing.*;\r
-import jalview.io.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
\r
-public class SequenceFeatureFetcher implements Runnable\r
-{\r
- AlignmentI align;\r
- AlignmentPanel ap;\r
- ArrayList unknownSequences;\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
- public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
- {\r
- unknownSequences = new ArrayList();\r
- this.align = align;\r
- this.ap = ap;\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- }\r
-\r
- public void run()\r
-{\r
-\r
- String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");\r
-\r
- RandomAccessFile out = null;\r
-\r
- try{\r
- if (cache == null)\r
- {\r
- jalview.bin.Cache.setProperty("UNIPROT_CACHE", System.getProperty("user.home")+"/uniprot.xml");\r
- cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");\r
- }\r
\r
+public class SequenceFeatureFetcher implements Runnable {\r
+ AlignmentI align;\r
+ AlignmentPanel ap;\r
+ ArrayList unknownSequences;\r
+ CutAndPasteTransfer output = new CutAndPasteTransfer();\r
+ StringBuffer sbuffer = new StringBuffer();\r
\r
+ public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap) {\r
+ unknownSequences = new ArrayList();\r
+ this.align = align;\r
+ this.ap = ap;\r
\r
- File test = new File(cache);\r
- if( !test.exists() )\r
- {\r
- out = new RandomAccessFile(cache, "rw");\r
- out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");\r
- out.writeBytes("<UNIPROT_CACHE>\n");\r
- }\r
- else\r
- {\r
- out = new RandomAccessFile(cache, "rw");\r
- // open exisiting cache and remove </UNIPROT_CACHE> from the end\r
- long lastLine = 0;\r
- String data;\r
- while ( (data = out.readLine()) != null)\r
- {\r
- if (data.indexOf("</entry>") > -1)\r
- lastLine = out.getFilePointer();\r
-\r
- }\r
- out.seek(lastLine);\r
+ Thread thread = new Thread(this);\r
+ thread.start();\r
}\r
\r
- int seqIndex = 0;\r
- Vector sequences = align.getSequences();\r
+ public void run() {\r
+ String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");\r
\r
- while (seqIndex < sequences.size())\r
- {\r
- ArrayList ids = new ArrayList();\r
- for (int i = 0; seqIndex < sequences.size() && i < 50; seqIndex++, i++)\r
- {\r
- SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
- ids.add(sequence.getName());\r
- }\r
+ RandomAccessFile out = null;\r
\r
- tryLocalCacheFirst(ids, align);\r
+ try {\r
+ if (cache == null) {\r
+ jalview.bin.Cache.setProperty("UNIPROT_CACHE",\r
+ System.getProperty("user.home") + "/uniprot.xml");\r
+ cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");\r
+ }\r
\r
- if (ids.size() > 0)\r
- {\r
- StringBuffer remainingIds = new StringBuffer("uniprot:");\r
- for (int i = 0; i < ids.size(); i++)\r
- remainingIds.append(ids.get(i) + ";");\r
+ File test = new File(cache);\r
\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);\r
+ if (!test.exists()) {\r
+ out = new RandomAccessFile(cache, "rw");\r
+ out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");\r
+ out.writeBytes("<UNIPROT_CACHE>\n");\r
+ } else {\r
+ out = new RandomAccessFile(cache, "rw");\r
\r
- if(result!=null)\r
- ReadUniprotFile(result, out, align);\r
- }\r
+ // open exisiting cache and remove </UNIPROT_CACHE> from the end\r
+ long lastLine = 0;\r
+ String data;\r
\r
- }\r
+ while ((data = out.readLine()) != null) {\r
+ if (data.indexOf("</entry>") > -1) {\r
+ lastLine = out.getFilePointer();\r
+ }\r
+ }\r
\r
- if (out != null)\r
- {\r
- out.writeBytes("</UNIPROT_CACHE>\n");\r
- out.close();\r
- }\r
- }catch(Exception ex){ex.printStackTrace();}\r
+ out.seek(lastLine);\r
+ }\r
\r
- ap.repaint();\r
- findMissingIds(align);\r
- if(sbuffer.length()>0)\r
- {\r
- output.setText("Your sequences have been matched to Uniprot. Some of the ids have been\n"\r
- +"altered, most likely the start/end residue will have been updated.\n"\r
- +"Save your alignment to maintain the updated id.\n\n"+sbuffer.toString());\r
- Desktop.addInternalFrame(output, "Sequence names updated ", 600,300);\r
+ int seqIndex = 0;\r
+ Vector sequences = align.getSequences();\r
\r
- }\r
+ while (seqIndex < sequences.size()) {\r
+ ArrayList ids = new ArrayList();\r
\r
- if(unknownSequences.size()>0)\r
- {\r
- //ignore for now!!!!!!!!!!\r
- // WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);\r
- }\r
+ for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
+ seqIndex++, i++) {\r
+ SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
+ ids.add(sequence.getName());\r
+ }\r
\r
-}\r
+ tryLocalCacheFirst(ids, align);\r
+\r
+ if (ids.size() > 0) {\r
+ StringBuffer remainingIds = new StringBuffer("uniprot:");\r
\r
-void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)\r
-{\r
- SequenceI sequence = null;\r
- Vector features = null;\r
- String type, description, status, start, end, pdb = null;\r
-\r
-\r
- for (int r = 0; r < result.length; r++)\r
- {\r
- if(sequence==null && result[r].indexOf("<name>")>-1)\r
- {\r
- long filePointer = 0;\r
-\r
- if(out!=null)\r
- try{\r
- filePointer=out.getFilePointer();\r
- out.writeBytes("<entry>\n");\r
- }catch(Exception ex){}\r
-\r
- String seqName = parseElement( result[r], "<name>" , out);\r
- sequence = align.findName( seqName ) ;\r
- if(sequence==null)\r
- {\r
- sequence = align.findName( seqName.substring(0, seqName.indexOf('_')));\r
- if(sequence!=null)\r
- {\r
- sbuffer.append("changing "+sequence.getName()+" to "+seqName+"\n");\r
- sequence.setName(seqName);\r
+ for (int i = 0; i < ids.size(); i++)\r
+ remainingIds.append(ids.get(i) + ";");\r
+\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String[] result = ebi.fetchData(remainingIds.toString(),\r
+ "xml", null);\r
+\r
+ if (result != null) {\r
+ ReadUniprotFile(result, out, align);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (out != null) {\r
+ out.writeBytes("</UNIPROT_CACHE>\n");\r
+ out.close();\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
}\r
- }\r
- if(sequence==null)\r
- {\r
- sbuffer.append("UNIPROT updated suggestion is "+result[r]+"\n");\r
- sequence = align.findName( result[r] ) ;\r
-\r
- // this entry has been suggested by ebi.\r
- // doesn't match id in alignment file\r
- try { out.setLength(filePointer); } catch (Exception ex) {}\r
- // now skip to next entry\r
- while( result[r].indexOf("</entry>")==-1)\r
- r++;\r
- }\r
-\r
- features = new Vector();\r
- type=""; start="0"; end="0"; description=""; status=""; pdb="";\r
\r
+ ap.repaint();\r
+ findMissingIds(align);\r
+\r
+ if (sbuffer.length() > 0) {\r
+ output.setText(\r
+ "Your sequences have been matched to Uniprot. Some of the ids have been\n" +\r
+ "altered, most likely the start/end residue will have been updated.\n" +\r
+ "Save your alignment to maintain the updated id.\n\n" +\r
+ sbuffer.toString());\r
+ Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
+ }\r
+\r
+ if (unknownSequences.size() > 0) {\r
+ //ignore for now!!!!!!!!!!\r
+ // WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);\r
+ }\r
}\r
\r
- if(sequence==null)\r
- continue;\r
-\r
- if( result[r].indexOf("<property type=\"pdb accession\"")>-1)\r
- {\r
- pdb = parseValue( result[r], "value=" , out);\r
- sequence.setPDBId(pdb);\r
- }\r
-\r
- if(result[r].indexOf("feature type")>-1)\r
- {\r
- type = parseValue( result[r], "type=" , out);\r
- description = parseValue( result[r], "description=" , null );\r
- status = parseValue ( result[r], "status=", null);\r
-\r
- while( result[r].indexOf("position")==-1)\r
- {\r
- r++; //<location>\r
- }\r
- // r++;\r
- if(result[r].indexOf("begin")>-1)\r
- {\r
- start = parseValue( result[r], "position=" , out);\r
- end = parseValue( result[++r], "position=" , out);\r
- }\r
- else\r
- {\r
- start = parseValue( result[r], "position=" , out);\r
- end = parseValue( result[r], "position=" , null);\r
- }\r
- int sstart = Integer.parseInt(start);\r
- int eend = Integer.parseInt(end);\r
- if(out!=null)\r
- try{ out.writeBytes("</feature>\n"); }catch(Exception ex){}\r
-\r
- SequenceFeature sf = new SequenceFeature(type,\r
- sstart,\r
- eend,\r
- description,\r
- status);\r
- features.add(sf);\r
- }\r
-\r
- if(result[r].indexOf("<sequence")>-1)\r
- {\r
- StringBuffer seqString = new StringBuffer();\r
-\r
- if(out!=null)\r
- try { out.writeBytes(result[r]+"\n"); } catch (Exception ex){}\r
-\r
- while(result[++r].indexOf("</sequence>")==-1)\r
- {\r
- seqString.append(result[r]);\r
- if(out!=null)\r
- try { out.writeBytes(result[r]+"\n"); } catch (Exception ex){}\r
- }\r
-\r
- if(out!=null)\r
- try { out.writeBytes(result[r]+"\n"); } catch (Exception ex){}\r
-\r
- StringBuffer nonGapped = new StringBuffer();\r
- for (int i = 0; i < sequence.getSequence().length(); i++)\r
- {\r
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))\r
- nonGapped.append(sequence.getCharAt(i));\r
- }\r
-\r
- int absStart = seqString.toString().indexOf(nonGapped.toString());\r
- if(absStart==-1)\r
- {\r
- unknownSequences.add(sequence.getName());\r
- features = null;\r
- sbuffer.append(sequence.getName()+ " SEQUENCE NOT %100 MATCH \n");\r
- continue;\r
- }\r
-\r
- int absEnd = absStart + nonGapped.toString().length();\r
- absStart+=1;\r
-\r
- if(absStart!=sequence.getStart() || absEnd!=sequence.getEnd())\r
- sbuffer.append("Updated: "+sequence.getName()+" "+\r
- sequence.getStart()+"/"+sequence.getEnd()+" to "+ absStart+"/"+absEnd+"\n");\r
-\r
-\r
- sequence.setStart(absStart);\r
- sequence.setEnd(absEnd);\r
-\r
- }\r
-\r
- if(result[r].indexOf("</entry>")>-1)\r
- {\r
- if(features!=null)\r
- sequence.setSequenceFeatures( features );\r
- features = null;\r
- sequence = null;\r
- if(out!=null)\r
- try{ out.writeBytes("</entry>\n"); }catch(Exception ex){}\r
-\r
- }\r
- }\r
-}\r
+ void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align) {\r
+ SequenceI sequence = null;\r
+ Vector features = null;\r
+ String type;\r
+ String description;\r
+ String status;\r
+ String start;\r
+ String end;\r
+ String pdb = null;\r
+\r
+ for (int r = 0; r < result.length; r++) {\r
+ if ((sequence == null) && (result[r].indexOf("<name>") > -1)) {\r
+ long filePointer = 0;\r
+\r
+ if (out != null) {\r
+ try {\r
+ filePointer = out.getFilePointer();\r
+ out.writeBytes("<entry>\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+\r
+ String seqName = parseElement(result[r], "<name>", out);\r
+ sequence = align.findName(seqName);\r
+\r
+ if (sequence == null) {\r
+ sequence = align.findName(seqName.substring(0,\r
+ seqName.indexOf('_')));\r
+\r
+ if (sequence != null) {\r
+ sbuffer.append("changing " + sequence.getName() +\r
+ " to " + seqName + "\n");\r
+ sequence.setName(seqName);\r
+ }\r
+ }\r
+\r
+ if (sequence == null) {\r
+ sbuffer.append("UNIPROT updated suggestion is " +\r
+ result[r] + "\n");\r
+ sequence = align.findName(result[r]);\r
+\r
+ // this entry has been suggested by ebi.\r
+ // doesn't match id in alignment file\r
+ try {\r
+ out.setLength(filePointer);\r
+ } catch (Exception ex) {\r
+ }\r
+\r
+ // now skip to next entry\r
+ while (result[r].indexOf("</entry>") == -1)\r
+ r++;\r
+ }\r
+\r
+ features = new Vector();\r
+ type = "";\r
+ start = "0";\r
+ end = "0";\r
+ description = "";\r
+ status = "";\r
+ pdb = "";\r
+ }\r
+\r
+ if (sequence == null) {\r
+ continue;\r
+ }\r
+\r
+ if (result[r].indexOf("<property type=\"pdb accession\"") > -1) {\r
+ pdb = parseValue(result[r], "value=", out);\r
+ sequence.setPDBId(pdb);\r
+ }\r
+\r
+ if (result[r].indexOf("feature type") > -1) {\r
+ type = parseValue(result[r], "type=", out);\r
+ description = parseValue(result[r], "description=", null);\r
+ status = parseValue(result[r], "status=", null);\r
+\r
+ while (result[r].indexOf("position") == -1) {\r
+ r++; //<location>\r
+ }\r
+\r
+ // r++;\r
+ if (result[r].indexOf("begin") > -1) {\r
+ start = parseValue(result[r], "position=", out);\r
+ end = parseValue(result[++r], "position=", out);\r
+ } else {\r
+ start = parseValue(result[r], "position=", out);\r
+ end = parseValue(result[r], "position=", null);\r
+ }\r
+\r
+ int sstart = Integer.parseInt(start);\r
+ int eend = Integer.parseInt(end);\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes("</feature>\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+\r
+ SequenceFeature sf = new SequenceFeature(type, sstart, eend,\r
+ description, status);\r
+ features.add(sf);\r
+ }\r
+\r
+ if (result[r].indexOf("<sequence") > -1) {\r
+ StringBuffer seqString = new StringBuffer();\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(result[r] + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+\r
+ while (result[++r].indexOf("</sequence>") == -1) {\r
+ seqString.append(result[r]);\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(result[r] + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+ }\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(result[r] + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+\r
+ StringBuffer nonGapped = new StringBuffer();\r
+\r
+ for (int i = 0; i < sequence.getSequence().length(); i++) {\r
+ if (!jalview.util.Comparison.isGap(sequence.getCharAt(i))) {\r
+ nonGapped.append(sequence.getCharAt(i));\r
+ }\r
+ }\r
+\r
+ int absStart = seqString.toString().indexOf(nonGapped.toString());\r
+\r
+ if (absStart == -1) {\r
+ unknownSequences.add(sequence.getName());\r
+ features = null;\r
+ sbuffer.append(sequence.getName() +\r
+ " SEQUENCE NOT %100 MATCH \n");\r
+\r
+ continue;\r
+ }\r
+\r
+ int absEnd = absStart + nonGapped.toString().length();\r
+ absStart += 1;\r
+\r
+ if ((absStart != sequence.getStart()) ||\r
+ (absEnd != sequence.getEnd())) {\r
+ sbuffer.append("Updated: " + sequence.getName() + " " +\r
+ sequence.getStart() + "/" + sequence.getEnd() +\r
+ " to " + absStart + "/" + absEnd + "\n");\r
+ }\r
+\r
+ sequence.setStart(absStart);\r
+ sequence.setEnd(absEnd);\r
+ }\r
+\r
+ if (result[r].indexOf("</entry>") > -1) {\r
+ if (features != null) {\r
+ sequence.setSequenceFeatures(features);\r
+ }\r
+\r
+ features = null;\r
+ sequence = null;\r
+\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes("</entry>\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
-void findMissingIds(AlignmentI align)\r
-{\r
- String data;\r
- ArrayList cachedIds = new ArrayList();\r
-\r
- try\r
- {\r
- BufferedReader in = new BufferedReader(\r
- new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
-\r
- while ( (data = in.readLine()) != null)\r
- {\r
- if (data.indexOf("name") > -1)\r
- {\r
- String name = parseElement(data, "<name>", null);\r
- cachedIds.add(name);\r
- }\r
+ void findMissingIds(AlignmentI align) {\r
+ String data;\r
+ ArrayList cachedIds = new ArrayList();\r
+\r
+ try {\r
+ BufferedReader in = new BufferedReader(new FileReader(\r
+ jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
+\r
+ while ((data = in.readLine()) != null) {\r
+ if (data.indexOf("name") > -1) {\r
+ String name = parseElement(data, "<name>", null);\r
+ cachedIds.add(name);\r
+ }\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ for (int i = 0; i < align.getHeight(); i++)\r
+ if (!cachedIds.contains(align.getSequenceAt(i).getName())) {\r
+ unknownSequences.add(align.getSequenceAt(i).getName());\r
+ }\r
}\r
- }\r
- catch (Exception ex)\r
- { ex.printStackTrace(); }\r
\r
- for(int i=0; i<align.getHeight(); i++)\r
- if( !cachedIds.contains( align.getSequenceAt(i).getName() ) )\r
- unknownSequences.add( align.getSequenceAt(i).getName() );\r
+ void tryLocalCacheFirst(ArrayList ids, AlignmentI align) {\r
+ ArrayList cacheData = new ArrayList();\r
\r
+ try {\r
+ BufferedReader in = new BufferedReader(new FileReader(\r
+ jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
\r
-}\r
+ // read through cache file, if the cache has sequences we're looking for\r
+ // add the lines to a new String array, Readthis new array and\r
+ // make sure we remove the ids from the list to retrieve from EBI\r
+ String data;\r
\r
-void tryLocalCacheFirst(ArrayList ids, AlignmentI align)\r
-{\r
- ArrayList cacheData = new ArrayList();\r
- try{\r
- BufferedReader in = new BufferedReader(\r
- new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
-\r
- // read through cache file, if the cache has sequences we're looking for\r
- // add the lines to a new String array, Readthis new array and\r
- // make sure we remove the ids from the list to retrieve from EBI\r
- String data;\r
- while( ( data=in.readLine())!=null)\r
- {\r
- if(data.indexOf("name")>-1)\r
- {\r
- String name = parseElement( data, "<name>" , null) ;\r
- if(ids.contains( name ) )\r
- {\r
- cacheData.add("<entry>");\r
- cacheData.add(data);\r
- while( data.indexOf("</entry>")==-1)\r
- {\r
- data = in.readLine();\r
- cacheData.add(data);\r
- }\r
- cacheData.add(data);\r
-\r
- ids.remove( name );\r
- }\r
- }\r
- }\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\r
+ while ((data = in.readLine()) != null) {\r
+ if (data.indexOf("name") > -1) {\r
+ String name = parseElement(data, "<name>", null);\r
\r
- String [] localData = new String[cacheData.size()];\r
- cacheData.toArray( localData );\r
- if(localData!=null && localData.length>0)\r
- ReadUniprotFile(localData, null, align);\r
-}\r
+ if (ids.contains(name)) {\r
+ cacheData.add("<entry>");\r
+ cacheData.add(data);\r
\r
+ while (data.indexOf("</entry>") == -1) {\r
+ data = in.readLine();\r
+ cacheData.add(data);\r
+ }\r
\r
-String parseValue(String line, String tag, RandomAccessFile out)\r
-{\r
- if(out!=null)\r
- try{ out.writeBytes(line+"\n"); }catch(Exception ex){}\r
+ cacheData.add(data);\r
\r
+ ids.remove(name);\r
+ }\r
+ }\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
\r
- int index = line.indexOf(tag)+tag.length()+1;\r
- if(index==tag.length())\r
- return "";\r
+ String[] localData = new String[cacheData.size()];\r
+ cacheData.toArray(localData);\r
\r
- return line.substring( index, line.indexOf("\"", index+1) );\r
-}\r
+ if ((localData != null) && (localData.length > 0)) {\r
+ ReadUniprotFile(localData, null, align);\r
+ }\r
+ }\r
+\r
+ String parseValue(String line, String tag, RandomAccessFile out) {\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(line + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
\r
+ int index = line.indexOf(tag) + tag.length() + 1;\r
\r
-String parseElement(String line, String tag, RandomAccessFile out)\r
-{\r
- if (out != null)\r
- try\r
- {\r
- out.writeBytes(line + "\n");\r
+ if (index == tag.length()) {\r
+ return "";\r
+ }\r
+\r
+ return line.substring(index, line.indexOf("\"", index + 1));\r
}\r
- catch (Exception ex)\r
- {}\r
\r
- int index = line.indexOf(tag) + tag.length();\r
- return line.substring(index, line.indexOf("</"));\r
+ String parseElement(String line, String tag, RandomAccessFile out) {\r
+ if (out != null) {\r
+ try {\r
+ out.writeBytes(line + "\n");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
\r
- }\r
+ int index = line.indexOf(tag) + tag.length();\r
+\r
+ return line.substring(index, line.indexOf("</"));\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
-import org.apache.axis.client.*;\r
-import javax.xml.namespace.QName;\r
-import java.util.*;\r
import jalview.datamodel.*;\r
+\r
import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
+\r
+import org.apache.axis.client.*;\r
+\r
import java.awt.*;\r
\r
-public class WSWUBlastClient\r
-{\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
- int jobsRunning = 0;\r
-\r
- public WSWUBlastClient(AlignmentI al, ArrayList ids)\r
- {\r
- output.setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."\r
- +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r
- Desktop.addInternalFrame(output, "BLASTing for unidentified sequences ", 800,300);\r
-\r
- for(int i=0; i<ids.size(); i++)\r
- {\r
- SequenceI sequence = al.findName( ids.get(i).toString() );\r
- StringBuffer nonGapped = new StringBuffer();\r
- for (int n = 0; n < sequence.getSequence().length(); n++)\r
- {\r
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))\r
- nonGapped.append(sequence.getCharAt(n));\r
- }\r
-\r
- BlastThread thread = new BlastThread(ids.get(i).toString(), nonGapped.toString());\r
- thread.start();\r
- jobsRunning ++;\r
- }\r
- ImageTwirler thread = new ImageTwirler();\r
- thread.start();\r
- }\r
-\r
- class ImageTwirler extends Thread\r
- {\r
- ImageIcon [] imageIcon;\r
- int imageIndex = 0;\r
- public ImageTwirler()\r
- {\r
- imageIcon = new ImageIcon[9];\r
- for(int i=0; i<9; i++)\r
- {\r
- java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
- if (url != null)\r
- imageIcon[i] = new ImageIcon(url);\r
- }\r
- }\r
+import java.util.*;\r
\r
- public void run()\r
- {\r
- while(jobsRunning>0)\r
- {\r
- try{\r
- Thread.sleep(100);\r
- imageIndex++;\r
- imageIndex %=9;\r
- output.setFrameIcon( imageIcon[imageIndex]);\r
- output.setTitle("BLASTing for unidentified sequences - "+jobsRunning+" jobs running.");\r
+import javax.swing.*;\r
\r
- }catch(Exception ex){}\r
+import javax.xml.namespace.QName;\r
\r
- }\r
- }\r
- }\r
\r
+public class WSWUBlastClient {\r
+ CutAndPasteTransfer output = new CutAndPasteTransfer();\r
+ int jobsRunning = 0;\r
\r
+ public WSWUBlastClient(AlignmentI al, ArrayList ids) {\r
+ output.setText(\r
+ "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +\r
+ "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r
+ Desktop.addInternalFrame(output,\r
+ "BLASTing for unidentified sequences ", 800, 300);\r
\r
+ for (int i = 0; i < ids.size(); i++) {\r
+ SequenceI sequence = al.findName(ids.get(i).toString());\r
+ StringBuffer nonGapped = new StringBuffer();\r
\r
- class BlastThread extends Thread\r
- {\r
- String sequence;\r
- String seqid;\r
- String jobid;\r
- boolean jobComplete = false;\r
+ for (int n = 0; n < sequence.getSequence().length(); n++) {\r
+ if (!jalview.util.Comparison.isGap(sequence.getCharAt(n))) {\r
+ nonGapped.append(sequence.getCharAt(n));\r
+ }\r
+ }\r
+\r
+ BlastThread thread = new BlastThread(ids.get(i).toString(),\r
+ nonGapped.toString());\r
+ thread.start();\r
+ jobsRunning++;\r
+ }\r
\r
- BlastThread(String id, String sequence)\r
- {\r
- this.sequence = sequence;\r
- seqid = id;\r
+ ImageTwirler thread = new ImageTwirler();\r
+ thread.start();\r
}\r
\r
- public void run()\r
- {\r
- StartJob();\r
-\r
- while (!jobComplete)\r
- {\r
- try\r
- {\r
- Call call = (Call)new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
- call.setOperationName(new QName("WSWUBlast", "polljob"));\r
- String result = (String) call.invoke(new Object[]\r
- {jobid, "xml"});\r
- if(result.indexOf("JOB PENDING")==-1 && result.indexOf("JOB RUNNING")==-1)\r
- {\r
- parseResult(seqid, result);\r
- jobComplete = true;\r
- jobsRunning --;\r
- }\r
- Thread.sleep(5000);\r
- // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
+ void parseResult(String id1, String res) {\r
+ StringTokenizer st = new StringTokenizer(res, "\n");\r
+ String data;\r
+ String id2;\r
+ int maxFound = 90;\r
+ StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");\r
+\r
+ while (st.hasMoreTokens()) {\r
+ data = st.nextToken();\r
+\r
+ if (data.indexOf("database=\"uniprot\" id=") > -1) {\r
+ int index = data.indexOf("database=\"uniprot\" id=") + 23;\r
+ id2 = data.substring(index, data.indexOf("\"", index));\r
+\r
+ while (data.indexOf("</alignment>") == -1) {\r
+ data = st.nextToken();\r
+\r
+ if (data.indexOf("<identity>") > -1) {\r
+ int value = Integer.parseInt(data.substring(data.indexOf(\r
+ "<identity>") + 10,\r
+ data.indexOf("</identity>")));\r
+\r
+ if (value >= maxFound) {\r
+ maxFound = value;\r
+ buffer.append(" " + id2 + " " + value + "%; ");\r
+ }\r
+ }\r
+ }\r
+ }\r
}\r
- catch (Exception ex)\r
- {}\r
- }\r
- }\r
\r
- void StartJob()\r
- {\r
- HashMap params = new HashMap();\r
- params.put("database", "uniprot");\r
- params.put("sensitivity", "low");\r
- params.put("sort", "totalscore");\r
- params.put("matrix", "pam10");\r
- params.put("program", "blastp");\r
- params.put("alignments", "5");\r
- params.put("outformat", "xml");\r
- params.put("searchtype", "1");\r
- byte[] seqbytes = sequence.getBytes();\r
-\r
- try\r
- {\r
- Call call = (Call)new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
- call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
- String result = (String) call.invoke(new Object[]\r
- {params, seqbytes});\r
- jobid = result;\r
- System.out.println("http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '"+jobid+"'");\r
-\r
- }\r
- catch (Exception exp)\r
- {\r
- System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
- exp.printStackTrace();\r
- }\r
+ output.setText(output.getText() + buffer.toString());\r
}\r
- }\r
-\r
- void parseResult(String id1, String res)\r
- {\r
- StringTokenizer st = new StringTokenizer(res, "\n");\r
- String data;\r
- String id2;\r
- int maxFound = 90;\r
- StringBuffer buffer = new StringBuffer("\n\n"+id1+" :");\r
-\r
- while( st.hasMoreTokens() )\r
- {\r
- data = st.nextToken();\r
-\r
- if(data.indexOf("database=\"uniprot\" id=")>-1)\r
- {\r
- int index = data.indexOf("database=\"uniprot\" id=")+ 23;\r
- id2 = data.substring( index, data.indexOf("\"", index) );\r
- while( data.indexOf("</alignment>")==-1)\r
- {\r
- data = st.nextToken();\r
- if(data.indexOf("<identity>")>-1)\r
- {\r
- int value = Integer.parseInt( data.substring(data.indexOf("<identity>")+10, data.indexOf("</identity>")));\r
- if(value>=maxFound)\r
- {\r
- maxFound = value;\r
- buffer.append(" "+ id2 + " " + value+"%; ");\r
- }\r
+\r
+ class ImageTwirler extends Thread {\r
+ ImageIcon[] imageIcon;\r
+ int imageIndex = 0;\r
+\r
+ public ImageTwirler() {\r
+ imageIcon = new ImageIcon[9];\r
+\r
+ for (int i = 0; i < 9; i++) {\r
+ java.net.URL url = getClass().getResource("/images/dna" +\r
+ (i + 1) + ".gif");\r
+\r
+ if (url != null) {\r
+ imageIcon[i] = new ImageIcon(url);\r
+ }\r
}\r
- }\r
+ }\r
\r
+ public void run() {\r
+ while (jobsRunning > 0) {\r
+ try {\r
+ Thread.sleep(100);\r
+ imageIndex++;\r
+ imageIndex %= 9;\r
+ output.setFrameIcon(imageIcon[imageIndex]);\r
+ output.setTitle("BLASTing for unidentified sequences - " +\r
+ jobsRunning + " jobs running.");\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
}\r
+ }\r
\r
+ class BlastThread extends Thread {\r
+ String sequence;\r
+ String seqid;\r
+ String jobid;\r
+ boolean jobComplete = false;\r
\r
- }\r
+ BlastThread(String id, String sequence) {\r
+ this.sequence = sequence;\r
+ seqid = id;\r
+ }\r
\r
- output.setText(output.getText()+buffer.toString());\r
- }\r
+ public void run() {\r
+ StartJob();\r
+\r
+ while (!jobComplete) {\r
+ try {\r
+ Call call = (Call) new Service().createCall();\r
+ call.setTargetEndpointAddress(new java.net.URL(\r
+ "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
+ call.setOperationName(new QName("WSWUBlast", "polljob"));\r
+\r
+ String result = (String) call.invoke(new Object[] {\r
+ jobid, "xml"\r
+ });\r
\r
+ if ((result.indexOf("JOB PENDING") == -1) &&\r
+ (result.indexOf("JOB RUNNING") == -1)) {\r
+ parseResult(seqid, result);\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ }\r
+\r
+ Thread.sleep(5000);\r
+\r
+ // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+ }\r
+\r
+ void StartJob() {\r
+ HashMap params = new HashMap();\r
+ params.put("database", "uniprot");\r
+ params.put("sensitivity", "low");\r
+ params.put("sort", "totalscore");\r
+ params.put("matrix", "pam10");\r
+ params.put("program", "blastp");\r
+ params.put("alignments", "5");\r
+ params.put("outformat", "xml");\r
+ params.put("searchtype", "1");\r
+\r
+ byte[] seqbytes = sequence.getBytes();\r
+\r
+ try {\r
+ Call call = (Call) new Service().createCall();\r
+ call.setTargetEndpointAddress(new java.net.URL(\r
+ "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
+ call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
+\r
+ String result = (String) call.invoke(new Object[] {\r
+ params, seqbytes\r
+ });\r
+ jobid = result;\r
+ System.out.println(\r
+ "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +\r
+ jobid + "'");\r
+ } catch (Exception exp) {\r
+ System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
+ exp.printStackTrace();\r
+ }\r
+ }\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
-import java.awt.event.*;\r
import java.awt.*;\r
-\r
-public class GAlignFrame extends Frame\r
-{\r
- protected MenuBar alignFrameMenuBar = new MenuBar();\r
- protected Menu fileMenu = new Menu();\r
- protected MenuItem closeMenuItem = new MenuItem();\r
- protected Menu editMenu = new Menu();\r
- protected Menu viewMenu = new Menu();\r
- protected Menu colourMenu = new Menu();\r
- protected Menu calculateMenu = new Menu();\r
- protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem invertSequenceMenuItem = new MenuItem();\r
- protected MenuItem remove2LeftMenuItem = new MenuItem();\r
- protected MenuItem remove2RightMenuItem = new MenuItem();\r
- protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
- protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
- protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
- protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
- protected MenuItem sortIDMenuItem = new MenuItem();\r
- protected MenuItem sortGroupMenuItem = new MenuItem();\r
- protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
- protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
- protected MenuItem PCAMenuItem = new MenuItem();\r
- protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
- protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public Label statusBar = new Label();\r
- protected Menu outputTextboxMenu = new Menu();\r
- protected MenuItem clustalColour = new MenuItem();\r
- protected MenuItem zappoColour = new MenuItem();\r
- protected MenuItem taylorColour = new MenuItem();\r
- protected MenuItem hydrophobicityColour = new MenuItem();\r
- protected MenuItem helixColour = new MenuItem();\r
- protected MenuItem strandColour = new MenuItem();\r
- protected MenuItem turnColour = new MenuItem();\r
- protected MenuItem buriedColour = new MenuItem();\r
- protected MenuItem userDefinedColour = new MenuItem();\r
- protected MenuItem PIDColour = new MenuItem();\r
- protected MenuItem BLOSUM62Colour = new MenuItem();\r
- MenuItem njTreeBlosumMenuItem = new MenuItem();\r
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
- protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
- MenuItem overviewMenuItem = new MenuItem();\r
- protected MenuItem undoMenuItem = new MenuItem();\r
- protected MenuItem redoMenuItem = new MenuItem();\r
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
- MenuItem noColourmenuItem = new MenuItem();\r
- protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
- MenuItem findMenuItem = new MenuItem();\r
- Menu searchMenu = new Menu();\r
- protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
- protected MenuItem nucleotideColour = new MenuItem();\r
- MenuItem deleteGroups = new MenuItem();\r
- MenuItem delete = new MenuItem();\r
- MenuItem copy = new MenuItem();\r
- MenuItem cut = new MenuItem();\r
- Menu Menu1 = new Menu();\r
- MenuItem pasteNew = new MenuItem();\r
- MenuItem pasteThis = new MenuItem();\r
- protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
- protected MenuItem font = new MenuItem();\r
- protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
- MenuItem modifyPID = new MenuItem();\r
- MenuItem modifyConservation = new MenuItem();\r
- protected Menu sortByTreeMenu = new Menu();\r
- Menu sort = new Menu();\r
- Menu calculate = new Menu();\r
- MenuItem inputText = new MenuItem();\r
- Menu helpMenu = new Menu();\r
- MenuItem documentation = new MenuItem();\r
- MenuItem about = new MenuItem();\r
- public GAlignFrame()\r
- {\r
- try\r
- {\r
- jbInit();\r
- setMenuBar(alignFrameMenuBar);\r
-\r
- MenuItem item;\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
- item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveAs_actionPerformed(e);\r
- }\r
- });\r
-\r
- item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add( item );\r
- }\r
-\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- fileMenu.setLabel("File");\r
- closeMenuItem.setLabel("Close");\r
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- closeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- editMenu.setLabel("Edit");\r
- viewMenu.setLabel("View");\r
- colourMenu.setLabel("Colour");\r
- calculateMenu.setLabel("Calculate");\r
- selectAllSequenceMenuItem.setLabel("Select all");\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- deselectAllSequenceMenuItem.setLabel("Deselect All");\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- invertSequenceMenuItem.setLabel("Invert Selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- invertSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2LeftMenuItem.setLabel("Remove Left");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2LeftMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2RightMenuItem.setLabel("Remove Right");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2RightMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeAllGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewBoxesMenuItem.setLabel("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- viewBoxesMenuItem_actionPerformed(null);\r
- }\r
- });\r
- viewTextMenuItem.setLabel("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- viewTextMenuItem_actionPerformed(null);\r
- }\r
- });\r
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortPairwiseMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortIDMenuItem.setLabel("by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortIDMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortGroupMenuItem.setLabel("by Group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeRedundancyMenuItem_actionPerformed(e);\r
- }\r
- });\r
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
- }\r
- });\r
- PCAMenuItem.setLabel("Principal Component Analysis...");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PCAMenuItem_actionPerformed(e);\r
- }\r
- });\r
- averageDistanceTreeMenuItem.setLabel("Average Distance Using % Identity...");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- neighbourTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setLabel("Output to Textbox");\r
- clustalColour.setLabel("Clustalx");\r
-\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setLabel("Helix Propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setLabel("Strand Propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setLabel("Turn Propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.setLabel("User Defined...");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- avDistanceTreeBlosumMenuItem.setLabel("Average Distance Using BLOSUM62...");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62...");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- njTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- annotationPanelMenuItem.setActionCommand("");\r
- annotationPanelMenuItem.setState(true);\r
- annotationPanelMenuItem.setLabel("Show Annotations");\r
- annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- annotationPanelMenuItem_actionPerformed(null);\r
- }\r
- });\r
- colourTextMenuItem.setLabel("Colour Text");\r
- colourTextMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- colourTextMenuItem_actionPerformed(null);\r
- }\r
- });\r
- overviewMenuItem.setLabel("Overview Window...");\r
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- overviewMenuItem_actionPerformed(e);\r
- }\r
- });\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- undoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- redoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setLabel("by Conservation");\r
- conservationMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(null);\r
- }\r
- });\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
- wrapMenuItem.setLabel("Wrap");\r
- wrapMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- wrapMenuItem_actionPerformed(null);\r
- }\r
- });\r
- renderGapsMenuItem.setLabel("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
-\r
- renderGapsMenuItem_actionPerformed(null);\r
- }\r
- });\r
- findMenuItem.setLabel("Find...");\r
- findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- findMenuItem_actionPerformed(e);\r
- }\r
- });\r
- searchMenu.setLabel("Search");\r
-\r
- abovePIDThreshold.setLabel("Above Identity Threshold");\r
- abovePIDThreshold.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- abovePIDThreshold_actionPerformed(null);\r
- }\r
- });\r
- nucleotideColour.setLabel("Nucleotide");\r
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideColour_actionPerformed(e);\r
- }\r
- });\r
- deleteGroups.setLabel("Undefine Groups");\r
- deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deleteGroups_actionPerformed(e);\r
- }\r
- });\r
- copy.setLabel("Copy");\r
- copy.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed(e);\r
- }\r
- });\r
- cut.setLabel("Cut");\r
- cut.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed(e);\r
- }\r
- });\r
- delete.setLabel("Delete");\r
- delete.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- delete_actionPerformed(e);\r
- }\r
- });\r
- Menu1.setLabel("Paste");\r
- pasteNew.setLabel("To New Alignment");\r
- pasteNew.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteNew_actionPerformed(e);\r
- }\r
- });\r
- pasteThis.setLabel("Add To This Alignment");\r
- pasteThis.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteThis_actionPerformed(e);\r
- }\r
- });\r
- applyToAllGroups.setLabel("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- applyToAllGroups_actionPerformed(null);\r
- }\r
- });\r
- font.setLabel("Font...");\r
- font.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- font_actionPerformed(e);\r
- }\r
- });\r
- fullSeqId.setLabel("Show Full Sequence ID");\r
- fullSeqId.setState(true);\r
- fullSeqId.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- fullSeqId_actionPerformed(null);\r
- }\r
- });\r
- scaleAbove.setLabel("Scale Above");\r
- scaleAbove.setState(true);\r
- scaleAbove.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
-\r
- scaleAbove_actionPerformed(null);\r
- }\r
- });\r
- scaleLeft.setEnabled(false);\r
- scaleLeft.setState(true);\r
- scaleLeft.setLabel("Scale Left");\r
- scaleLeft.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
-\r
- scaleLeft_actionPerformed(null);\r
- }\r
- });\r
- scaleRight.setEnabled(false);\r
- scaleRight.setState(true);\r
- scaleRight.setLabel("Scale Right");\r
- scaleRight.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
-\r
- scaleRight_actionPerformed(null);\r
- }\r
- });\r
- modifyPID.setLabel("Modify Identity Threshold...");\r
- modifyPID.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- modifyPID_actionPerformed(e);\r
- }\r
- });\r
- modifyConservation.setLabel("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- modifyConservation_actionPerformed(e);\r
- }\r
- });\r
- sortByTreeMenu.setLabel("By Tree Order");\r
- sort.setLabel("Sort");\r
- calculate.setLabel("Calculate Tree");\r
- inputText.setLabel("Input from textbox");\r
- inputText.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- helpMenu.setLabel("Help");\r
- documentation.setLabel("Documentation");\r
- documentation.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- documentation_actionPerformed(e);\r
- }\r
- });\r
-\r
- about.setLabel("About...");\r
- about.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- about_actionPerformed(e);\r
- }\r
- });\r
-\r
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
- alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(helpMenu);\r
- fileMenu.add(inputText);\r
- fileMenu.add(outputTextboxMenu);\r
- fileMenu.addSeparator();\r
- fileMenu.add(closeMenuItem);\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.add(cut);\r
- editMenu.add(copy);\r
- editMenu.add(Menu1);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.addSeparator();\r
- viewMenu.add(fullSeqId);\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.addSeparator();\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(applyToAllGroups);\r
- colourMenu.addSeparator();\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
- calculateMenu.add(sort);\r
- calculateMenu.add(calculate);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- this.add(statusBar, BorderLayout.SOUTH);\r
- Menu1.add(pasteNew);\r
- Menu1.add(pasteThis);\r
- sort.add(sortIDMenuItem);\r
- sort.add(sortByTreeMenu);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- helpMenu.add(documentation);\r
- helpMenu.add(about);\r
- }\r
-\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
+import java.awt.event.*;\r
\r
\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
+public class GAlignFrame extends Frame {\r
+ protected MenuBar alignFrameMenuBar = new MenuBar();\r
+ protected Menu fileMenu = new Menu();\r
+ protected MenuItem closeMenuItem = new MenuItem();\r
+ protected Menu editMenu = new Menu();\r
+ protected Menu viewMenu = new Menu();\r
+ protected Menu colourMenu = new Menu();\r
+ protected Menu calculateMenu = new Menu();\r
+ protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem();\r
+ protected MenuItem remove2LeftMenuItem = new MenuItem();\r
+ protected MenuItem remove2RightMenuItem = new MenuItem();\r
+ protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+ protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+ protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
+ protected MenuItem sortIDMenuItem = new MenuItem();\r
+ protected MenuItem sortGroupMenuItem = new MenuItem();\r
+ protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
+ protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+ protected MenuItem PCAMenuItem = new MenuItem();\r
+ protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+ protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public Label statusBar = new Label();\r
+ protected Menu outputTextboxMenu = new Menu();\r
+ protected MenuItem clustalColour = new MenuItem();\r
+ protected MenuItem zappoColour = new MenuItem();\r
+ protected MenuItem taylorColour = new MenuItem();\r
+ protected MenuItem hydrophobicityColour = new MenuItem();\r
+ protected MenuItem helixColour = new MenuItem();\r
+ protected MenuItem strandColour = new MenuItem();\r
+ protected MenuItem turnColour = new MenuItem();\r
+ protected MenuItem buriedColour = new MenuItem();\r
+ protected MenuItem userDefinedColour = new MenuItem();\r
+ protected MenuItem PIDColour = new MenuItem();\r
+ protected MenuItem BLOSUM62Colour = new MenuItem();\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+ protected MenuItem undoMenuItem = new MenuItem();\r
+ protected MenuItem redoMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+ protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+ MenuItem findMenuItem = new MenuItem();\r
+ Menu searchMenu = new Menu();\r
+ protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+ protected MenuItem nucleotideColour = new MenuItem();\r
+ MenuItem deleteGroups = new MenuItem();\r
+ MenuItem delete = new MenuItem();\r
+ MenuItem copy = new MenuItem();\r
+ MenuItem cut = new MenuItem();\r
+ Menu Menu1 = new Menu();\r
+ MenuItem pasteNew = new MenuItem();\r
+ MenuItem pasteThis = new MenuItem();\r
+ protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+ protected MenuItem font = new MenuItem();\r
+ protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+ MenuItem modifyPID = new MenuItem();\r
+ MenuItem modifyConservation = new MenuItem();\r
+ protected Menu sortByTreeMenu = new Menu();\r
+ Menu sort = new Menu();\r
+ Menu calculate = new Menu();\r
+ MenuItem inputText = new MenuItem();\r
+ Menu helpMenu = new Menu();\r
+ MenuItem documentation = new MenuItem();\r
+ MenuItem about = new MenuItem();\r
+\r
+ public GAlignFrame() {\r
+ try {\r
+ jbInit();\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
+ item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ saveAs_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
\r
- }\r
+ private void jbInit() throws Exception {\r
+ fileMenu.setLabel("File");\r
+ closeMenuItem.setLabel("Close");\r
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ closeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ editMenu.setLabel("Edit");\r
+ viewMenu.setLabel("View");\r
+ colourMenu.setLabel("Colour");\r
+ calculateMenu.setLabel("Calculate");\r
+ selectAllSequenceMenuItem.setLabel("Select all");\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ selectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ deselectAllSequenceMenuItem.setLabel("Deselect All");\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deselectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ invertSequenceMenuItem.setLabel("Invert Selection");\r
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ invertSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2LeftMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2RightMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeGappedColumnMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeAllGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ viewBoxesMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ viewTextMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortPairwiseMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortIDMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortGroupMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeRedundancyMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pairwiseAlignmentMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ PCAMenuItem.setLabel("Principal Component Analysis...");\r
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PCAMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ averageDistanceTreeMenuItem.setLabel(\r
+ "Average Distance Using % Identity...");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ averageDistanceTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");\r
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ neighbourTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ clustalColour_actionPerformed(e);\r
+ }\r
+ });\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ zappoColour_actionPerformed(e);\r
+ }\r
+ });\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ taylorColour_actionPerformed(e);\r
+ }\r
+ });\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ hydrophobicityColour_actionPerformed(e);\r
+ }\r
+ });\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ helixColour_actionPerformed(e);\r
+ }\r
+ });\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ strandColour_actionPerformed(e);\r
+ }\r
+ });\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ turnColour_actionPerformed(e);\r
+ }\r
+ });\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setLabel(\r
+ "Average Distance Using BLOSUM62...");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62...");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setState(true);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ annotationPanelMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ colourTextMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ overviewMenuItem.setLabel("Overview Window...");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ undoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ conservationMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ renderGapsMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ searchMenu.setLabel("Search");\r
+\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ abovePIDThreshold_actionPerformed(null);\r
+ }\r
+ });\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ Menu1.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ applyToAllGroups_actionPerformed(null);\r
+ }\r
+ });\r
+ font.setLabel("Font...");\r
+ font.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+ fullSeqId.setLabel("Show Full Sequence ID");\r
+ fullSeqId.setState(true);\r
+ fullSeqId.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fullSeqId_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleAbove_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleLeft_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleRight_actionPerformed(null);\r
+ }\r
+ });\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ inputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ documentation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ about_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(searchMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(helpMenu);\r
+ fileMenu.add(inputText);\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(Menu1);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(selectAllSequenceMenuItem);\r
+ editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(invertSequenceMenuItem);\r
+ editMenu.add(deleteGroups);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ searchMenu.add(findMenuItem);\r
+ viewMenu.add(font);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(wrapMenuItem);\r
+ viewMenu.add(scaleAbove);\r
+ viewMenu.add(scaleLeft);\r
+ viewMenu.add(scaleRight);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(fullSeqId);\r
+ viewMenu.add(viewBoxesMenuItem);\r
+ viewMenu.add(viewTextMenuItem);\r
+ viewMenu.add(colourTextMenuItem);\r
+ viewMenu.add(renderGapsMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ Menu1.add(pasteNew);\r
+ Menu1.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ helpMenu.add(documentation);\r
+ helpMenu.add(about);\r
+ }\r
\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
+ protected void saveAs_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void outputText_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void printMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
- {\r
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void copy_actionPerformed(ActionEvent e)\r
- {\r
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void cut_actionPerformed(ActionEvent e)\r
- {\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void delete_actionPerformed(ActionEvent e)\r
- {\r
+ protected void clustalColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void zappoColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
- {\r
+ protected void taylorColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
- {\r
+ protected void helixColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void strandColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
+ protected void turnColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void buriedColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
- {\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void PIDColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void font_actionPerformed(ActionEvent e)\r
- {\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
- {\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void printMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
- {\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void findMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
+ }\r
\r
- protected void jpred_actionPerformed(ActionEvent e)\r
- {\r
+ protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void deleteGroups_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
+ protected void copy_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void cut_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
+ protected void delete_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void pasteNew_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
+ protected void pasteThis_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
- {\r
+ protected void createPNG_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void font_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
- {\r
+ protected void fullSeqId_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void epsFile_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void jpred_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ protected void scaleAbove_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void scaleLeft_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void inputText_actionPerformed(ActionEvent e) {\r
+ protected void scaleRight_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void modifyPID_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void documentation_actionPerformed(ActionEvent e) {\r
+ protected void modifyConservation_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void preferences_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void about_actionPerformed(ActionEvent e) {\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void inputText_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void documentation_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void about_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
\r
-public class GAlignmentPanel extends Panel\r
-{\r
- protected Panel sequenceHolderPanel = new Panel();\r
- protected Scrollbar vscroll = new Scrollbar();\r
- protected Scrollbar hscroll = new Scrollbar();\r
- protected Panel seqPanelHolder = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout3 = new BorderLayout();\r
- protected Panel scalePanelHolder = new Panel();\r
- protected Panel idPanelHolder = new Panel();\r
- BorderLayout borderLayout5 = new BorderLayout();\r
- protected Panel idSpaceFillerPanel1 = new Panel();\r
- public Panel annotationSpaceFillerHolder = new Panel();\r
- BorderLayout borderLayout6 = new BorderLayout();\r
- BorderLayout borderLayout7 = new BorderLayout();\r
- Panel hscrollHolder = new Panel();\r
- BorderLayout borderLayout10 = new BorderLayout();\r
- protected Panel hscrollFillerPanel = new Panel();\r
- BorderLayout borderLayout11 = new BorderLayout();\r
- public Panel annotationScroller = new Panel();\r
- BorderLayout borderLayout4 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
\r
- public GAlignmentPanel()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
+public class GAlignmentPanel extends Panel {\r
+ protected Panel sequenceHolderPanel = new Panel();\r
+ protected Scrollbar vscroll = new Scrollbar();\r
+ protected Scrollbar hscroll = new Scrollbar();\r
+ protected Panel seqPanelHolder = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ protected Panel scalePanelHolder = new Panel();\r
+ protected Panel idPanelHolder = new Panel();\r
+ BorderLayout borderLayout5 = new BorderLayout();\r
+ protected Panel idSpaceFillerPanel1 = new Panel();\r
+ public Panel annotationSpaceFillerHolder = new Panel();\r
+ BorderLayout borderLayout6 = new BorderLayout();\r
+ BorderLayout borderLayout7 = new BorderLayout();\r
+ Panel hscrollHolder = new Panel();\r
+ BorderLayout borderLayout10 = new BorderLayout();\r
+ protected Panel hscrollFillerPanel = new Panel();\r
+ BorderLayout borderLayout11 = new BorderLayout();\r
+ public Panel annotationScroller = new Panel();\r
+ BorderLayout borderLayout4 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+\r
+ public GAlignmentPanel() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- // idPanelHolder.setPreferredSize(new Dimension(70, 10));\r
- this.setLayout(borderLayout7);\r
- // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));\r
- sequenceHolderPanel.setLayout(borderLayout3);\r
- seqPanelHolder.setLayout(borderLayout1);\r
- scalePanelHolder.setBackground(Color.white);\r
- // scalePanelHolder.setPreferredSize(new Dimension(10, 30));\r
- scalePanelHolder.setLayout(borderLayout6);\r
- idPanelHolder.setLayout(borderLayout5);\r
- idSpaceFillerPanel1.setBackground(Color.white);\r
- // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));\r
- idSpaceFillerPanel1.setLayout(borderLayout11);\r
- annotationSpaceFillerHolder.setBackground(Color.white);\r
- // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));\r
- annotationSpaceFillerHolder.setLayout(borderLayout4);\r
- hscroll.setOrientation(Scrollbar.HORIZONTAL);\r
- hscrollHolder.setLayout(borderLayout10);\r
- hscrollFillerPanel.setBackground(Color.white);\r
- // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));\r
- hscrollHolder.setBackground(Color.white);\r
- // annotationScroller.setPreferredSize(new Dimension(10, 80));\r
- // this.setPreferredSize(new Dimension(220, 166));\r
- seqPanelHolder.setBackground(Color.white);\r
- idPanelHolder.setBackground(Color.white);\r
- annotationScroller.setLayout(borderLayout2);\r
- sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
- sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
- seqPanelHolder.add(vscroll, BorderLayout.EAST);\r
- sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);\r
- // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);\r
- this.add(idPanelHolder, BorderLayout.WEST);\r
- idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);\r
- idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);\r
- this.add(hscrollHolder, BorderLayout.SOUTH);\r
- hscrollHolder.add(hscroll, BorderLayout.CENTER);\r
- hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);\r
- this.add(sequenceHolderPanel, BorderLayout.CENTER);\r
- }\r
\r
+ private void jbInit() throws Exception {\r
+ // idPanelHolder.setPreferredSize(new Dimension(70, 10));\r
+ this.setLayout(borderLayout7);\r
+\r
+ // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));\r
+ sequenceHolderPanel.setLayout(borderLayout3);\r
+ seqPanelHolder.setLayout(borderLayout1);\r
+ scalePanelHolder.setBackground(Color.white);\r
+\r
+ // scalePanelHolder.setPreferredSize(new Dimension(10, 30));\r
+ scalePanelHolder.setLayout(borderLayout6);\r
+ idPanelHolder.setLayout(borderLayout5);\r
+ idSpaceFillerPanel1.setBackground(Color.white);\r
\r
+ // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));\r
+ idSpaceFillerPanel1.setLayout(borderLayout11);\r
+ annotationSpaceFillerHolder.setBackground(Color.white);\r
+\r
+ // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));\r
+ annotationSpaceFillerHolder.setLayout(borderLayout4);\r
+ hscroll.setOrientation(Scrollbar.HORIZONTAL);\r
+ hscrollHolder.setLayout(borderLayout10);\r
+ hscrollFillerPanel.setBackground(Color.white);\r
+\r
+ // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));\r
+ hscrollHolder.setBackground(Color.white);\r
+\r
+ // annotationScroller.setPreferredSize(new Dimension(10, 80));\r
+ // this.setPreferredSize(new Dimension(220, 166));\r
+ seqPanelHolder.setBackground(Color.white);\r
+ idPanelHolder.setBackground(Color.white);\r
+ annotationScroller.setLayout(borderLayout2);\r
+ sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
+ sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
+ seqPanelHolder.add(vscroll, BorderLayout.EAST);\r
+ sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);\r
+\r
+ // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);\r
+ this.add(idPanelHolder, BorderLayout.WEST);\r
+ idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);\r
+ idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);\r
+ this.add(hscrollHolder, BorderLayout.SOUTH);\r
+ hscrollHolder.add(hscroll, BorderLayout.CENTER);\r
+ hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);\r
+ this.add(sequenceHolderPanel, BorderLayout.CENTER);\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
\r
-public class GCutAndPasteTransfer extends Panel\r
-{\r
- protected TextArea textarea = new TextArea();\r
- Button ok = new Button();\r
- Button cancel = new Button();\r
- protected Panel buttonPanel = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public GCutAndPasteTransfer()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- textarea.setFont(new java.awt.Font("Verdana", 0, 12));\r
- textarea.setText("Paste your alignment file here");\r
- textarea.addMouseListener(new java.awt.event.MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent e)\r
- {\r
- textarea_mousePressed(e);\r
- }\r
- });\r
- this.setLayout(borderLayout1);\r
- ok.setLabel("OK");\r
- ok.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- cancel.setLabel("Cancel");\r
- cancel.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- cancel_actionPerformed(e);\r
- }\r
- });\r
- this.add(buttonPanel, BorderLayout.SOUTH);\r
- buttonPanel.add(ok, null);\r
- buttonPanel.add(cancel, null);\r
- this.add(textarea, java.awt.BorderLayout.CENTER);\r
- }\r
-\r
-\r
-\r
+public class GCutAndPasteTransfer extends Panel {\r
+ protected TextArea textarea = new TextArea();\r
+ Button ok = new Button();\r
+ Button cancel = new Button();\r
+ protected Panel buttonPanel = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
\r
- void textarea_mousePressed(MouseEvent e)\r
- {\r
- if(textarea.getText().equals("Paste your alignment file here"))\r
- textarea.setText("");\r
- }\r
-\r
- protected void ok_actionPerformed(ActionEvent e) {\r
+ public GCutAndPasteTransfer() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
\r
- }\r
+ private void jbInit() throws Exception {\r
+ textarea.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ textarea.setText("Paste your alignment file here");\r
+ textarea.addMouseListener(new java.awt.event.MouseAdapter() {\r
+ public void mousePressed(MouseEvent e) {\r
+ textarea_mousePressed(e);\r
+ }\r
+ });\r
+ this.setLayout(borderLayout1);\r
+ ok.setLabel("OK");\r
+ ok.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ok_actionPerformed(e);\r
+ }\r
+ });\r
+ cancel.setLabel("Cancel");\r
+ cancel.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancel_actionPerformed(e);\r
+ }\r
+ });\r
+ this.add(buttonPanel, BorderLayout.SOUTH);\r
+ buttonPanel.add(ok, null);\r
+ buttonPanel.add(cancel, null);\r
+ this.add(textarea, java.awt.BorderLayout.CENTER);\r
+ }\r
\r
- protected void cancel_actionPerformed(ActionEvent e) {\r
+ void textarea_mousePressed(MouseEvent e) {\r
+ if (textarea.getText().equals("Paste your alignment file here")) {\r
+ textarea.setText("");\r
+ }\r
+ }\r
\r
- }\r
+ protected void ok_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void cancel_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
\r
-public class GFinder extends Panel\r
-{\r
- Label jLabel1 = new Label();\r
- protected TextField textfield = new TextField();\r
- protected Button findAll = new Button();\r
- protected Button findNext = new Button();\r
- Panel jPanel1 = new Panel();\r
- GridLayout gridLayout1 = new GridLayout();\r
- protected Button createNewGroup = new Button();\r
-\r
- public GFinder()\r
- {\r
- try\r
- {\r
- jbInit();\r
+public class GFinder extends Panel {\r
+ Label jLabel1 = new Label();\r
+ protected TextField textfield = new TextField();\r
+ protected Button findAll = new Button();\r
+ protected Button findNext = new Button();\r
+ Panel jPanel1 = new Panel();\r
+ GridLayout gridLayout1 = new GridLayout();\r
+ protected Button createNewGroup = new Button();\r
+\r
+ public GFinder() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel1.setText("Find");\r
- jLabel1.setBounds(new Rectangle(3, 30, 34, 15));\r
- this.setLayout(null);\r
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
- textfield.setText("");\r
- textfield.setBounds(new Rectangle(40, 27, 133, 21));\r
- textfield.addKeyListener(new java.awt.event.KeyAdapter()\r
- {\r
- public void keyTyped(KeyEvent e)\r
- {\r
- textfield_keyTyped(e);\r
- }\r
- });\r
- textfield.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- textfield_actionPerformed(e);\r
- }\r
- });\r
- findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
- findAll.setLabel("Find all");\r
- findAll.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- findAll_actionPerformed(e);\r
- }\r
- });\r
- findNext.setEnabled(false);\r
- findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
- findNext.setLabel("Find Next");\r
- findNext.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- findNext_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.setBounds(new Rectangle(180, 5, 141, 64));\r
- jPanel1.setLayout(gridLayout1);\r
- gridLayout1.setHgap(0);\r
- gridLayout1.setRows(3);\r
- gridLayout1.setVgap(2);\r
- createNewGroup.setEnabled(false);\r
- createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
- createNewGroup.setLabel("Create new group");\r
- createNewGroup.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- createNewGroup_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.add(findNext, null);\r
- jPanel1.add(findAll, null);\r
- jPanel1.add(createNewGroup, null);\r
- this.add(textfield, null);\r
- this.add(jLabel1, null);\r
- this.add(jPanel1, null);\r
- }\r
-\r
- protected void findNext_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void findAll_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
\r
+ private void jbInit() throws Exception {\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel1.setText("Find");\r
+ jLabel1.setBounds(new Rectangle(3, 30, 34, 15));\r
+ this.setLayout(null);\r
+ textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ textfield.setText("");\r
+ textfield.setBounds(new Rectangle(40, 27, 133, 21));\r
+ textfield.addKeyListener(new java.awt.event.KeyAdapter() {\r
+ public void keyTyped(KeyEvent e) {\r
+ textfield_keyTyped(e);\r
+ }\r
+ });\r
+ textfield.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ textfield_actionPerformed(e);\r
+ }\r
+ });\r
+ findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ findAll.setLabel("Find all");\r
+ findAll.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findAll_actionPerformed(e);\r
+ }\r
+ });\r
+ findNext.setEnabled(false);\r
+ findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ findNext.setLabel("Find Next");\r
+ findNext.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findNext_actionPerformed(e);\r
+ }\r
+ });\r
+ jPanel1.setBounds(new Rectangle(180, 5, 141, 64));\r
+ jPanel1.setLayout(gridLayout1);\r
+ gridLayout1.setHgap(0);\r
+ gridLayout1.setRows(3);\r
+ gridLayout1.setVgap(2);\r
+ createNewGroup.setEnabled(false);\r
+ createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ createNewGroup.setLabel("Create new group");\r
+ createNewGroup.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ createNewGroup_actionPerformed(e);\r
+ }\r
+ });\r
+ jPanel1.add(findNext, null);\r
+ jPanel1.add(findAll, null);\r
+ jPanel1.add(createNewGroup, null);\r
+ this.add(textfield, null);\r
+ this.add(jLabel1, null);\r
+ this.add(jPanel1, null);\r
+ }\r
\r
- protected void textfield_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+ protected void findNext_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- void textfield_keyTyped(KeyEvent e)\r
- {\r
- findNext.setEnabled(true);\r
- }\r
+ protected void findAll_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void createNewGroup_actionPerformed(ActionEvent e)\r
- {\r
+ protected void textfield_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ void textfield_keyTyped(KeyEvent e) {\r
+ findNext.setEnabled(true);\r
+ }\r
\r
+ public void createNewGroup_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
\r
-public class GFontChooser extends Panel\r
-{\r
- Label label1 = new Label();\r
- protected Choice fontSize = new Choice();\r
- protected Choice fontStyle = new Choice();\r
- Label label2 = new Label();\r
- Label label3 = new Label();\r
- protected Choice fontName = new Choice();\r
- Button ok = new Button();\r
- Button cancel = new Button();\r
- Panel panel1 = new Panel();\r
- Panel panel2 = new Panel();\r
- Panel panel3 = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- BorderLayout borderLayout3 = new BorderLayout();\r
- Panel panel4 = new Panel();\r
- Panel panel5 = new Panel();\r
- BorderLayout borderLayout4 = new BorderLayout();\r
-\r
- public GFontChooser()\r
- {\r
- try\r
- {\r
- jbInit();\r
+public class GFontChooser extends Panel {\r
+ Label label1 = new Label();\r
+ protected Choice fontSize = new Choice();\r
+ protected Choice fontStyle = new Choice();\r
+ Label label2 = new Label();\r
+ Label label3 = new Label();\r
+ protected Choice fontName = new Choice();\r
+ Button ok = new Button();\r
+ Button cancel = new Button();\r
+ Panel panel1 = new Panel();\r
+ Panel panel2 = new Panel();\r
+ Panel panel3 = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ Panel panel4 = new Panel();\r
+ Panel panel5 = new Panel();\r
+ BorderLayout borderLayout4 = new BorderLayout();\r
+\r
+ public GFontChooser() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- label1.setFont(new java.awt.Font("Verdana", 0, 11));\r
- label1.setAlignment(Label.RIGHT);\r
- label1.setText("Font: ");\r
- this.setLayout(borderLayout4);\r
- fontSize.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontSize.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- fontSize_actionPerformed();\r
- }\r
- });\r
- fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontStyle.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- fontStyle_actionPerformed();\r
- }\r
- });\r
- label2.setAlignment(Label.RIGHT);\r
- label2.setFont(new java.awt.Font("Verdana", 0, 11));\r
- label2.setText("Size: ");\r
- label3.setAlignment(Label.RIGHT);\r
- label3.setFont(new java.awt.Font("Verdana", 0, 11));\r
- label3.setText("Style: ");\r
- fontName.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontName.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- fontName_actionPerformed();\r
- }\r
- });\r
- ok.setFont(new java.awt.Font("Verdana", 0, 11));\r
- ok.setLabel("OK");\r
- ok.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed();\r
- }\r
- });\r
- cancel.setFont(new java.awt.Font("Verdana", 0, 11));\r
- cancel.setLabel("Cancel");\r
- cancel.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancel_actionPerformed();\r
- }\r
- });\r
- this.setBackground(Color.white);\r
- panel1.setLayout(borderLayout1);\r
- panel2.setLayout(borderLayout3);\r
- panel3.setLayout(borderLayout2);\r
- panel5.setBackground(Color.white);\r
- panel4.setBackground(Color.white);\r
- panel1.setBackground(Color.white);\r
- panel2.setBackground(Color.white);\r
- panel3.setBackground(Color.white);\r
- panel1.add(label1, BorderLayout.WEST);\r
- panel1.add(fontName, BorderLayout.CENTER);\r
- panel5.add(panel1, null);\r
- panel5.add(panel3, null);\r
- panel5.add(panel2, null);\r
- panel2.add(label3, BorderLayout.WEST);\r
- panel2.add(fontStyle, BorderLayout.CENTER);\r
- panel3.add(label2, BorderLayout.WEST);\r
- panel3.add(fontSize, BorderLayout.CENTER);\r
- this.add(panel4, BorderLayout.SOUTH);\r
- panel4.add(ok, null);\r
- panel4.add(cancel, null);\r
- this.add(panel5, BorderLayout.CENTER);\r
-\r
- }\r
-\r
- protected void ok_actionPerformed()\r
- {\r
-\r
- }\r
-\r
- protected void cancel_actionPerformed()\r
- {\r
-\r
- }\r
\r
- protected void fontName_actionPerformed()\r
- {\r
-\r
- }\r
+ private void jbInit() throws Exception {\r
+ label1.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label1.setAlignment(Label.RIGHT);\r
+ label1.setText("Font: ");\r
+ this.setLayout(borderLayout4);\r
+ fontSize.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontSize.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fontSize_actionPerformed();\r
+ }\r
+ });\r
+ fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontStyle.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fontStyle_actionPerformed();\r
+ }\r
+ });\r
+ label2.setAlignment(Label.RIGHT);\r
+ label2.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label2.setText("Size: ");\r
+ label3.setAlignment(Label.RIGHT);\r
+ label3.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label3.setText("Style: ");\r
+ fontName.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontName.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fontName_actionPerformed();\r
+ }\r
+ });\r
+ ok.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ ok.setLabel("OK");\r
+ ok.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ok_actionPerformed();\r
+ }\r
+ });\r
+ cancel.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ cancel.setLabel("Cancel");\r
+ cancel.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancel_actionPerformed();\r
+ }\r
+ });\r
+ this.setBackground(Color.white);\r
+ panel1.setLayout(borderLayout1);\r
+ panel2.setLayout(borderLayout3);\r
+ panel3.setLayout(borderLayout2);\r
+ panel5.setBackground(Color.white);\r
+ panel4.setBackground(Color.white);\r
+ panel1.setBackground(Color.white);\r
+ panel2.setBackground(Color.white);\r
+ panel3.setBackground(Color.white);\r
+ panel1.add(label1, BorderLayout.WEST);\r
+ panel1.add(fontName, BorderLayout.CENTER);\r
+ panel5.add(panel1, null);\r
+ panel5.add(panel3, null);\r
+ panel5.add(panel2, null);\r
+ panel2.add(label3, BorderLayout.WEST);\r
+ panel2.add(fontStyle, BorderLayout.CENTER);\r
+ panel3.add(label2, BorderLayout.WEST);\r
+ panel3.add(fontSize, BorderLayout.CENTER);\r
+ this.add(panel4, BorderLayout.SOUTH);\r
+ panel4.add(ok, null);\r
+ panel4.add(cancel, null);\r
+ this.add(panel5, BorderLayout.CENTER);\r
+ }\r
\r
- protected void fontSize_actionPerformed()\r
- {\r
+ protected void ok_actionPerformed() {\r
+ }\r
\r
- }\r
+ protected void cancel_actionPerformed() {\r
+ }\r
\r
- protected void fontStyle_actionPerformed()\r
- {\r
+ protected void fontName_actionPerformed() {\r
+ }\r
\r
- }\r
+ protected void fontSize_actionPerformed() {\r
+ }\r
\r
+ protected void fontStyle_actionPerformed() {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class GPCAPanel extends Panel\r
-{\r
- Panel jPanel2 = new Panel();\r
- Label jLabel1 = new Label();\r
- Label jLabel2 = new Label();\r
- Label jLabel3 = new Label();\r
- protected Choice xCombobox = new Choice();\r
- protected Choice yCombobox = new Choice();\r
- protected Choice zCombobox = new Choice();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
-\r
- public GPCAPanel()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- for(int i=1; i<8; i++)\r
- {\r
- xCombobox.addItem("dim "+i);\r
- yCombobox.addItem("dim "+i);\r
- zCombobox.addItem("dim "+i);\r
- }\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- this.setLayout(borderLayout1);\r
- jPanel2.setLayout(flowLayout1);\r
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel1.setText("x=");\r
- jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel2.setText("y=");\r
- jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel3.setText("z=");\r
- jPanel2.setBackground(Color.white);\r
- zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- zCombobox.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- zCombobox_actionPerformed(null);\r
- }\r
- });\r
- yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- yCombobox.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- yCombobox_actionPerformed(null);\r
- }\r
- });\r
- xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- xCombobox.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- xCombobox_actionPerformed(null);\r
- }\r
- });\r
- this.add(jPanel2, BorderLayout.SOUTH);\r
- jPanel2.add(jLabel1, null);\r
- jPanel2.add(xCombobox, null);\r
- jPanel2.add(jLabel2, null);\r
- jPanel2.add(yCombobox, null);\r
- jPanel2.add(jLabel3, null);\r
- jPanel2.add(zCombobox, null);\r
- }\r
\r
- protected void xCombobox_actionPerformed(ActionEvent e)\r
- {\r
+public class GPCAPanel extends Panel {\r
+ Panel jPanel2 = new Panel();\r
+ Label jLabel1 = new Label();\r
+ Label jLabel2 = new Label();\r
+ Label jLabel3 = new Label();\r
+ protected Choice xCombobox = new Choice();\r
+ protected Choice yCombobox = new Choice();\r
+ protected Choice zCombobox = new Choice();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
\r
- }\r
+ public GPCAPanel() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
\r
- protected void yCombobox_actionPerformed(ActionEvent e)\r
- {\r
+ for (int i = 1; i < 8; i++) {\r
+ xCombobox.addItem("dim " + i);\r
+ yCombobox.addItem("dim " + i);\r
+ zCombobox.addItem("dim " + i);\r
+ }\r
+ }\r
\r
- }\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(borderLayout1);\r
+ jPanel2.setLayout(flowLayout1);\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel1.setText("x=");\r
+ jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel2.setText("y=");\r
+ jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel3.setText("z=");\r
+ jPanel2.setBackground(Color.white);\r
+ zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ zCombobox.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ zCombobox_actionPerformed(null);\r
+ }\r
+ });\r
+ yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ yCombobox.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ yCombobox_actionPerformed(null);\r
+ }\r
+ });\r
+ xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ xCombobox.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ xCombobox_actionPerformed(null);\r
+ }\r
+ });\r
+ this.add(jPanel2, BorderLayout.SOUTH);\r
+ jPanel2.add(jLabel1, null);\r
+ jPanel2.add(xCombobox, null);\r
+ jPanel2.add(jLabel2, null);\r
+ jPanel2.add(yCombobox, null);\r
+ jPanel2.add(jLabel3, null);\r
+ jPanel2.add(zCombobox, null);\r
+ }\r
\r
- protected void zCombobox_actionPerformed(ActionEvent e)\r
- {\r
+ protected void xCombobox_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void yCombobox_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void zCombobox_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
\r
-public class GPairwiseAlignPanel extends Panel\r
-{\r
- protected ScrollPane scrollPane = new ScrollPane();\r
- protected TextArea textarea = new TextArea();\r
- protected Button viewInEditorButton = new Button();\r
- Panel jPanel1 = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
+public class GPairwiseAlignPanel extends Panel {\r
+ protected ScrollPane scrollPane = new ScrollPane();\r
+ protected TextArea textarea = new TextArea();\r
+ protected Button viewInEditorButton = new Button();\r
+ Panel jPanel1 = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
\r
- public GPairwiseAlignPanel()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
+ public GPairwiseAlignPanel() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- this.setLayout(borderLayout1);\r
- textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
- textarea.setText("");\r
- viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
- viewInEditorButton.setLabel("View in alignment editor");\r
- viewInEditorButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- viewInEditorButton_actionPerformed(e);\r
- }\r
- });\r
- this.add(scrollPane, BorderLayout.CENTER);\r
- scrollPane.add(textarea);\r
- this.add(jPanel1, BorderLayout.SOUTH);\r
- jPanel1.add(viewInEditorButton, null);\r
- }\r
-\r
- protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
- {\r
\r
- }\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(borderLayout1);\r
+ textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
+ textarea.setText("");\r
+ viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ viewInEditorButton.setLabel("View in alignment editor");\r
+ viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ viewInEditorButton_actionPerformed(e);\r
+ }\r
+ });\r
+ this.add(scrollPane, BorderLayout.CENTER);\r
+ scrollPane.add(textarea);\r
+ this.add(jPanel1, BorderLayout.SOUTH);\r
+ jPanel1.add(viewInEditorButton, null);\r
+ }\r
\r
+ protected void viewInEditorButton_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class GSliderPanel extends Panel\r
-{\r
- // this is used for conservation colours, PID colours and redundancy threshold\r
- protected Scrollbar slider = new Scrollbar();\r
- protected TextField valueField = new TextField();\r
- protected Label label = new Label();\r
- Panel jPanel1 = new Panel();\r
- Panel jPanel2 = new Panel();\r
- protected Button applyButton = new Button();\r
- protected Button undoButton = new Button();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- protected Checkbox allGroupsCheck = new Checkbox();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- FlowLayout flowLayout2 = new FlowLayout();\r
-\r
- public GSliderPanel()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- this.setLayout(borderLayout2);\r
- // slider.setMajorTickSpacing(10);\r
- // slider.setMinorTickSpacing(1);\r
- // slider.setPaintTicks(true);\r
- slider.setBackground(Color.white);\r
- slider.setFont(new java.awt.Font("Verdana", 0, 11));\r
- slider.setOrientation(0);\r
- valueField.setFont(new java.awt.Font("Verdana", 0, 11));\r
- valueField.setText(" ");\r
- valueField.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- valueField_actionPerformed(e);\r
- }\r
- });\r
- label.setFont(new java.awt.Font("Verdana", 0, 11));\r
- label.setText("set this label text");\r
- jPanel1.setLayout(borderLayout1);\r
- jPanel2.setLayout(flowLayout1);\r
- applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- applyButton.setLabel("Apply");\r
- applyButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- applyButton_actionPerformed(e);\r
- }\r
- });\r
- undoButton.setEnabled(false);\r
- undoButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- undoButton.setLabel("Undo");\r
- undoButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- undoButton_actionPerformed(e);\r
- }\r
- });\r
- allGroupsCheck.setEnabled(false);\r
- allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));\r
- allGroupsCheck.setLabel("Apply threshold to all groups");\r
- allGroupsCheck.setName("Apply to all Groups");\r
- allGroupsCheck.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- allGroupsCheck_actionPerformed();\r
- }\r
- });\r
- this.setBackground(Color.white);\r
- this.setForeground(Color.black);\r
- jPanel2.add(label, null);\r
- jPanel2.add(applyButton, null);\r
- jPanel2.add(undoButton, null);\r
- jPanel2.add(allGroupsCheck);\r
- jPanel1.add(valueField, java.awt.BorderLayout.EAST);\r
- jPanel1.add(slider, java.awt.BorderLayout.CENTER);\r
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
- this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
- }\r
-\r
- protected void valueField_actionPerformed(ActionEvent e)\r
- {\r
\r
- }\r
+public class GSliderPanel extends Panel {\r
+ // this is used for conservation colours, PID colours and redundancy threshold\r
+ protected Scrollbar slider = new Scrollbar();\r
+ protected TextField valueField = new TextField();\r
+ protected Label label = new Label();\r
+ Panel jPanel1 = new Panel();\r
+ Panel jPanel2 = new Panel();\r
+ protected Button applyButton = new Button();\r
+ protected Button undoButton = new Button();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ protected Checkbox allGroupsCheck = new Checkbox();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ FlowLayout flowLayout2 = new FlowLayout();\r
\r
- protected void applyButton_actionPerformed(ActionEvent e)\r
- {\r
+ public GSliderPanel() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
\r
- }\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(borderLayout2);\r
\r
- protected void undoButton_actionPerformed(ActionEvent e)\r
- {\r
+ // slider.setMajorTickSpacing(10);\r
+ // slider.setMinorTickSpacing(1);\r
+ // slider.setPaintTicks(true);\r
+ slider.setBackground(Color.white);\r
+ slider.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ slider.setOrientation(0);\r
+ valueField.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ valueField.setText(" ");\r
+ valueField.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ valueField_actionPerformed(e);\r
+ }\r
+ });\r
+ label.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label.setText("set this label text");\r
+ jPanel1.setLayout(borderLayout1);\r
+ jPanel2.setLayout(flowLayout1);\r
+ applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ applyButton.setLabel("Apply");\r
+ applyButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ applyButton_actionPerformed(e);\r
+ }\r
+ });\r
+ undoButton.setEnabled(false);\r
+ undoButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ undoButton.setLabel("Undo");\r
+ undoButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ undoButton_actionPerformed(e);\r
+ }\r
+ });\r
+ allGroupsCheck.setEnabled(false);\r
+ allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ allGroupsCheck.setLabel("Apply threshold to all groups");\r
+ allGroupsCheck.setName("Apply to all Groups");\r
+ allGroupsCheck.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ allGroupsCheck_actionPerformed();\r
+ }\r
+ });\r
+ this.setBackground(Color.white);\r
+ this.setForeground(Color.black);\r
+ jPanel2.add(label, null);\r
+ jPanel2.add(applyButton, null);\r
+ jPanel2.add(undoButton, null);\r
+ jPanel2.add(allGroupsCheck);\r
+ jPanel1.add(valueField, java.awt.BorderLayout.EAST);\r
+ jPanel1.add(slider, java.awt.BorderLayout.CENTER);\r
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+ this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
+ }\r
\r
- }\r
+ protected void valueField_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void allGroupsCheck_actionPerformed()\r
- {\r
+ protected void applyButton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void undoButton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void allGroupsCheck_actionPerformed() {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class GTreePanel extends Frame\r
-{\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- protected ScrollPane scrollPane = new ScrollPane();\r
- MenuBar jMenuBar1 = new MenuBar();\r
- Menu jMenu2 = new Menu();\r
- protected MenuItem fontSize = new MenuItem();\r
- protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
- Menu fileMenu = new Menu();\r
- MenuItem newickOutput = new MenuItem();\r
\r
- public GTreePanel()\r
- {\r
- try\r
- {\r
- jbInit();\r
- this.setMenuBar(jMenuBar1);\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
+public class GTreePanel extends Frame {\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ protected ScrollPane scrollPane = new ScrollPane();\r
+ MenuBar jMenuBar1 = new MenuBar();\r
+ Menu jMenu2 = new Menu();\r
+ protected MenuItem fontSize = new MenuItem();\r
+ protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
+ Menu fileMenu = new Menu();\r
+ MenuItem newickOutput = new MenuItem();\r
+\r
+ public GTreePanel() {\r
+ try {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- setLayout(borderLayout1);\r
- this.setBackground(Color.white);\r
- this.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jMenu2.setLabel("View");\r
- fontSize.setLabel("Font Size - 12");\r
- fontSize.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fontSize_actionPerformed(e);\r
- }\r
- });\r
- bootstrapMenu.setLabel("Show Bootstrap Values");\r
- bootstrapMenu.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- bootstrapMenu_actionPerformed(null);\r
- }\r
- });\r
- distanceMenu.setLabel("Show Distances");\r
- distanceMenu.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- distanceMenu_actionPerformed(null);\r
- }\r
- });\r
- placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
- placeholdersMenu.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- placeholdersMenu_actionPerformed(null);\r
- }\r
- });\r
- fitToWindow.setState(true);\r
- fitToWindow.setLabel("Fit To Window");\r
- fitToWindow.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- fitToWindow_actionPerformed(null);\r
- }\r
- });\r
- fileMenu.setLabel("File");\r
- newickOutput.setLabel("Newick Format");\r
- newickOutput.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- newickOutput_actionPerformed(actionEvent);\r
- }\r
- });\r
- add(scrollPane, BorderLayout.CENTER);\r
- jMenuBar1.add(fileMenu);\r
- jMenuBar1.add(jMenu2);\r
- jMenu2.add(fitToWindow);\r
- jMenu2.add(fontSize);\r
- jMenu2.add(distanceMenu);\r
- jMenu2.add(bootstrapMenu);\r
- jMenu2.add(placeholdersMenu);\r
- fileMenu.add(newickOutput);\r
- }\r
-\r
-\r
- protected void printMenu_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void fontSize_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void distanceMenu_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+ private void jbInit() throws Exception {\r
+ setLayout(borderLayout1);\r
+ this.setBackground(Color.white);\r
+ this.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jMenu2.setLabel("View");\r
+ fontSize.setLabel("Font Size - 12");\r
+ fontSize.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fontSize_actionPerformed(e);\r
+ }\r
+ });\r
+ bootstrapMenu.setLabel("Show Bootstrap Values");\r
+ bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ bootstrapMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ distanceMenu.setLabel("Show Distances");\r
+ distanceMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ distanceMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
+ placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ placeholdersMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ fitToWindow.setState(true);\r
+ fitToWindow.setLabel("Fit To Window");\r
+ fitToWindow.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fitToWindow_actionPerformed(null);\r
+ }\r
+ });\r
+ fileMenu.setLabel("File");\r
+ newickOutput.setLabel("Newick Format");\r
+ newickOutput.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent actionEvent) {\r
+ newickOutput_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ add(scrollPane, BorderLayout.CENTER);\r
+ jMenuBar1.add(fileMenu);\r
+ jMenuBar1.add(jMenu2);\r
+ jMenu2.add(fitToWindow);\r
+ jMenu2.add(fontSize);\r
+ jMenu2.add(distanceMenu);\r
+ jMenu2.add(bootstrapMenu);\r
+ jMenu2.add(placeholdersMenu);\r
+ fileMenu.add(newickOutput);\r
+ }\r
\r
- protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
+ protected void printMenu_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void fontSize_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
+ protected void distanceMenu_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void bootstrapMenu_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void newickOutput_actionPerformed(ActionEvent actionEvent)\r
- {\r
+ protected void placeholdersMenu_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void fitToWindow_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ public void newickOutput_actionPerformed(ActionEvent actionEvent) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
\r
-public class GUserDefinedColours extends Panel\r
-{\r
- protected Panel buttonPanel = new Panel();\r
- protected GridLayout gridLayout = new GridLayout();\r
- Panel jPanel2 = new Panel();\r
- protected Button okButton = new Button();\r
- protected Button applyButton = new Button();\r
- protected Button cancelButton = new Button();\r
- protected Scrollbar rScroller = new Scrollbar();\r
- Label label1 = new Label();\r
- Panel panel2 = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- protected TextField rText = new TextField();\r
- Panel panel3 = new Panel();\r
- Label label4 = new Label();\r
- protected Scrollbar gScroller = new Scrollbar();\r
- protected TextField gText = new TextField();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- Panel panel4 = new Panel();\r
- Label label5 = new Label();\r
- protected Scrollbar bScroller = new Scrollbar();\r
- protected TextField bText = new TextField();\r
- BorderLayout borderLayout3 = new BorderLayout();\r
- protected Panel target = new Panel();\r
-\r
- public GUserDefinedColours()\r
- {\r
- try\r
- {\r
- jbInit();\r
+public class GUserDefinedColours extends Panel {\r
+ protected Panel buttonPanel = new Panel();\r
+ protected GridLayout gridLayout = new GridLayout();\r
+ Panel jPanel2 = new Panel();\r
+ protected Button okButton = new Button();\r
+ protected Button applyButton = new Button();\r
+ protected Button cancelButton = new Button();\r
+ protected Scrollbar rScroller = new Scrollbar();\r
+ Label label1 = new Label();\r
+ Panel panel2 = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ protected TextField rText = new TextField();\r
+ Panel panel3 = new Panel();\r
+ Label label4 = new Label();\r
+ protected Scrollbar gScroller = new Scrollbar();\r
+ protected TextField gText = new TextField();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ Panel panel4 = new Panel();\r
+ Label label5 = new Label();\r
+ protected Scrollbar bScroller = new Scrollbar();\r
+ protected TextField bText = new TextField();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ protected Panel target = new Panel();\r
+\r
+ public GUserDefinedColours() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- this.setLayout(null);\r
- buttonPanel.setLayout(gridLayout);\r
- gridLayout.setColumns(6);\r
- gridLayout.setRows(4);\r
- okButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- okButton.setLabel("OK");\r
- okButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- okButton_actionPerformed(e);\r
- }\r
- });\r
- applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- applyButton.setLabel("Apply");\r
- applyButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- applyButton_actionPerformed(e);\r
- }\r
- });\r
- cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- cancelButton.setLabel("Cancel");\r
- cancelButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancelButton_actionPerformed(e);\r
- }\r
- });\r
- this.setBackground(new Color(212, 208, 223));\r
- jPanel2.setBounds(new Rectangle(0, 265, 400, 35));\r
- buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));\r
- rScroller.setMaximum(255);\r
- rScroller.setMinimum(0);\r
- rScroller.setOrientation(0);\r
- rScroller.setUnitIncrement(1);\r
- rScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
- public void adjustmentValueChanged(AdjustmentEvent e) {\r
- rScroller_adjustmentValueChanged(e);\r
- }\r
- });\r
- label1.setText("R");\r
- panel2.setBounds(new Rectangle(20, 29, 180, 19));\r
- panel2.setLayout(borderLayout1);\r
- rText.setText(" 0");\r
- rText.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- rText_actionPerformed(e);\r
- }\r
- });\r
- panel3.setLayout(borderLayout2);\r
- label4.setText("G");\r
- gScroller.setMaximum(255);\r
- gScroller.setMinimum(0);\r
- gScroller.setOrientation(0);\r
- gScroller.setUnitIncrement(1);\r
- gScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
- public void adjustmentValueChanged(AdjustmentEvent e) {\r
- gScroller_adjustmentValueChanged(e);\r
- }\r
- });\r
- gText.setText(" 0");\r
- gText.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- gText_actionPerformed(e);\r
- }\r
- });\r
- panel3.setBounds(new Rectangle(19, 54, 181, 20));\r
- panel4.setLayout(borderLayout3);\r
- label5.setText("B");\r
- bScroller.setMaximum(255);\r
- bScroller.setMinimum(0);\r
- bScroller.setOrientation(0);\r
- bScroller.setUnitIncrement(1);\r
- bScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
- public void adjustmentValueChanged(AdjustmentEvent e) {\r
- bScroller_adjustmentValueChanged(e);\r
- }\r
- });\r
- bText.setSelectionStart(6);\r
- bText.setText(" 0");\r
- bText.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- bText_actionPerformed(e);\r
- }\r
- });\r
- panel4.setBounds(new Rectangle(19, 87, 180, 20));\r
- target.setBackground(Color.black);\r
- target.setBounds(new Rectangle(229, 26, 134, 79));\r
- this.add(jPanel2, null);\r
- jPanel2.add(okButton, null);\r
- jPanel2.add(applyButton, null);\r
- jPanel2.add(cancelButton, null);\r
- this.add(buttonPanel, null);\r
- panel2.add(label1, BorderLayout.WEST);\r
- panel2.add(rScroller, BorderLayout.CENTER);\r
- panel2.add(rText, BorderLayout.EAST);\r
- this.add(target, null);\r
- this.add(panel4, null);\r
- panel3.add(label4, BorderLayout.WEST);\r
- panel3.add(gScroller, BorderLayout.CENTER);\r
- panel3.add(gText, BorderLayout.EAST);\r
- this.add(panel2, null);\r
- panel4.add(label5, BorderLayout.WEST);\r
- panel4.add(bScroller, BorderLayout.CENTER);\r
- panel4.add(bText, BorderLayout.EAST);\r
- this.add(panel3, null);\r
- }\r
-\r
-\r
- protected void okButton_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void applyButton_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
- protected void cancelButton_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
-\r
- }\r
\r
- protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
-\r
- }\r
-\r
- protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
-\r
- }\r
-\r
- protected void rText_actionPerformed(ActionEvent e) {\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(null);\r
+ buttonPanel.setLayout(gridLayout);\r
+ gridLayout.setColumns(6);\r
+ gridLayout.setRows(4);\r
+ okButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ okButton.setLabel("OK");\r
+ okButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ okButton_actionPerformed(e);\r
+ }\r
+ });\r
+ applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ applyButton.setLabel("Apply");\r
+ applyButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ applyButton_actionPerformed(e);\r
+ }\r
+ });\r
+ cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ cancelButton.setLabel("Cancel");\r
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancelButton_actionPerformed(e);\r
+ }\r
+ });\r
+ this.setBackground(new Color(212, 208, 223));\r
+ jPanel2.setBounds(new Rectangle(0, 265, 400, 35));\r
+ buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));\r
+ rScroller.setMaximum(255);\r
+ rScroller.setMinimum(0);\r
+ rScroller.setOrientation(0);\r
+ rScroller.setUnitIncrement(1);\r
+ rScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
+ public void adjustmentValueChanged(AdjustmentEvent e) {\r
+ rScroller_adjustmentValueChanged(e);\r
+ }\r
+ });\r
+ label1.setText("R");\r
+ panel2.setBounds(new Rectangle(20, 29, 180, 19));\r
+ panel2.setLayout(borderLayout1);\r
+ rText.setText(" 0");\r
+ rText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ rText_actionPerformed(e);\r
+ }\r
+ });\r
+ panel3.setLayout(borderLayout2);\r
+ label4.setText("G");\r
+ gScroller.setMaximum(255);\r
+ gScroller.setMinimum(0);\r
+ gScroller.setOrientation(0);\r
+ gScroller.setUnitIncrement(1);\r
+ gScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
+ public void adjustmentValueChanged(AdjustmentEvent e) {\r
+ gScroller_adjustmentValueChanged(e);\r
+ }\r
+ });\r
+ gText.setText(" 0");\r
+ gText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ gText_actionPerformed(e);\r
+ }\r
+ });\r
+ panel3.setBounds(new Rectangle(19, 54, 181, 20));\r
+ panel4.setLayout(borderLayout3);\r
+ label5.setText("B");\r
+ bScroller.setMaximum(255);\r
+ bScroller.setMinimum(0);\r
+ bScroller.setOrientation(0);\r
+ bScroller.setUnitIncrement(1);\r
+ bScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
+ public void adjustmentValueChanged(AdjustmentEvent e) {\r
+ bScroller_adjustmentValueChanged(e);\r
+ }\r
+ });\r
+ bText.setSelectionStart(6);\r
+ bText.setText(" 0");\r
+ bText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ bText_actionPerformed(e);\r
+ }\r
+ });\r
+ panel4.setBounds(new Rectangle(19, 87, 180, 20));\r
+ target.setBackground(Color.black);\r
+ target.setBounds(new Rectangle(229, 26, 134, 79));\r
+ this.add(jPanel2, null);\r
+ jPanel2.add(okButton, null);\r
+ jPanel2.add(applyButton, null);\r
+ jPanel2.add(cancelButton, null);\r
+ this.add(buttonPanel, null);\r
+ panel2.add(label1, BorderLayout.WEST);\r
+ panel2.add(rScroller, BorderLayout.CENTER);\r
+ panel2.add(rText, BorderLayout.EAST);\r
+ this.add(target, null);\r
+ this.add(panel4, null);\r
+ panel3.add(label4, BorderLayout.WEST);\r
+ panel3.add(gScroller, BorderLayout.CENTER);\r
+ panel3.add(gText, BorderLayout.EAST);\r
+ this.add(panel2, null);\r
+ panel4.add(label5, BorderLayout.WEST);\r
+ panel4.add(bScroller, BorderLayout.CENTER);\r
+ panel4.add(bText, BorderLayout.EAST);\r
+ this.add(panel3, null);\r
+ }\r
\r
- }\r
+ protected void okButton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void gText_actionPerformed(ActionEvent e) {\r
+ protected void applyButton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void cancelButton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void bText_actionPerformed(ActionEvent e) {\r
+ protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
+ }\r
\r
- }\r
+ protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
+ }\r
\r
+ protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
+ }\r
\r
+ protected void rText_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void gText_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void bText_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import java.awt.*;\r
-\r
import jalview.gui.Preferences;\r
-import jalview.schemes.ColourSchemeProperty;\r
-import javax.swing.event.AncestorListener;\r
-import javax.swing.event.AncestorEvent;\r
-\r
-public class GAlignFrame extends JInternalFrame\r
-{\r
- protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
- protected JMenu fileMenu = new JMenu();\r
- protected JMenuItem closeMenuItem = new JMenuItem();\r
- protected JMenu editMenu = new JMenu();\r
- protected JMenu viewMenu = new JMenu();\r
- protected JMenu colourMenu = new JMenu();\r
- protected JMenu calculateMenu = new JMenu();\r
- protected JMenu webService = new JMenu();\r
- protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
- protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
- protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
- protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
- protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
- protected JMenuItem sortIDMenuItem = new JMenuItem();\r
- protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
- protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
- protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
- protected JMenuItem PCAMenuItem = new JMenuItem();\r
- protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
- protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
- protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public JLabel statusBar = new JLabel();\r
- protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
- protected JMenu outputTextboxMenu = new JMenu();\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
- JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem htmlMenuItem = new JMenuItem();\r
- JMenuItem overviewMenuItem = new JMenuItem();\r
- protected JMenuItem undoMenuItem = new JMenuItem();\r
- protected JMenuItem redoMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
- protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem printMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem findMenuItem = new JMenuItem();\r
- JMenu searchMenu = new JMenu();\r
- protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
- JMenuItem deleteGroups = new JMenuItem();\r
- JMenuItem delete = new JMenuItem();\r
- JMenuItem copy = new JMenuItem();\r
- JMenuItem cut = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
- JMenuItem pasteNew = new JMenuItem();\r
- JMenuItem pasteThis = new JMenuItem();\r
- protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
- JMenuItem createPNG = new JMenuItem();\r
- protected JMenuItem font = new JMenuItem();\r
- protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
- JMenuItem epsFile = new JMenuItem();\r
- JMenuItem LoadtreeMenuItem = new JMenuItem();\r
- JMenuItem jpred = new JMenuItem();\r
- protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
- JMenuItem modifyPID = new JMenuItem();\r
- JMenuItem modifyConservation = new JMenuItem();\r
- protected JMenu sortByTreeMenu = new JMenu();\r
- protected JMenu sort = new JMenu();\r
- JMenu calculate = new JMenu();\r
- JMenuItem msaAlignMenuItem = new JMenuItem();\r
- JMenu jMenu2 = new JMenu();\r
- JMenuItem padGapsMenuitem = new JMenuItem();\r
- JMenuItem ClustalRealign = new JMenuItem();\r
- public GAlignFrame()\r
- {\r
- ButtonGroup colours = new ButtonGroup();\r
- colours.add(noColourmenuItem);\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- colours.add(strandColour);\r
- colours.add(turnColour);\r
- colours.add(buriedColour);\r
- colours.add(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
- colours.add(nucleotideColour);\r
-\r
- noColourmenuItem.setSelected(true);\r
- String defaultColour = Preferences.defaultColour;\r
- if(defaultColour!=null)\r
- {\r
- int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
- switch(index)\r
- {\r
- case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;\r
- case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;\r
- case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;\r
- case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;\r
- case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;\r
- case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;\r
- case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;\r
- case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;\r
- case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;\r
- case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;\r
- case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;\r
- }\r
- }\r
-\r
-\r
- try\r
- {\r
- jbInit();\r
- setJMenuBar(alignFrameMenuBar);\r
-\r
- JMenuItem item;\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
- item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add( item );\r
- }\r
-\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- fileMenu.setMnemonic('F');\r
- fileMenu.setText("File");\r
- saveAlignmentMenu.setMnemonic('L');\r
- saveAlignmentMenu.setText("Save As");\r
- saveAlignmentMenu.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveAlignmentMenu_actionPerformed(e);\r
- }\r
- });\r
- closeMenuItem.setMnemonic('C');\r
- closeMenuItem.setText("Close");\r
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- closeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- editMenu.setText("Edit");\r
- viewMenu.setText("View");\r
- colourMenu.setText("Colour");\r
- calculateMenu.setText("Calculate");\r
- webService.setText("Web Service");\r
- selectAllSequenceMenuItem.setText("Select all");\r
- selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- deselectAllSequenceMenuItem.setText("Deselect All");\r
- deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
- getKeyStroke(java.awt.event.\r
- KeyEvent.VK_ESCAPE, 0, false));\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- invertSequenceMenuItem.setText("Invert Selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- invertSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2LeftMenuItem.setText("Remove Left");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2LeftMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2RightMenuItem.setText("Remove Right");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2RightMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeAllGapsMenuItem.setText("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeAllGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewBoxesMenuItem.setText("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- viewBoxesMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewTextMenuItem.setText("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- viewTextMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortPairwiseMenuItem.setText("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortPairwiseMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortIDMenuItem.setText("by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortIDMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortGroupMenuItem.setText("by Group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeRedundancyMenuItem.setText("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeRedundancyMenuItem_actionPerformed(e);\r
- }\r
- });\r
- pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
- }\r
- });\r
- PCAMenuItem.setText("Principal Component Analysis...");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PCAMenuItem_actionPerformed(e);\r
- }\r
- });\r
- averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- neighbourTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- clustalAlignMenuItem.setText("Clustal Alignment...");\r
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalAlignMenuItem_actionPerformed(e);\r
- }\r
- });\r
- this.getContentPane().setLayout(borderLayout1);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
- {\r
- public void ancestorAdded(AncestorEvent event)\r
- {\r
- alignFrameMenuBar_ancestorAdded(event);\r
- }\r
-\r
- public void ancestorRemoved(AncestorEvent event)\r
- {\r
- }\r
-\r
- public void ancestorMoved(AncestorEvent event)\r
- {\r
- }\r
- });\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setMnemonic('T');\r
- outputTextboxMenu.setText("Output to Textbox");\r
- clustalColour.setText("Clustalx");\r
-\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setText("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setText("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setText("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setText("Helix Propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setText("Strand Propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setText("Turn Propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setText("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.setText("User Defined...");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setText("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setText("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62...");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- njTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- annotationPanelMenuItem.setActionCommand("");\r
- annotationPanelMenuItem.setText("Show Annotations");\r
- annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );\r
- annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- annotationPanelMenuItem_actionPerformed(e);\r
- }\r
- });\r
- colourTextMenuItem.setText("Colour Text");\r
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- colourTextMenuItem_actionPerformed(e);\r
- }\r
- });\r
- htmlMenuItem.setText("HTML");\r
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- htmlMenuItem_actionPerformed(e);\r
- }\r
- });\r
- overviewMenuItem.setText("Overview Window...");\r
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- overviewMenuItem_actionPerformed(e);\r
- }\r
- });\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setMnemonic('Z');\r
- undoMenuItem.setText("Undo");\r
- undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
- event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- undoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setMnemonic('0');\r
- redoMenuItem.setText("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- redoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setText("By Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
- wrapMenuItem.setText("Wrap");\r
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- wrapMenuItem_actionPerformed(e);\r
- }\r
- });\r
- printMenuItem.setText("Print");\r
- printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- printMenuItem_actionPerformed(e);\r
- }\r
- });\r
- renderGapsMenuItem.setText("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- renderGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- findMenuItem.setText("Find...");\r
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
- event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- findMenuItem_actionPerformed(e);\r
- }\r
- });\r
- searchMenu.setText("Search");\r
-\r
- abovePIDThreshold.setText("Above Identity Threshold");\r
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- abovePIDThreshold_actionPerformed(e);\r
- }\r
- });\r
- sequenceFeatures.setText("Sequence Features");\r
- sequenceFeatures.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- sequenceFeatures_actionPerformed(actionEvent);\r
- }\r
- });\r
- nucleotideColour.setText("Nucleotide");\r
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideColour_actionPerformed(e);\r
- }\r
- });\r
- deleteGroups.setText("Undefine groups");\r
- deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deleteGroups_actionPerformed(e);\r
- }\r
- });\r
- copy.setText("Copy");\r
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
- KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- copy.setMnemonic(KeyEvent.VK_C);\r
-\r
- copy.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed(e);\r
- }\r
- });\r
- cut.setText("Cut");\r
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
- KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- cut.setMnemonic(KeyEvent.VK_X);\r
- cut.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed(e);\r
- }\r
- });\r
- delete.setText("Delete");\r
- delete.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- delete_actionPerformed(e);\r
- }\r
- });\r
- jMenu1.setMnemonic('V');\r
- jMenu1.setText("Paste");\r
- pasteNew.setText("To New Alignment");\r
- pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
- KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- pasteNew.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteNew_actionPerformed(e);\r
- }\r
- });\r
- pasteThis.setText("Add To This Alignment");\r
- pasteThis.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteThis_actionPerformed(e);\r
- }\r
- });\r
- applyToAllGroups.setText("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- applyToAllGroups_actionPerformed(e);\r
- }\r
- });\r
- createPNG.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- createPNG_actionPerformed(e);\r
- }\r
- });\r
- createPNG.setActionCommand("Save As PNG Image");\r
- createPNG.setText("PNG");\r
- font.setText("Font...");\r
- font.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- font_actionPerformed(e);\r
- }\r
- });\r
- fullSeqId.setText("Show Full Sequence ID");\r
- fullSeqId.setState(true);\r
- fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fullSeqId_actionPerformed(e);\r
- }\r
- });\r
- epsFile.setText("EPS");\r
- epsFile.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- epsFile_actionPerformed(e);\r
- }\r
- });\r
- LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
- LoadtreeMenuItem.setText("Load Assocated Tree");\r
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- LoadtreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- jpred.setText("JPred...");\r
- jpred.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- jpred_actionPerformed(e);\r
- }\r
- });\r
- scaleAbove.setVisible(false);\r
- scaleAbove.setText("Scale Above");\r
- scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- scaleAbove_actionPerformed(e);\r
- }\r
- });\r
- scaleLeft.setVisible(false);\r
- scaleLeft.setSelected(true);\r
- scaleLeft.setText("Scale Left");\r
- scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- scaleLeft_actionPerformed(e);\r
- }\r
- });\r
- scaleRight.setVisible(false);\r
- scaleRight.setSelected(true);\r
- scaleRight.setText("Scale Right");\r
- scaleRight.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- scaleRight_actionPerformed(e);\r
- }\r
- });\r
- modifyPID.setText("Modify Identity Threshold...");\r
- modifyPID.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- modifyPID_actionPerformed(e);\r
- }\r
- });\r
- modifyConservation.setText("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- modifyConservation_actionPerformed(e);\r
- }\r
- });\r
- sortByTreeMenu.setText("By Tree Order");\r
- sort.setText("Sort");\r
- calculate.setText("Calculate Tree");\r
- msaAlignMenuItem.setText("Muscle Alignment...");\r
- msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- msaAlignMenuItem_actionPerformed(e);\r
- }\r
- });\r
- jMenu2.setText("Export");\r
- padGapsMenuitem.setText("Pad Gaps");\r
- padGapsMenuitem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- padGapsMenuitem_actionPerformed(e);\r
- }\r
- });\r
- ClustalRealign.setText("Clustal Realign...");\r
- ClustalRealign.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ClustalRealign_actionPerformed(e);\r
- }\r
- });\r
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
- alignFrameMenuBar.add(calculateMenu);\r
- fileMenu.add(saveAlignmentMenu);\r
- fileMenu.add(jMenu2);\r
- fileMenu.add(outputTextboxMenu);\r
- fileMenu.add(printMenuItem);\r
- fileMenu.addSeparator();\r
- fileMenu.add(LoadtreeMenuItem);\r
- fileMenu.addSeparator();\r
- fileMenu.add(closeMenuItem);\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.add(cut);\r
- editMenu.add(copy);\r
- editMenu.add(jMenu1);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(padGapsMenuitem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(fullSeqId);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.add(sequenceFeatures);\r
- viewMenu.addSeparator();\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(applyToAllGroups);\r
- colourMenu.addSeparator();\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
- calculateMenu.add(sort);\r
- calculateMenu.add(calculate);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(webService);\r
- webService.add(clustalAlignMenuItem);\r
- webService.add(msaAlignMenuItem);\r
- webService.add(jpred);\r
- webService.add(ClustalRealign);\r
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
- jMenu1.add(pasteNew);\r
- jMenu1.add(pasteThis);\r
- sort.add(sortIDMenuItem);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- jMenu2.add(htmlMenuItem);\r
- jMenu2.add(epsFile);\r
- jMenu2.add(createPNG);\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+import jalview.schemes.ColourSchemeProperty;\r
\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
+import java.awt.*;\r
+import java.awt.event.*;\r
\r
- }\r
+import javax.swing.*;\r
+import javax.swing.event.AncestorEvent;\r
+import javax.swing.event.AncestorListener;\r
\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
\r
- }\r
+public class GAlignFrame extends JInternalFrame {\r
+ protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
+ protected JMenu fileMenu = new JMenu();\r
+ protected JMenuItem closeMenuItem = new JMenuItem();\r
+ protected JMenu editMenu = new JMenu();\r
+ protected JMenu viewMenu = new JMenu();\r
+ protected JMenu colourMenu = new JMenu();\r
+ protected JMenu calculateMenu = new JMenu();\r
+ protected JMenu webService = new JMenu();\r
+ protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
+ protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
+ protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
+ protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
+ protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
+ protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
+ protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
+ protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
+ protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
+ protected JMenuItem sortIDMenuItem = new JMenuItem();\r
+ protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
+ protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
+ protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
+ protected JMenuItem PCAMenuItem = new JMenuItem();\r
+ protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
+ protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
+ protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public JLabel statusBar = new JLabel();\r
+ protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
+ protected JMenu outputTextboxMenu = new JMenu();\r
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
+ JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
+ JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
+ protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
+ JMenuItem htmlMenuItem = new JMenuItem();\r
+ JMenuItem overviewMenuItem = new JMenuItem();\r
+ protected JMenuItem undoMenuItem = new JMenuItem();\r
+ protected JMenuItem redoMenuItem = new JMenuItem();\r
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
+ protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
+ JMenuItem printMenuItem = new JMenuItem();\r
+ protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
+ JMenuItem findMenuItem = new JMenuItem();\r
+ JMenu searchMenu = new JMenu();\r
+ protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
+ JMenuItem deleteGroups = new JMenuItem();\r
+ JMenuItem delete = new JMenuItem();\r
+ JMenuItem copy = new JMenuItem();\r
+ JMenuItem cut = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
+ JMenuItem pasteNew = new JMenuItem();\r
+ JMenuItem pasteThis = new JMenuItem();\r
+ protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
+ JMenuItem createPNG = new JMenuItem();\r
+ protected JMenuItem font = new JMenuItem();\r
+ protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+ JMenuItem epsFile = new JMenuItem();\r
+ JMenuItem LoadtreeMenuItem = new JMenuItem();\r
+ JMenuItem jpred = new JMenuItem();\r
+ protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
+ JMenuItem modifyPID = new JMenuItem();\r
+ JMenuItem modifyConservation = new JMenuItem();\r
+ protected JMenu sortByTreeMenu = new JMenu();\r
+ protected JMenu sort = new JMenu();\r
+ JMenu calculate = new JMenu();\r
+ JMenuItem msaAlignMenuItem = new JMenuItem();\r
+ JMenu jMenu2 = new JMenu();\r
+ JMenuItem padGapsMenuitem = new JMenuItem();\r
+ JMenuItem ClustalRealign = new JMenuItem();\r
+\r
+ public GAlignFrame() {\r
+ ButtonGroup colours = new ButtonGroup();\r
+ colours.add(noColourmenuItem);\r
+ colours.add(clustalColour);\r
+ colours.add(zappoColour);\r
+ colours.add(taylorColour);\r
+ colours.add(hydrophobicityColour);\r
+ colours.add(helixColour);\r
+ colours.add(strandColour);\r
+ colours.add(turnColour);\r
+ colours.add(buriedColour);\r
+ colours.add(userDefinedColour);\r
+ colours.add(PIDColour);\r
+ colours.add(BLOSUM62Colour);\r
+ colours.add(nucleotideColour);\r
+\r
+ noColourmenuItem.setSelected(true);\r
+\r
+ String defaultColour = Preferences.defaultColour;\r
+\r
+ if (defaultColour != null) {\r
+ int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
+\r
+ switch (index) {\r
+ case ColourSchemeProperty.CLUSTAL:\r
+ clustalColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BLOSUM:\r
+ BLOSUM62Colour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.PID:\r
+ PIDColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.ZAPPO:\r
+ zappoColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.HYDROPHOBIC:\r
+ hydrophobicityColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.HELIX:\r
+ helixColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.STRAND:\r
+ strandColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.TURN:\r
+ turnColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BURIED:\r
+ buriedColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.NUCLEOTIDE:\r
+ nucleotideColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.USER_DEFINED:\r
+ userDefinedColour.setSelected(true);\r
+\r
+ break;\r
+ }\r
+ }\r
\r
+ try {\r
+ jbInit();\r
+ setJMenuBar(alignFrameMenuBar);\r
\r
+ JMenuItem item;\r
\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
+ item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
\r
- }\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
+ private void jbInit() throws Exception {\r
+ fileMenu.setMnemonic('F');\r
+ fileMenu.setText("File");\r
+ saveAlignmentMenu.setMnemonic('L');\r
+ saveAlignmentMenu.setText("Save As");\r
+ saveAlignmentMenu.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ saveAlignmentMenu_actionPerformed(e);\r
+ }\r
+ });\r
+ closeMenuItem.setMnemonic('C');\r
+ closeMenuItem.setText("Close");\r
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ closeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ editMenu.setText("Edit");\r
+ viewMenu.setText("View");\r
+ colourMenu.setText("Colour");\r
+ calculateMenu.setText("Calculate");\r
+ webService.setText("Web Service");\r
+ selectAllSequenceMenuItem.setText("Select all");\r
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_A,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ selectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ deselectAllSequenceMenuItem.setText("Deselect All");\r
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deselectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ invertSequenceMenuItem.setText("Invert Selection");\r
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ invertSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2LeftMenuItem.setText("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2LeftMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2RightMenuItem.setText("Remove Right");\r
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2RightMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeGappedColumnMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeAllGapsMenuItem.setText("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeAllGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewBoxesMenuItem.setText("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ viewBoxesMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewTextMenuItem.setText("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ viewTextMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortPairwiseMenuItem.setText("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortPairwiseMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortIDMenuItem.setText("by ID");\r
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortIDMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortGroupMenuItem.setText("by Group");\r
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortGroupMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeRedundancyMenuItem.setText("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeRedundancyMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pairwiseAlignmentMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ PCAMenuItem.setText("Principal Component Analysis...");\r
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PCAMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ averageDistanceTreeMenuItem.setText(\r
+ "Average Distance Using % Identity...");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ averageDistanceTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");\r
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ neighbourTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ clustalAlignMenuItem.setText("Clustal Alignment...");\r
+ clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ clustalAlignMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ this.getContentPane().setLayout(borderLayout1);\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ alignFrameMenuBar.addAncestorListener(new AncestorListener() {\r
+ public void ancestorAdded(AncestorEvent event) {\r
+ alignFrameMenuBar_ancestorAdded(event);\r
+ }\r
+\r
+ public void ancestorRemoved(AncestorEvent event) {\r
+ }\r
+\r
+ public void ancestorMoved(AncestorEvent event) {\r
+ }\r
+ });\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setMnemonic('T');\r
+ outputTextboxMenu.setText("Output to Textbox");\r
+ clustalColour.setText("Clustalx");\r
+\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ clustalColour_actionPerformed(e);\r
+ }\r
+ });\r
+ zappoColour.setText("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ zappoColour_actionPerformed(e);\r
+ }\r
+ });\r
+ taylorColour.setText("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ taylorColour_actionPerformed(e);\r
+ }\r
+ });\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ hydrophobicityColour_actionPerformed(e);\r
+ }\r
+ });\r
+ helixColour.setText("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ helixColour_actionPerformed(e);\r
+ }\r
+ });\r
+ strandColour.setText("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ strandColour_actionPerformed(e);\r
+ }\r
+ });\r
+ turnColour.setText("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ turnColour_actionPerformed(e);\r
+ }\r
+ });\r
+ buriedColour.setText("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setText("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setText("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setText("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setText(\r
+ "Average Distance Using BLOSUM62...");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setText("Show Annotations");\r
+ annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
+ annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ annotationPanelMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ colourTextMenuItem.setText("Colour Text");\r
+ colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ colourTextMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ htmlMenuItem.setText("HTML");\r
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ htmlMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ overviewMenuItem.setText("Overview Window...");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setMnemonic('Z');\r
+ undoMenuItem.setText("Undo");\r
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_Z,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ undoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setMnemonic('0');\r
+ redoMenuItem.setText("Redo");\r
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setText("By Conservation");\r
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ conservationMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ noColourmenuItem.setText("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setText("Wrap");\r
+ wrapMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ wrapMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ printMenuItem.setText("Print");\r
+ printMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ printMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setText("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ renderGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ findMenuItem.setText("Find...");\r
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_F,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ searchMenu.setText("Search");\r
+\r
+ abovePIDThreshold.setText("Above Identity Threshold");\r
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ abovePIDThreshold_actionPerformed(e);\r
+ }\r
+ });\r
+ sequenceFeatures.setText("Sequence Features");\r
+ sequenceFeatures.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent actionEvent) {\r
+ sequenceFeatures_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ nucleotideColour.setText("Nucleotide");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setText("Undefine groups");\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_C,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ copy.setMnemonic(KeyEvent.VK_C);\r
+\r
+ copy.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setText("Cut");\r
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_X,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ cut.setMnemonic(KeyEvent.VK_X);\r
+ cut.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setText("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu1.setMnemonic('V');\r
+ jMenu1.setText("Paste");\r
+ pasteNew.setText("To New Alignment");\r
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_V,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setText("Add To This Alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setText("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ applyToAllGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ createPNG.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ createPNG_actionPerformed(e);\r
+ }\r
+ });\r
+ createPNG.setActionCommand("Save As PNG Image");\r
+ createPNG.setText("PNG");\r
+ font.setText("Font...");\r
+ font.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+ fullSeqId.setText("Show Full Sequence ID");\r
+ fullSeqId.setState(true);\r
+ fullSeqId.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fullSeqId_actionPerformed(e);\r
+ }\r
+ });\r
+ epsFile.setText("EPS");\r
+ epsFile.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ epsFile_actionPerformed(e);\r
+ }\r
+ });\r
+ LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
+ LoadtreeMenuItem.setText("Load Assocated Tree");\r
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ LoadtreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ jpred.setText("JPred...");\r
+ jpred.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ jpred_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleAbove.setVisible(false);\r
+ scaleAbove.setText("Scale Above");\r
+ scaleAbove.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ scaleAbove_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleLeft.setVisible(false);\r
+ scaleLeft.setSelected(true);\r
+ scaleLeft.setText("Scale Left");\r
+ scaleLeft.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ scaleLeft_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleRight.setVisible(false);\r
+ scaleRight.setSelected(true);\r
+ scaleRight.setText("Scale Right");\r
+ scaleRight.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ scaleRight_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyPID.setText("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setText("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setText("By Tree Order");\r
+ sort.setText("Sort");\r
+ calculate.setText("Calculate Tree");\r
+ msaAlignMenuItem.setText("Muscle Alignment...");\r
+ msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ msaAlignMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu2.setText("Export");\r
+ padGapsMenuitem.setText("Pad Gaps");\r
+ padGapsMenuitem.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ padGapsMenuitem_actionPerformed(e);\r
+ }\r
+ });\r
+ ClustalRealign.setText("Clustal Realign...");\r
+ ClustalRealign.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ClustalRealign_actionPerformed(e);\r
+ }\r
+ });\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(searchMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ fileMenu.add(saveAlignmentMenu);\r
+ fileMenu.add(jMenu2);\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(printMenuItem);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(LoadtreeMenuItem);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(jMenu1);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(selectAllSequenceMenuItem);\r
+ editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(invertSequenceMenuItem);\r
+ editMenu.add(deleteGroups);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ editMenu.addSeparator();\r
+ editMenu.add(padGapsMenuitem);\r
+ searchMenu.add(findMenuItem);\r
+ viewMenu.add(font);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(wrapMenuItem);\r
+ viewMenu.add(fullSeqId);\r
+ viewMenu.add(scaleAbove);\r
+ viewMenu.add(scaleLeft);\r
+ viewMenu.add(scaleRight);\r
+ viewMenu.add(viewBoxesMenuItem);\r
+ viewMenu.add(viewTextMenuItem);\r
+ viewMenu.add(colourTextMenuItem);\r
+ viewMenu.add(renderGapsMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.add(sequenceFeatures);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(webService);\r
+ webService.add(clustalAlignMenuItem);\r
+ webService.add(msaAlignMenuItem);\r
+ webService.add(jpred);\r
+ webService.add(ClustalRealign);\r
+ this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ jMenu1.add(pasteNew);\r
+ jMenu1.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ jMenu2.add(htmlMenuItem);\r
+ jMenu2.add(epsFile);\r
+ jMenu2.add(createPNG);\r
+ }\r
\r
- }\r
+ protected void outputText_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void printMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
- {\r
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void copy_actionPerformed(ActionEvent e)\r
- {\r
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void cut_actionPerformed(ActionEvent e)\r
- {\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void delete_actionPerformed(ActionEvent e)\r
- {\r
+ protected void clustalColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void zappoColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
- {\r
+ protected void taylorColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
- {\r
+ protected void helixColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void strandColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
+ protected void turnColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void buriedColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
- {\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void PIDColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void font_actionPerformed(ActionEvent e)\r
- {\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
- {\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void printMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
- {\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void findMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
+ }\r
\r
- protected void jpred_actionPerformed(ActionEvent e)\r
- {\r
+ protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void deleteGroups_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
+ protected void copy_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void cut_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
+ protected void delete_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void pasteNew_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
+ protected void pasteThis_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
- {\r
+ protected void createPNG_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void font_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
- {\r
+ protected void fullSeqId_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void epsFile_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void jpred_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ protected void scaleAbove_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void scaleLeft_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
- {\r
+ protected void scaleRight_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void modifyPID_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
- {\r
+ protected void modifyConservation_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void preferences_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) {\r
+ }\r
\r
- protected void ClustalRealign_actionPerformed(ActionEvent e)\r
- {\r
+ protected void saveAlignmentMenu_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void ClustalRealign_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.jbgui;
-
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.border.*;
-
-public class GAlignmentPanel extends JPanel
-{
- protected JPanel sequenceHolderPanel = new JPanel();
- protected JScrollBar vscroll = new JScrollBar();
- protected JScrollBar hscroll = new JScrollBar();
- protected JPanel seqPanelHolder = new JPanel();
- BorderLayout borderLayout1 = new BorderLayout();
- BorderLayout borderLayout3 = new BorderLayout();
- protected JPanel scalePanelHolder = new JPanel();
- protected JPanel idPanelHolder = new JPanel();
- BorderLayout borderLayout5 = new BorderLayout();
- protected JPanel idSpaceFillerPanel1 = new JPanel();
- public JPanel annotationSpaceFillerHolder = new JPanel();
- BorderLayout borderLayout6 = new BorderLayout();
- ButtonGroup buttonGroup1 = new ButtonGroup();
- BorderLayout borderLayout7 = new BorderLayout();
- JPanel hscrollHolder = new JPanel();
- BorderLayout borderLayout10 = new BorderLayout();
- protected JPanel hscrollFillerPanel = new JPanel();
- BorderLayout borderLayout11 = new BorderLayout();
- public JScrollPane annotationScroller = new JScrollPane();
- Border border1;
- BorderLayout borderLayout4 = new BorderLayout();
-
- public GAlignmentPanel()
- {
- try
- {
- jbInit();
- }
- catch(Exception e)
- {
- e.printStackTrace();
- }
- }
- private void jbInit() throws Exception
- {
- border1 = BorderFactory.createLineBorder(Color.gray,1);
- idPanelHolder.setBorder(null);
- idPanelHolder.setPreferredSize(new Dimension(70, 10));
- this.setLayout(borderLayout7);
- sequenceHolderPanel.setMaximumSize(new Dimension(2147483647, 2147483647));
- sequenceHolderPanel.setMinimumSize(new Dimension(150, 150));
- sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
- sequenceHolderPanel.setLayout(borderLayout3);
- seqPanelHolder.setLayout(borderLayout1);
- scalePanelHolder.setBackground(Color.white);
- scalePanelHolder.setMinimumSize(new Dimension(10, 80));
- scalePanelHolder.setPreferredSize(new Dimension(10, 30));
- scalePanelHolder.setLayout(borderLayout6);
- idPanelHolder.setLayout(borderLayout5);
- idSpaceFillerPanel1.setBackground(Color.white);
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
- idSpaceFillerPanel1.setLayout(borderLayout11);
- annotationSpaceFillerHolder.setBackground(Color.white);
- annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
- annotationSpaceFillerHolder.setLayout(borderLayout4);
- hscroll.setOrientation(JScrollBar.HORIZONTAL);
- hscrollHolder.setLayout(borderLayout10);
- hscrollFillerPanel.setBackground(Color.white);
- hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
- hscrollHolder.setBackground(Color.white);
- annotationScroller.setBorder(null);
- annotationScroller.setPreferredSize(new Dimension(10, 80));
- this.setPreferredSize(new Dimension(220, 166));
- this.setRequestFocusEnabled(true);
- sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
- sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
- seqPanelHolder.add(vscroll, BorderLayout.EAST);
- sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
- // jPanel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
- this.add(idPanelHolder, BorderLayout.WEST);
- idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
- idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
- this.add(hscrollHolder, BorderLayout.SOUTH);
- hscrollHolder.add(hscroll, BorderLayout.CENTER);
- hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
- this.add(sequenceHolderPanel, BorderLayout.CENTER);
- }
-
-
-}
+*/\r
+package jalview.jbgui;\r
+\r
+import java.awt.*;\r
+\r
+import javax.swing.*;\r
+import javax.swing.border.*;\r
+\r
+\r
+public class GAlignmentPanel extends JPanel {\r
+ protected JPanel sequenceHolderPanel = new JPanel();\r
+ protected JScrollBar vscroll = new JScrollBar();\r
+ protected JScrollBar hscroll = new JScrollBar();\r
+ protected JPanel seqPanelHolder = new JPanel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ protected JPanel scalePanelHolder = new JPanel();\r
+ protected JPanel idPanelHolder = new JPanel();\r
+ BorderLayout borderLayout5 = new BorderLayout();\r
+ protected JPanel idSpaceFillerPanel1 = new JPanel();\r
+ public JPanel annotationSpaceFillerHolder = new JPanel();\r
+ BorderLayout borderLayout6 = new BorderLayout();\r
+ ButtonGroup buttonGroup1 = new ButtonGroup();\r
+ BorderLayout borderLayout7 = new BorderLayout();\r
+ JPanel hscrollHolder = new JPanel();\r
+ BorderLayout borderLayout10 = new BorderLayout();\r
+ protected JPanel hscrollFillerPanel = new JPanel();\r
+ BorderLayout borderLayout11 = new BorderLayout();\r
+ public JScrollPane annotationScroller = new JScrollPane();\r
+ Border border1;\r
+ BorderLayout borderLayout4 = new BorderLayout();\r
+\r
+ public GAlignmentPanel() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception {\r
+ border1 = BorderFactory.createLineBorder(Color.gray, 1);\r
+ idPanelHolder.setBorder(null);\r
+ idPanelHolder.setPreferredSize(new Dimension(70, 10));\r
+ this.setLayout(borderLayout7);\r
+ sequenceHolderPanel.setMaximumSize(new Dimension(2147483647, 2147483647));\r
+ sequenceHolderPanel.setMinimumSize(new Dimension(150, 150));\r
+ sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));\r
+ sequenceHolderPanel.setLayout(borderLayout3);\r
+ seqPanelHolder.setLayout(borderLayout1);\r
+ scalePanelHolder.setBackground(Color.white);\r
+ scalePanelHolder.setMinimumSize(new Dimension(10, 80));\r
+ scalePanelHolder.setPreferredSize(new Dimension(10, 30));\r
+ scalePanelHolder.setLayout(borderLayout6);\r
+ idPanelHolder.setLayout(borderLayout5);\r
+ idSpaceFillerPanel1.setBackground(Color.white);\r
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));\r
+ idSpaceFillerPanel1.setLayout(borderLayout11);\r
+ annotationSpaceFillerHolder.setBackground(Color.white);\r
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));\r
+ annotationSpaceFillerHolder.setLayout(borderLayout4);\r
+ hscroll.setOrientation(JScrollBar.HORIZONTAL);\r
+ hscrollHolder.setLayout(borderLayout10);\r
+ hscrollFillerPanel.setBackground(Color.white);\r
+ hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));\r
+ hscrollHolder.setBackground(Color.white);\r
+ annotationScroller.setBorder(null);\r
+ annotationScroller.setPreferredSize(new Dimension(10, 80));\r
+ this.setPreferredSize(new Dimension(220, 166));\r
+ this.setRequestFocusEnabled(true);\r
+ sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
+ sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
+ seqPanelHolder.add(vscroll, BorderLayout.EAST);\r
+ sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);\r
+\r
+ // jPanel3.add(secondaryPanelHolder, BorderLayout.SOUTH);\r
+ this.add(idPanelHolder, BorderLayout.WEST);\r
+ idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);\r
+ idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);\r
+ this.add(hscrollHolder, BorderLayout.SOUTH);\r
+ hscrollHolder.add(hscroll, BorderLayout.CENTER);\r
+ hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);\r
+ this.add(sequenceHolderPanel, BorderLayout.CENTER);\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.beans.VetoableChangeListener;\r
+\r
import java.beans.PropertyChangeEvent;\r
import java.beans.PropertyVetoException;\r
+import java.beans.VetoableChangeListener;\r
\r
-public class GCutAndPasteTransfer extends JInternalFrame\r
-{\r
- protected JTextArea textarea = new JTextArea();\r
- protected JScrollPane scrollPane = new JScrollPane();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- JMenuBar editMenubar = new JMenuBar();\r
- JMenu editMenu = new JMenu();\r
- JMenuItem copyItem = new JMenuItem();\r
- JMenuItem pasteMenu = new JMenuItem();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- protected JPanel inputButtonPanel = new JPanel();\r
- JButton ok = new JButton();\r
- JButton cancel = new JButton();\r
- public GCutAndPasteTransfer()\r
- {\r
- try\r
- {\r
- setJMenuBar(editMenubar);\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- scrollPane.setBorder(null);\r
- ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- ok.setText("Accept");\r
- ok.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- cancel.setText("Cancel");\r
- cancel.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancel_actionPerformed(e);\r
- }\r
- });\r
- textarea.setBorder(null);\r
- textarea.addVetoableChangeListener(new VetoableChangeListener()\r
- {\r
- public void vetoableChange(PropertyChangeEvent evt)\r
- {\r
- try\r
- {\r
- textarea_vetoableChange(evt);\r
- }\r
- catch (java.beans.PropertyVetoException exception0)\r
- {\r
- exception0.printStackTrace();\r
- }\r
-\r
- }\r
- });\r
- editMenubar.add(editMenu);\r
- textarea.setFont(new java.awt.Font("Verdana", 0, 12));\r
- textarea.addMouseListener(new java.awt.event.MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent e)\r
- {\r
- textarea_mousePressed(e);\r
- }\r
- });\r
- editMenu.setText("Edit");\r
- pasteMenu.setText("Paste");\r
- pasteMenu.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteMenu_actionPerformed(e);\r
- }\r
- });\r
- copyItem.setText("Copy");\r
- copyItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copyItem_actionPerformed(e);\r
- }\r
- });\r
- this.getContentPane().setLayout(borderLayout2);\r
- scrollPane.setBorder(null);\r
- scrollPane.getViewport().add(textarea, null);\r
- editMenu.add(copyItem);\r
- editMenu.add(pasteMenu);\r
- this.getContentPane().add(scrollPane, java.awt.BorderLayout.CENTER);\r
- inputButtonPanel.add(ok);\r
- inputButtonPanel.add(cancel);\r
-\r
- }\r
-\r
- void textarea_mousePressed(MouseEvent e)\r
- {\r
- if(textarea.getText().equals("Paste your alignment file here"))\r
- textarea.setText("");\r
- }\r
-\r
- public void copyItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+import javax.swing.*;\r
\r
- public void pasteMenu_actionPerformed(ActionEvent e)\r
- {\r
\r
- }\r
+public class GCutAndPasteTransfer extends JInternalFrame {\r
+ protected JTextArea textarea = new JTextArea();\r
+ protected JScrollPane scrollPane = new JScrollPane();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ JMenuBar editMenubar = new JMenuBar();\r
+ JMenu editMenu = new JMenu();\r
+ JMenuItem copyItem = new JMenuItem();\r
+ JMenuItem pasteMenu = new JMenuItem();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ protected JPanel inputButtonPanel = new JPanel();\r
+ JButton ok = new JButton();\r
+ JButton cancel = new JButton();\r
+\r
+ public GCutAndPasteTransfer() {\r
+ try {\r
+ setJMenuBar(editMenubar);\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
+ private void jbInit() throws Exception {\r
+ scrollPane.setBorder(null);\r
+ ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ ok.setText("Accept");\r
+ ok.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ok_actionPerformed(e);\r
+ }\r
+ });\r
+ cancel.setText("Cancel");\r
+ cancel.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancel_actionPerformed(e);\r
+ }\r
+ });\r
+ textarea.setBorder(null);\r
+ textarea.addVetoableChangeListener(new VetoableChangeListener() {\r
+ public void vetoableChange(PropertyChangeEvent evt) {\r
+ try {\r
+ textarea_vetoableChange(evt);\r
+ } catch (java.beans.PropertyVetoException exception0) {\r
+ exception0.printStackTrace();\r
+ }\r
+ }\r
+ });\r
+ editMenubar.add(editMenu);\r
+ textarea.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ textarea.addMouseListener(new java.awt.event.MouseAdapter() {\r
+ public void mousePressed(MouseEvent e) {\r
+ textarea_mousePressed(e);\r
+ }\r
+ });\r
+ editMenu.setText("Edit");\r
+ pasteMenu.setText("Paste");\r
+ pasteMenu.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteMenu_actionPerformed(e);\r
+ }\r
+ });\r
+ copyItem.setText("Copy");\r
+ copyItem.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ copyItem_actionPerformed(e);\r
+ }\r
+ });\r
+ this.getContentPane().setLayout(borderLayout2);\r
+ scrollPane.setBorder(null);\r
+ scrollPane.getViewport().add(textarea, null);\r
+ editMenu.add(copyItem);\r
+ editMenu.add(pasteMenu);\r
+ this.getContentPane().add(scrollPane, java.awt.BorderLayout.CENTER);\r
+ inputButtonPanel.add(ok);\r
+ inputButtonPanel.add(cancel);\r
+ }\r
\r
- }\r
+ void textarea_mousePressed(MouseEvent e) {\r
+ if (textarea.getText().equals("Paste your alignment file here")) {\r
+ textarea.setText("");\r
+ }\r
+ }\r
\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
+ public void copyItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ public void pasteMenu_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void textarea_vetoableChange(PropertyChangeEvent evt)\r
- throws PropertyVetoException\r
- {\r
+ public void ok_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ public void cancel_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ public void textarea_vetoableChange(PropertyChangeEvent evt)\r
+ throws PropertyVetoException {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+\r
+\r
+public class GDesktop extends JFrame {\r
+ protected static JMenu windowMenu = new JMenu();\r
+ JMenuBar DesktopMenubar = new JMenuBar();\r
+ JMenu FileMenu = new JMenu();\r
+ JMenu HelpMenu = new JMenu();\r
+ JMenuItem inputLocalFileMenuItem = new JMenuItem();\r
+ JMenuItem inputURLMenuItem = new JMenuItem();\r
+ JMenuItem inputTextboxMenuItem = new JMenuItem();\r
+ JMenuItem quit = new JMenuItem();\r
+ JMenuItem aboutMenuItem = new JMenuItem();\r
+ JMenuItem documentationMenuItem = new JMenuItem();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ JMenu toolsMenu = new JMenu();\r
+ JMenuItem preferences = new JMenuItem();\r
+ JMenuItem saveState = new JMenuItem();\r
+ JMenuItem loadState = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
+\r
+ public GDesktop() {\r
+ try {\r
+ jbInit();\r
+ this.setJMenuBar(DesktopMenubar);\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception {\r
+ FileMenu.setMnemonic('F');\r
+ FileMenu.setText("File");\r
+ HelpMenu.setText("Help");\r
+ inputLocalFileMenuItem.setMnemonic('L');\r
+ inputLocalFileMenuItem.setText("from File");\r
+ inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ inputLocalFileMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ inputURLMenuItem.setMnemonic('U');\r
+ inputURLMenuItem.setText("from URL");\r
+ inputURLMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ inputURLMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ inputTextboxMenuItem.setMnemonic('C');\r
+ inputTextboxMenuItem.setText("from Textbox");\r
+ inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ inputTextboxMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ quit.setMnemonic('Q');\r
+ quit.setText("Quit");\r
+ quit.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ quit_actionPerformed(e);\r
+ }\r
+ });\r
+ aboutMenuItem.setText("About");\r
+ aboutMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ aboutMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ documentationMenuItem.setText("Documentation");\r
+ documentationMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ documentationMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ this.getContentPane().setLayout(flowLayout1);\r
+ windowMenu.setText("Window");\r
+ preferences.setText("Preferences...");\r
+ preferences.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ preferences_actionPerformed(e);\r
+ }\r
+ });\r
+ toolsMenu.setText("Tools");\r
+ saveState.setMnemonic('S');\r
+ saveState.setText("Save Project");\r
+ saveState.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ saveState_actionPerformed(e);\r
+ }\r
+ });\r
+ loadState.setMnemonic('L');\r
+ loadState.setText("Load Project");\r
+ loadState.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ loadState_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu1.setMnemonic('I');\r
+ jMenu1.setText("Input Alignment");\r
+ DesktopMenubar.add(FileMenu);\r
+ DesktopMenubar.add(toolsMenu);\r
+ DesktopMenubar.add(HelpMenu);\r
+ DesktopMenubar.add(windowMenu);\r
+ FileMenu.addSeparator();\r
+ FileMenu.add(jMenu1);\r
+ FileMenu.addSeparator();\r
+ FileMenu.add(saveState);\r
+ FileMenu.add(loadState);\r
+ FileMenu.addSeparator();\r
+ FileMenu.add(quit);\r
+ HelpMenu.add(aboutMenuItem);\r
+ HelpMenu.add(documentationMenuItem);\r
+ toolsMenu.add(preferences);\r
+ jMenu1.add(inputLocalFileMenuItem);\r
+ jMenu1.add(inputURLMenuItem);\r
+ jMenu1.add(inputTextboxMenuItem);\r
+ }\r
+\r
+ protected void inputLocalFileMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void inputURLMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void inputTextboxMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void quit_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void aboutMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void documentationMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ public void SaveState_actionPerformed(ActionEvent e) {\r
+ }\r
\r
-public class GDesktop extends JFrame\r
-{\r
- JMenuBar DesktopMenubar = new JMenuBar();\r
- JMenu FileMenu = new JMenu();\r
- JMenu HelpMenu = new JMenu();\r
- JMenuItem inputLocalFileMenuItem = new JMenuItem();\r
- JMenuItem inputURLMenuItem = new JMenuItem();\r
- JMenuItem inputTextboxMenuItem = new JMenuItem();\r
- JMenuItem quit = new JMenuItem();\r
- JMenuItem aboutMenuItem = new JMenuItem();\r
- JMenuItem documentationMenuItem = new JMenuItem();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- protected static JMenu windowMenu = new JMenu();\r
- JMenu toolsMenu = new JMenu();\r
- JMenuItem preferences = new JMenuItem();\r
- JMenuItem saveState = new JMenuItem();\r
- JMenuItem loadState = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
- public GDesktop()\r
- {\r
- try\r
- {\r
- jbInit();\r
- this.setJMenuBar(DesktopMenubar);\r
+ protected void preferences_actionPerformed(ActionEvent e) {\r
}\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
+\r
+ public void saveState_actionPerformed(ActionEvent e) {\r
}\r
\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- FileMenu.setMnemonic('F');\r
- FileMenu.setText("File");\r
- HelpMenu.setText("Help");\r
- inputLocalFileMenuItem.setMnemonic('L');\r
- inputLocalFileMenuItem.setText("from File");\r
- inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputLocalFileMenuItem_actionPerformed(e);\r
- }\r
- });\r
- inputURLMenuItem.setMnemonic('U');\r
- inputURLMenuItem.setText("from URL");\r
- inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputURLMenuItem_actionPerformed(e);\r
- }\r
- });\r
- inputTextboxMenuItem.setMnemonic('C');\r
- inputTextboxMenuItem.setText("from Textbox");\r
- inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputTextboxMenuItem_actionPerformed(e);\r
- }\r
- });\r
- quit.setMnemonic('Q');\r
- quit.setText("Quit");\r
- quit.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- quit_actionPerformed(e);\r
- }\r
- });\r
- aboutMenuItem.setText("About");\r
- aboutMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- aboutMenuItem_actionPerformed(e);\r
- }\r
- });\r
- documentationMenuItem.setText("Documentation");\r
- documentationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- documentationMenuItem_actionPerformed(e);\r
- }\r
- });\r
- this.getContentPane().setLayout(flowLayout1);\r
- windowMenu.setText("Window");\r
- preferences.setText("Preferences...");\r
- preferences.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
-\r
- preferences_actionPerformed(e);\r
- }\r
- });\r
- toolsMenu.setText("Tools");\r
- saveState.setMnemonic('S');\r
- saveState.setText("Save Project");\r
- saveState.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveState_actionPerformed(e);\r
- }\r
- });\r
- loadState.setMnemonic('L');\r
- loadState.setText("Load Project");\r
- loadState.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- loadState_actionPerformed(e);\r
- }\r
- });\r
- jMenu1.setMnemonic('I');\r
- jMenu1.setText("Input Alignment");\r
- DesktopMenubar.add(FileMenu);\r
- DesktopMenubar.add(toolsMenu);\r
- DesktopMenubar.add(HelpMenu);\r
- DesktopMenubar.add(windowMenu);\r
- FileMenu.addSeparator();\r
- FileMenu.add(jMenu1);\r
- FileMenu.addSeparator();\r
- FileMenu.add(saveState);\r
- FileMenu.add(loadState);\r
- FileMenu.addSeparator();\r
- FileMenu.add(quit);\r
- HelpMenu.add(aboutMenuItem);\r
- HelpMenu.add(documentationMenuItem);\r
- toolsMenu.add(preferences);\r
- jMenu1.add(inputLocalFileMenuItem);\r
- jMenu1.add(inputURLMenuItem);\r
- jMenu1.add(inputTextboxMenuItem);\r
-\r
- }\r
-\r
- protected void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- { }\r
-\r
- protected void inputURLMenuItem_actionPerformed(ActionEvent e)\r
- { }\r
-\r
- protected void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- { }\r
-\r
- protected void quit_actionPerformed(ActionEvent e)\r
- { }\r
-\r
- protected void aboutMenuItem_actionPerformed(ActionEvent e)\r
- { }\r
-\r
- protected void documentationMenuItem_actionPerformed(ActionEvent e)\r
- { }\r
-\r
- public void SaveState_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void saveState_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void loadState_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void loadJalviewAlign_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+ public void loadState_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ public void loadJalviewAlign_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
+import javax.swing.*;\r
\r
-public class GFinder extends JPanel\r
-{\r
- JLabel jLabel1 = new JLabel();\r
- protected JTextField textfield = new JTextField();\r
- protected JButton findAll = new JButton();\r
- protected JButton findNext = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- GridLayout gridLayout1 = new GridLayout();\r
- protected JButton createNewGroup = new JButton();\r
\r
- public GFinder()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
+public class GFinder extends JPanel {\r
+ JLabel jLabel1 = new JLabel();\r
+ protected JTextField textfield = new JTextField();\r
+ protected JButton findAll = new JButton();\r
+ protected JButton findNext = new JButton();\r
+ JPanel jPanel1 = new JPanel();\r
+ GridLayout gridLayout1 = new GridLayout();\r
+ protected JButton createNewGroup = new JButton();\r
+\r
+ public GFinder() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel1.setText("Find");\r
- jLabel1.setBounds(new Rectangle(3, 30, 34, 15));\r
- this.setLayout(null);\r
- textfield.setFont(new java.awt.Font("Verdana", 0, 12));\r
- textfield.setText("");\r
- textfield.setBounds(new Rectangle(40, 27, 133, 21));\r
- textfield.addKeyListener(new java.awt.event.KeyAdapter()\r
- {\r
- public void keyTyped(KeyEvent e)\r
- {\r
- textfield_keyTyped(e);\r
- }\r
- });\r
- textfield.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- textfield_actionPerformed(e);\r
- }\r
- });\r
- findAll.setFont(new java.awt.Font("Verdana", 0, 12));\r
- findAll.setText("Find all");\r
- findAll.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- findAll_actionPerformed(e);\r
- }\r
- });\r
- findNext.setEnabled(false);\r
- findNext.setFont(new java.awt.Font("Verdana", 0, 12));\r
- findNext.setText("Find Next");\r
- findNext.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- findNext_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.setBounds(new Rectangle(180, 5, 141, 64));\r
- jPanel1.setLayout(gridLayout1);\r
- gridLayout1.setHgap(0);\r
- gridLayout1.setRows(3);\r
- gridLayout1.setVgap(2);\r
- createNewGroup.setEnabled(false);\r
- createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));\r
- createNewGroup.setToolTipText("");\r
- createNewGroup.setMargin(new Insets(0, 0, 0, 0));\r
- createNewGroup.setText("Create new group");\r
- createNewGroup.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- createNewGroup_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.add(findNext, null);\r
- jPanel1.add(findAll, null);\r
- jPanel1.add(createNewGroup, null);\r
- this.add(textfield, null);\r
- this.add(jLabel1, null);\r
- this.add(jPanel1, null);\r
- }\r
-\r
- protected void findNext_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void findAll_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
\r
+ private void jbInit() throws Exception {\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel1.setText("Find");\r
+ jLabel1.setBounds(new Rectangle(3, 30, 34, 15));\r
+ this.setLayout(null);\r
+ textfield.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ textfield.setText("");\r
+ textfield.setBounds(new Rectangle(40, 27, 133, 21));\r
+ textfield.addKeyListener(new java.awt.event.KeyAdapter() {\r
+ public void keyTyped(KeyEvent e) {\r
+ textfield_keyTyped(e);\r
+ }\r
+ });\r
+ textfield.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ textfield_actionPerformed(e);\r
+ }\r
+ });\r
+ findAll.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ findAll.setText("Find all");\r
+ findAll.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findAll_actionPerformed(e);\r
+ }\r
+ });\r
+ findNext.setEnabled(false);\r
+ findNext.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ findNext.setText("Find Next");\r
+ findNext.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findNext_actionPerformed(e);\r
+ }\r
+ });\r
+ jPanel1.setBounds(new Rectangle(180, 5, 141, 64));\r
+ jPanel1.setLayout(gridLayout1);\r
+ gridLayout1.setHgap(0);\r
+ gridLayout1.setRows(3);\r
+ gridLayout1.setVgap(2);\r
+ createNewGroup.setEnabled(false);\r
+ createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ createNewGroup.setToolTipText("");\r
+ createNewGroup.setMargin(new Insets(0, 0, 0, 0));\r
+ createNewGroup.setText("Create new group");\r
+ createNewGroup.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ createNewGroup_actionPerformed(e);\r
+ }\r
+ });\r
+ jPanel1.add(findNext, null);\r
+ jPanel1.add(findAll, null);\r
+ jPanel1.add(createNewGroup, null);\r
+ this.add(textfield, null);\r
+ this.add(jLabel1, null);\r
+ this.add(jPanel1, null);\r
+ }\r
\r
- protected void textfield_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+ protected void findNext_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- void textfield_keyTyped(KeyEvent e)\r
- {\r
- findNext.setEnabled(true);\r
- }\r
+ protected void findAll_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void createNewGroup_actionPerformed(ActionEvent e)\r
- {\r
+ protected void textfield_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ void textfield_keyTyped(KeyEvent e) {\r
+ findNext.setEnabled(true);\r
+ }\r
\r
+ public void createNewGroup_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
+import javax.swing.*;\r
\r
-public class GFontChooser extends JPanel\r
-{\r
- JLabel jLabel1 = new JLabel();\r
- protected JComboBox fontSize = new JComboBox();\r
- protected JComboBox fontStyle = new JComboBox();\r
- JLabel jLabel2 = new JLabel();\r
- JLabel jLabel3 = new JLabel();\r
- protected JComboBox fontName = new JComboBox();\r
- JButton ok = new JButton();\r
- JButton cancel = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- JPanel jPanel2 = new JPanel();\r
- JPanel jPanel3 = new JPanel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- BorderLayout borderLayout3 = new BorderLayout();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- JButton defaultButton = new JButton();\r
\r
- public GFontChooser()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
+public class GFontChooser extends JPanel {\r
+ JLabel jLabel1 = new JLabel();\r
+ protected JComboBox fontSize = new JComboBox();\r
+ protected JComboBox fontStyle = new JComboBox();\r
+ JLabel jLabel2 = new JLabel();\r
+ JLabel jLabel3 = new JLabel();\r
+ protected JComboBox fontName = new JComboBox();\r
+ JButton ok = new JButton();\r
+ JButton cancel = new JButton();\r
+ JPanel jPanel1 = new JPanel();\r
+ JPanel jPanel2 = new JPanel();\r
+ JPanel jPanel3 = new JPanel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ JButton defaultButton = new JButton();\r
+\r
+ public GFontChooser() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));\r
- jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel1.setText("Font: ");\r
- jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);\r
- this.setLayout(flowLayout1);\r
- fontSize.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontSize.setOpaque(false);\r
- fontSize.setPreferredSize(new Dimension(50, 21));\r
- fontSize.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fontSize_actionPerformed(e);\r
- }\r
- });\r
- fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontStyle.setOpaque(false);\r
- fontStyle.setPreferredSize(new Dimension(90, 21));\r
- fontStyle.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fontStyle_actionPerformed(e);\r
- }\r
- });\r
- jLabel2.setFont(new java.awt.Font("Verdana", 0, 11));\r
- jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel2.setText("Size: ");\r
- jLabel2.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);\r
- jLabel3.setFont(new java.awt.Font("Verdana", 0, 11));\r
- jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel3.setText("Style: ");\r
- jLabel3.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);\r
- fontName.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontName.setMaximumSize(new Dimension(32767, 32767));\r
- fontName.setMinimumSize(new Dimension(300, 21));\r
- fontName.setOpaque(false);\r
- fontName.setPreferredSize(new Dimension(180, 21));\r
- fontName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fontName_actionPerformed(e);\r
- }\r
- });\r
- ok.setFont(new java.awt.Font("Verdana", 0, 11));\r
- ok.setText("OK");\r
- ok.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- cancel.setFont(new java.awt.Font("Verdana", 0, 11));\r
- cancel.setText("Cancel");\r
- cancel.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancel_actionPerformed(e);\r
- }\r
- });\r
- this.setBackground(Color.white);\r
- jPanel1.setOpaque(false);\r
- jPanel1.setLayout(borderLayout1);\r
- jPanel2.setOpaque(false);\r
- jPanel2.setLayout(borderLayout3);\r
- jPanel3.setOpaque(false);\r
- jPanel3.setLayout(borderLayout2);\r
- flowLayout1.setAlignment(FlowLayout.CENTER);\r
- flowLayout1.setVgap(5);\r
- defaultButton.setText("Set as Default");\r
- defaultButton.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- defaultButton_actionPerformed(e);\r
- }\r
- });\r
- this.add(jPanel1, null);\r
- jPanel1.add(jLabel1, BorderLayout.WEST);\r
- jPanel1.add(fontName, BorderLayout.CENTER);\r
- this.add(jPanel3, null);\r
- this.add(jPanel2, null);\r
- jPanel2.add(jLabel3, BorderLayout.WEST);\r
- jPanel2.add(fontStyle, BorderLayout.CENTER);\r
- jPanel3.add(jLabel2, BorderLayout.WEST);\r
- jPanel3.add(fontSize, BorderLayout.CENTER);\r
- this.add(ok, null);\r
- this.add(cancel, null);\r
- this.add(defaultButton);\r
- }\r
-\r
- protected void ok_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void cancel_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
\r
- protected void fontName_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+ private void jbInit() throws Exception {\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ jLabel1.setText("Font: ");\r
+ jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);\r
+ this.setLayout(flowLayout1);\r
+ fontSize.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontSize.setOpaque(false);\r
+ fontSize.setPreferredSize(new Dimension(50, 21));\r
+ fontSize.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fontSize_actionPerformed(e);\r
+ }\r
+ });\r
+ fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontStyle.setOpaque(false);\r
+ fontStyle.setPreferredSize(new Dimension(90, 21));\r
+ fontStyle.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fontStyle_actionPerformed(e);\r
+ }\r
+ });\r
+ jLabel2.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ jLabel2.setText("Size: ");\r
+ jLabel2.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);\r
+ jLabel3.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ jLabel3.setText("Style: ");\r
+ jLabel3.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);\r
+ fontName.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontName.setMaximumSize(new Dimension(32767, 32767));\r
+ fontName.setMinimumSize(new Dimension(300, 21));\r
+ fontName.setOpaque(false);\r
+ fontName.setPreferredSize(new Dimension(180, 21));\r
+ fontName.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fontName_actionPerformed(e);\r
+ }\r
+ });\r
+ ok.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ ok.setText("OK");\r
+ ok.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ok_actionPerformed(e);\r
+ }\r
+ });\r
+ cancel.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ cancel.setText("Cancel");\r
+ cancel.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancel_actionPerformed(e);\r
+ }\r
+ });\r
+ this.setBackground(Color.white);\r
+ jPanel1.setOpaque(false);\r
+ jPanel1.setLayout(borderLayout1);\r
+ jPanel2.setOpaque(false);\r
+ jPanel2.setLayout(borderLayout3);\r
+ jPanel3.setOpaque(false);\r
+ jPanel3.setLayout(borderLayout2);\r
+ flowLayout1.setAlignment(FlowLayout.CENTER);\r
+ flowLayout1.setVgap(5);\r
+ defaultButton.setText("Set as Default");\r
+ defaultButton.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ defaultButton_actionPerformed(e);\r
+ }\r
+ });\r
+ this.add(jPanel1, null);\r
+ jPanel1.add(jLabel1, BorderLayout.WEST);\r
+ jPanel1.add(fontName, BorderLayout.CENTER);\r
+ this.add(jPanel3, null);\r
+ this.add(jPanel2, null);\r
+ jPanel2.add(jLabel3, BorderLayout.WEST);\r
+ jPanel2.add(fontStyle, BorderLayout.CENTER);\r
+ jPanel3.add(jLabel2, BorderLayout.WEST);\r
+ jPanel3.add(fontSize, BorderLayout.CENTER);\r
+ this.add(ok, null);\r
+ this.add(cancel, null);\r
+ this.add(defaultButton);\r
+ }\r
\r
- protected void fontSize_actionPerformed(ActionEvent e)\r
- {\r
+ protected void ok_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void cancel_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void fontStyle_actionPerformed(ActionEvent e)\r
- {\r
+ protected void fontName_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void fontSize_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void defaultButton_actionPerformed(ActionEvent e)\r
- {\r
+ protected void fontStyle_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ public void defaultButton_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.jbgui;
-
-import java.awt.*;
-import javax.swing.*;
-import java.awt.event.*;
-
-public class GPCAPanel extends JPanel
-{
- JPanel jPanel2 = new JPanel();
- JLabel jLabel1 = new JLabel();
- JLabel jLabel2 = new JLabel();
- JLabel jLabel3 = new JLabel();
- protected JComboBox xCombobox = new JComboBox();
- protected JComboBox yCombobox = new JComboBox();
- protected JComboBox zCombobox = new JComboBox();
- FlowLayout flowLayout1 = new FlowLayout();
- BorderLayout borderLayout1 = new BorderLayout();
-
- public GPCAPanel()
- {
- try
- {
- jbInit();
- }
- catch(Exception e)
- {
- e.printStackTrace();
- }
-
- for(int i=1; i<8; i++)
- {
- xCombobox.addItem("dim "+i);
- yCombobox.addItem("dim "+i);
- zCombobox.addItem("dim "+i);
- }
- }
- private void jbInit() throws Exception
- {
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel1.setText("x=");
- jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel2.setText("y=");
- jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel3.setText("z=");
- jPanel2.setBackground(Color.white);
- jPanel2.setBorder(null);
- zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
- zCombobox.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zCombobox_actionPerformed(e);
- }
- });
- yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
- yCombobox.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- yCombobox_actionPerformed(e);
- }
- });
- xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
- xCombobox.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- xCombobox_actionPerformed(e);
- }
- });
- this.add(jPanel2, BorderLayout.SOUTH);
- jPanel2.add(jLabel1, null);
- jPanel2.add(xCombobox, null);
- jPanel2.add(jLabel2, null);
- jPanel2.add(yCombobox, null);
- jPanel2.add(jLabel3, null);
- jPanel2.add(zCombobox, null);
- }
-
- protected void xCombobox_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void yCombobox_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void zCombobox_actionPerformed(ActionEvent e)
- {
-
- }
-
-}
+*/\r
+package jalview.jbgui;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+\r
+\r
+public class GPCAPanel extends JPanel {\r
+ JPanel jPanel2 = new JPanel();\r
+ JLabel jLabel1 = new JLabel();\r
+ JLabel jLabel2 = new JLabel();\r
+ JLabel jLabel3 = new JLabel();\r
+ protected JComboBox xCombobox = new JComboBox();\r
+ protected JComboBox yCombobox = new JComboBox();\r
+ protected JComboBox zCombobox = new JComboBox();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ public GPCAPanel() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ for (int i = 1; i < 8; i++) {\r
+ xCombobox.addItem("dim " + i);\r
+ yCombobox.addItem("dim " + i);\r
+ zCombobox.addItem("dim " + i);\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(borderLayout1);\r
+ jPanel2.setLayout(flowLayout1);\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel1.setText("x=");\r
+ jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel2.setText("y=");\r
+ jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel3.setText("z=");\r
+ jPanel2.setBackground(Color.white);\r
+ jPanel2.setBorder(null);\r
+ zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ zCombobox.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ zCombobox_actionPerformed(e);\r
+ }\r
+ });\r
+ yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ yCombobox.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ yCombobox_actionPerformed(e);\r
+ }\r
+ });\r
+ xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ xCombobox.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ xCombobox_actionPerformed(e);\r
+ }\r
+ });\r
+ this.add(jPanel2, BorderLayout.SOUTH);\r
+ jPanel2.add(jLabel1, null);\r
+ jPanel2.add(xCombobox, null);\r
+ jPanel2.add(jLabel2, null);\r
+ jPanel2.add(yCombobox, null);\r
+ jPanel2.add(jLabel3, null);\r
+ jPanel2.add(zCombobox, null);\r
+ }\r
+\r
+ protected void xCombobox_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void yCombobox_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void zCombobox_actionPerformed(ActionEvent e) {\r
+ }\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.jbgui;
-
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-
-
-public class GPairwiseAlignPanel extends JPanel
-{
- protected JScrollPane scrollPane = new JScrollPane();
- protected JTextArea textarea = new JTextArea();
- protected JButton viewInEditorButton = new JButton();
- JPanel jPanel1 = new JPanel();
- BorderLayout borderLayout1 = new BorderLayout();
-
- public GPairwiseAlignPanel()
- {
- try
- {
- jbInit();
- }
- catch(Exception e)
- {
- e.printStackTrace();
- }
- }
- private void jbInit() throws Exception
- {
- this.setLayout(borderLayout1);
- textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
- textarea.setText("");
- textarea.setWrapStyleWord(false);
- viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
- viewInEditorButton.setText("View in alignment editor");
- viewInEditorButton.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- viewInEditorButton_actionPerformed(e);
- }
- });
- this.add(scrollPane, BorderLayout.CENTER);
- scrollPane.getViewport().add(textarea, null);
- this.add(jPanel1, BorderLayout.SOUTH);
- jPanel1.add(viewInEditorButton, null);
- }
-
- protected void viewInEditorButton_actionPerformed(ActionEvent e)
- {
-
- }
-
-}
+*/\r
+package jalview.jbgui;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+\r
+\r
+public class GPairwiseAlignPanel extends JPanel {\r
+ protected JScrollPane scrollPane = new JScrollPane();\r
+ protected JTextArea textarea = new JTextArea();\r
+ protected JButton viewInEditorButton = new JButton();\r
+ JPanel jPanel1 = new JPanel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ public GPairwiseAlignPanel() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(borderLayout1);\r
+ textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
+ textarea.setText("");\r
+ textarea.setWrapStyleWord(false);\r
+ viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ viewInEditorButton.setText("View in alignment editor");\r
+ viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ viewInEditorButton_actionPerformed(e);\r
+ }\r
+ });\r
+ this.add(scrollPane, BorderLayout.CENTER);\r
+ scrollPane.getViewport().add(textarea, null);\r
+ this.add(jPanel1, BorderLayout.SOUTH);\r
+ jPanel1.add(viewInEditorButton, null);\r
+ }\r
+\r
+ protected void viewInEditorButton_actionPerformed(ActionEvent e) {\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
import java.awt.*;\r
-import java.awt.event.ActionListener;\r
import java.awt.event.ActionEvent;\r
-import javax.swing.border.TitledBorder;\r
+import java.awt.event.ActionListener;\r
import java.awt.event.MouseAdapter;\r
import java.awt.event.MouseEvent;\r
\r
-public class GPreferences\r
- extends JPanel\r
-{\r
- public GPreferences()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.setLayout(borderLayout1);\r
- ok.setText("OK");\r
- ok.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- cancel.setText("Cancel");\r
- cancel.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancel_actionPerformed(e);\r
- }\r
- });\r
- visual.setLayout(null);\r
- quality.setEnabled(false);\r
- quality.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
- quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
- quality.setSelected(true);\r
- quality.setText("Quality");\r
- quality.setBounds(new Rectangle(248, 53, 81, 23));\r
- jPanel2.setBorder(titledBorder1);\r
- jPanel2.setBounds(new Rectangle(9, 20, 442, 241));\r
- jPanel2.setLayout(null);\r
- fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fullID.setHorizontalAlignment(SwingConstants.RIGHT);\r
- fullID.setHorizontalTextPosition(SwingConstants.LEFT);\r
- fullID.setText("Full Sequence ID");\r
- fullID.setBounds(new Rectangle(9, 78, 129, 23));\r
- fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
- fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
- fullScreen.setText("Maximise Window");\r
- fullScreen.setBounds(new Rectangle(5, 29, 132, 23));\r
- conservation.setEnabled(false);\r
- conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
- conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
- conservation.setSelected(true);\r
- conservation.setText("Conservation");\r
- conservation.setBounds(new Rectangle(137, 53, 113, 23));\r
- identity.setEnabled(false);\r
- identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
- identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
- identity.setSelected(true);\r
- identity.setText("Consensus");\r
- identity.setBounds(new Rectangle(326, 53, 99, 23));\r
- annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
- annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
- annotations.setSelected(true);\r
- annotations.setText("Show Annotations");\r
- annotations.setBounds(new Rectangle(10, 53, 128, 23));\r
- annotations.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- annotations_actionPerformed(e);\r
- }\r
- });\r
- jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel1.setText("Gap Symbol");\r
- jLabel1.setBounds(new Rectangle(41, 142, 76, 15));\r
- colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- colour.setBounds(new Rectangle(121, 168, 154, 21));\r
- jLabel2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel2.setText("Colour");\r
- jLabel2.setBounds(new Rectangle(60, 172, 58, 15));\r
- jLabel3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel3.setText("Font");\r
- jLabel3.setBounds(new Rectangle(83, 114, 34, 15));\r
- fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontSizeCB.setBounds(new Rectangle(304, 109, 49, 21));\r
- fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontStyleCB.setBounds(new Rectangle(353, 109, 80, 21));\r
- fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontNameCB.setBounds(new Rectangle(121, 109, 183, 21));\r
- gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- gapSymbolCB.setBounds(new Rectangle(121, 140, 67, 21));\r
- startupCheckbox.setText("Open file");\r
- startupCheckbox.setBounds(new Rectangle(4, 200, 115, 23));\r
- startupCheckbox.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- jCheckBox1_actionPerformed(e);\r
- }\r
- });\r
- startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
- startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
- startupCheckbox.setSelected(true);\r
- startupFileTextfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- startupFileTextfield.setBounds(new Rectangle(122, 202, 309, 20));\r
- startupFileTextfield.addMouseListener(new MouseAdapter()\r
- {\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- startupFileTextfield_mouseClicked();\r
- }\r
- });\r
-\r
- jPanel2.add(annotations);\r
- jPanel2.add(conservation);\r
- jPanel2.add(quality);\r
- jPanel2.add(fullID);\r
- jPanel2.add(gapSymbolCB);\r
- jPanel2.add(jLabel1);\r
- jPanel2.add(fontNameCB);\r
- jPanel2.add(jLabel2);\r
- jPanel2.add(jLabel3);\r
- jPanel2.add(colour);\r
- jPanel2.add(fontSizeCB);\r
- jPanel2.add(fontStyleCB);\r
- jPanel2.add(identity);\r
- jPanel2.add(fullScreen);\r
- jPanel2.add(startupCheckbox);\r
- jPanel2.add(startupFileTextfield);\r
- jPanel1.add(ok);\r
- jPanel1.add(cancel);\r
- this.add(visaulTab, java.awt.BorderLayout.CENTER);\r
- visaulTab.add(visual, "visual");\r
- visual.add(jPanel2);\r
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();\r
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);\r
- gapSymbolCB.setRenderer(dlcr);\r
-\r
- }\r
-\r
- JTabbedPane visaulTab = new JTabbedPane();\r
- JPanel visual = new JPanel();\r
- JButton ok = new JButton();\r
- JButton cancel = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- protected JCheckBox quality = new JCheckBox();\r
- JPanel jPanel2 = new JPanel();\r
- TitledBorder titledBorder1 = new TitledBorder("Open new alignment");\r
- protected JCheckBox fullID = new JCheckBox();\r
- protected JCheckBox fullScreen = new JCheckBox();\r
- protected JCheckBox conservation = new JCheckBox();\r
- protected JCheckBox identity = new JCheckBox();\r
- protected JCheckBox annotations = new JCheckBox();\r
- JLabel jLabel1 = new JLabel();\r
- protected JComboBox colour = new JComboBox();\r
- JLabel jLabel2 = new JLabel();\r
- JLabel jLabel3 = new JLabel();\r
- protected JComboBox fontSizeCB = new JComboBox();\r
- protected JComboBox fontStyleCB = new JComboBox();\r
- protected JComboBox fontNameCB = new JComboBox();\r
- protected JComboBox gapSymbolCB = new JComboBox();\r
- protected JCheckBox startupCheckbox = new JCheckBox();\r
- protected JTextField startupFileTextfield = new JTextField();\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+import javax.swing.*;\r
+import javax.swing.border.TitledBorder;\r
\r
- public void annotations_actionPerformed(ActionEvent e)\r
- {\r
\r
- }\r
+public class GPreferences extends JPanel {\r
+ JTabbedPane visaulTab = new JTabbedPane();\r
+ JPanel visual = new JPanel();\r
+ JButton ok = new JButton();\r
+ JButton cancel = new JButton();\r
+ JPanel jPanel1 = new JPanel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ protected JCheckBox quality = new JCheckBox();\r
+ JPanel jPanel2 = new JPanel();\r
+ TitledBorder titledBorder1 = new TitledBorder("Open new alignment");\r
+ protected JCheckBox fullID = new JCheckBox();\r
+ protected JCheckBox fullScreen = new JCheckBox();\r
+ protected JCheckBox conservation = new JCheckBox();\r
+ protected JCheckBox identity = new JCheckBox();\r
+ protected JCheckBox annotations = new JCheckBox();\r
+ JLabel jLabel1 = new JLabel();\r
+ protected JComboBox colour = new JComboBox();\r
+ JLabel jLabel2 = new JLabel();\r
+ JLabel jLabel3 = new JLabel();\r
+ protected JComboBox fontSizeCB = new JComboBox();\r
+ protected JComboBox fontStyleCB = new JComboBox();\r
+ protected JComboBox fontNameCB = new JComboBox();\r
+ protected JComboBox gapSymbolCB = new JComboBox();\r
+ protected JCheckBox startupCheckbox = new JCheckBox();\r
+ protected JTextField startupFileTextfield = new JTextField();\r
+\r
+ public GPreferences() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
\r
- public void jCheckBox1_actionPerformed(ActionEvent e)\r
- {\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(borderLayout1);\r
+ ok.setText("OK");\r
+ ok.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ok_actionPerformed(e);\r
+ }\r
+ });\r
+ cancel.setText("Cancel");\r
+ cancel.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancel_actionPerformed(e);\r
+ }\r
+ });\r
+ visual.setLayout(null);\r
+ quality.setEnabled(false);\r
+ quality.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ quality.setSelected(true);\r
+ quality.setText("Quality");\r
+ quality.setBounds(new Rectangle(248, 53, 81, 23));\r
+ jPanel2.setBorder(titledBorder1);\r
+ jPanel2.setBounds(new Rectangle(9, 20, 442, 241));\r
+ jPanel2.setLayout(null);\r
+ fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fullID.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ fullID.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ fullID.setText("Full Sequence ID");\r
+ fullID.setBounds(new Rectangle(9, 78, 129, 23));\r
+ fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ fullScreen.setText("Maximise Window");\r
+ fullScreen.setBounds(new Rectangle(5, 29, 132, 23));\r
+ conservation.setEnabled(false);\r
+ conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ conservation.setSelected(true);\r
+ conservation.setText("Conservation");\r
+ conservation.setBounds(new Rectangle(137, 53, 113, 23));\r
+ identity.setEnabled(false);\r
+ identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ identity.setSelected(true);\r
+ identity.setText("Consensus");\r
+ identity.setBounds(new Rectangle(326, 53, 99, 23));\r
+ annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ annotations.setSelected(true);\r
+ annotations.setText("Show Annotations");\r
+ annotations.setBounds(new Rectangle(10, 53, 128, 23));\r
+ annotations.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ annotations_actionPerformed(e);\r
+ }\r
+ });\r
+ jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ jLabel1.setText("Gap Symbol");\r
+ jLabel1.setBounds(new Rectangle(41, 142, 76, 15));\r
+ colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ colour.setBounds(new Rectangle(121, 168, 154, 21));\r
+ jLabel2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ jLabel2.setText("Colour");\r
+ jLabel2.setBounds(new Rectangle(60, 172, 58, 15));\r
+ jLabel3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ jLabel3.setText("Font");\r
+ jLabel3.setBounds(new Rectangle(83, 114, 34, 15));\r
+ fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontSizeCB.setBounds(new Rectangle(304, 109, 49, 21));\r
+ fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontStyleCB.setBounds(new Rectangle(353, 109, 80, 21));\r
+ fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontNameCB.setBounds(new Rectangle(121, 109, 183, 21));\r
+ gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ gapSymbolCB.setBounds(new Rectangle(121, 140, 67, 21));\r
+ startupCheckbox.setText("Open file");\r
+ startupCheckbox.setBounds(new Rectangle(4, 200, 115, 23));\r
+ startupCheckbox.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ jCheckBox1_actionPerformed(e);\r
+ }\r
+ });\r
+ startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ startupCheckbox.setSelected(true);\r
+ startupFileTextfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ startupFileTextfield.setBounds(new Rectangle(122, 202, 309, 20));\r
+ startupFileTextfield.addMouseListener(new MouseAdapter() {\r
+ public void mouseClicked(MouseEvent e) {\r
+ startupFileTextfield_mouseClicked();\r
+ }\r
+ });\r
+\r
+ jPanel2.add(annotations);\r
+ jPanel2.add(conservation);\r
+ jPanel2.add(quality);\r
+ jPanel2.add(fullID);\r
+ jPanel2.add(gapSymbolCB);\r
+ jPanel2.add(jLabel1);\r
+ jPanel2.add(fontNameCB);\r
+ jPanel2.add(jLabel2);\r
+ jPanel2.add(jLabel3);\r
+ jPanel2.add(colour);\r
+ jPanel2.add(fontSizeCB);\r
+ jPanel2.add(fontStyleCB);\r
+ jPanel2.add(identity);\r
+ jPanel2.add(fullScreen);\r
+ jPanel2.add(startupCheckbox);\r
+ jPanel2.add(startupFileTextfield);\r
+ jPanel1.add(ok);\r
+ jPanel1.add(cancel);\r
+ this.add(visaulTab, java.awt.BorderLayout.CENTER);\r
+ visaulTab.add(visual, "visual");\r
+ visual.add(jPanel2);\r
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+\r
+ DefaultListCellRenderer dlcr = new DefaultListCellRenderer();\r
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);\r
+ gapSymbolCB.setRenderer(dlcr);\r
+ }\r
\r
- }\r
+ public void ok_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ public void cancel_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void startupFileTextfield_mouseClicked()\r
- {\r
+ public void annotations_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ public void jCheckBox1_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ public void startupFileTextfield_mouseClicked() {\r
+ }\r
}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.jbgui;
-
-import java.awt.*;
-import javax.swing.*;
-import java.awt.event.*;
-
-public class GSliderPanel extends JPanel
-{
- // this is used for conservation colours, PID colours and redundancy threshold
- protected JSlider slider = new JSlider();
- protected JTextField valueField = new JTextField();
- protected JLabel label = new JLabel();
- JPanel jPanel1 = new JPanel();
- GridLayout gridLayout1 = new GridLayout();
- JPanel jPanel2 = new JPanel();
- protected JButton applyButton = new JButton();
- protected JButton undoButton = new JButton();
- FlowLayout flowLayout1 = new FlowLayout();
- protected JCheckBox allGroupsCheck = new JCheckBox();
- BorderLayout borderLayout1 = new BorderLayout();
-
- public GSliderPanel()
- {
- try
- {
- jbInit();
- }
- catch(Exception e)
- {
- e.printStackTrace();
- }
- }
- private void jbInit() throws Exception
- {
- this.setLayout(gridLayout1);
- slider.setMajorTickSpacing(10);
- slider.setMinorTickSpacing(1);
- slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setFont(new java.awt.Font("Verdana", 0, 11));
- slider.setDoubleBuffered(true);
- valueField.setFont(new java.awt.Font("Verdana", 0, 11));
- valueField.setMinimumSize(new Dimension(6, 14));
- valueField.setPreferredSize(new Dimension(50, 12));
- valueField.setText("");
- valueField.setHorizontalAlignment(SwingConstants.CENTER);
- valueField.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- valueField_actionPerformed(e);
- }
- });
- label.setFont(new java.awt.Font("Verdana", 0, 11));
- label.setOpaque(false);
- label.setHorizontalAlignment(SwingConstants.CENTER);
- label.setText("set this label text");
- jPanel1.setLayout(borderLayout1);
- gridLayout1.setRows(2);
- jPanel2.setLayout(flowLayout1);
- applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
- applyButton.setOpaque(false);
- applyButton.setText("Apply");
- applyButton.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- applyButton_actionPerformed(e);
- }
- });
- undoButton.setEnabled(false);
- undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
- undoButton.setOpaque(false);
- undoButton.setText("Undo");
- undoButton.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- undoButton_actionPerformed(e);
- }
- });
- allGroupsCheck.setEnabled(false);
- allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
- allGroupsCheck.setOpaque(false);
- allGroupsCheck.setText("Apply to all Groups");
- allGroupsCheck.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- allGroupsCheck_actionPerformed(e);
- }
- });
- this.setBackground(Color.white);
- this.setPreferredSize(new Dimension(415, 84));
- jPanel2.setOpaque(false);
- jPanel1.setOpaque(false);
- this.add(jPanel2, null);
- jPanel2.add(label, null);
- jPanel2.add(applyButton, null);
- jPanel2.add(undoButton, null);this.add(jPanel1, null);
- jPanel1.add(slider, BorderLayout.WEST);
- jPanel1.add(valueField, BorderLayout.CENTER);
- jPanel1.add(allGroupsCheck, BorderLayout.EAST);
-
- }
-
- protected void valueField_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void applyButton_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void undoButton_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void allGroupsCheck_actionPerformed(ActionEvent e)
- {
-
- }
-
-}
+*/\r
+package jalview.jbgui;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+\r
+\r
+public class GSliderPanel extends JPanel {\r
+ // this is used for conservation colours, PID colours and redundancy threshold\r
+ protected JSlider slider = new JSlider();\r
+ protected JTextField valueField = new JTextField();\r
+ protected JLabel label = new JLabel();\r
+ JPanel jPanel1 = new JPanel();\r
+ GridLayout gridLayout1 = new GridLayout();\r
+ JPanel jPanel2 = new JPanel();\r
+ protected JButton applyButton = new JButton();\r
+ protected JButton undoButton = new JButton();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ protected JCheckBox allGroupsCheck = new JCheckBox();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ public GSliderPanel() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(gridLayout1);\r
+ slider.setMajorTickSpacing(10);\r
+ slider.setMinorTickSpacing(1);\r
+ slider.setPaintTicks(true);\r
+ slider.setBackground(Color.white);\r
+ slider.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ slider.setDoubleBuffered(true);\r
+ valueField.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ valueField.setMinimumSize(new Dimension(6, 14));\r
+ valueField.setPreferredSize(new Dimension(50, 12));\r
+ valueField.setText("");\r
+ valueField.setHorizontalAlignment(SwingConstants.CENTER);\r
+ valueField.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ valueField_actionPerformed(e);\r
+ }\r
+ });\r
+ label.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label.setOpaque(false);\r
+ label.setHorizontalAlignment(SwingConstants.CENTER);\r
+ label.setText("set this label text");\r
+ jPanel1.setLayout(borderLayout1);\r
+ gridLayout1.setRows(2);\r
+ jPanel2.setLayout(flowLayout1);\r
+ applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ applyButton.setOpaque(false);\r
+ applyButton.setText("Apply");\r
+ applyButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ applyButton_actionPerformed(e);\r
+ }\r
+ });\r
+ undoButton.setEnabled(false);\r
+ undoButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ undoButton.setOpaque(false);\r
+ undoButton.setText("Undo");\r
+ undoButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ undoButton_actionPerformed(e);\r
+ }\r
+ });\r
+ allGroupsCheck.setEnabled(false);\r
+ allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ allGroupsCheck.setOpaque(false);\r
+ allGroupsCheck.setText("Apply to all Groups");\r
+ allGroupsCheck.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ allGroupsCheck_actionPerformed(e);\r
+ }\r
+ });\r
+ this.setBackground(Color.white);\r
+ this.setPreferredSize(new Dimension(415, 84));\r
+ jPanel2.setOpaque(false);\r
+ jPanel1.setOpaque(false);\r
+ this.add(jPanel2, null);\r
+ jPanel2.add(label, null);\r
+ jPanel2.add(applyButton, null);\r
+ jPanel2.add(undoButton, null);\r
+ this.add(jPanel1, null);\r
+ jPanel1.add(slider, BorderLayout.WEST);\r
+ jPanel1.add(valueField, BorderLayout.CENTER);\r
+ jPanel1.add(allGroupsCheck, BorderLayout.EAST);\r
+ }\r
+\r
+ protected void valueField_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void applyButton_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void undoButton_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void allGroupsCheck_actionPerformed(ActionEvent e) {\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbgui;\r
\r
import java.awt.*;\r
-import javax.swing.*;\r
import java.awt.event.*;\r
\r
-public class GTreePanel extends JInternalFrame\r
-{\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- protected JScrollPane scrollPane = new JScrollPane();\r
- JMenuBar jMenuBar1 = new JMenuBar();\r
- JMenu jMenu1 = new JMenu();\r
- JMenuItem saveAsNewick = new JMenuItem();\r
- JMenuItem printMenu = new JMenuItem();\r
- JMenu jMenu2 = new JMenu();\r
- protected JMenuItem fontSize = new JMenuItem();\r
- protected JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();\r
- JMenuItem pngTree = new JMenuItem();\r
- JMenuItem epsTree = new JMenuItem();\r
- JMenu saveAsMenu = new JMenu();\r
- JMenuItem textbox = new JMenuItem();\r
-\r
- public GTreePanel()\r
- {\r
- try\r
- {\r
- jbInit();\r
- this.setJMenuBar(jMenuBar1);\r
+import javax.swing.*;\r
+\r
+\r
+public class GTreePanel extends JInternalFrame {\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ protected JScrollPane scrollPane = new JScrollPane();\r
+ JMenuBar jMenuBar1 = new JMenuBar();\r
+ JMenu jMenu1 = new JMenu();\r
+ JMenuItem saveAsNewick = new JMenuItem();\r
+ JMenuItem printMenu = new JMenuItem();\r
+ JMenu jMenu2 = new JMenu();\r
+ protected JMenuItem fontSize = new JMenuItem();\r
+ protected JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();\r
+ JMenuItem pngTree = new JMenuItem();\r
+ JMenuItem epsTree = new JMenuItem();\r
+ JMenu saveAsMenu = new JMenu();\r
+ JMenuItem textbox = new JMenuItem();\r
+\r
+ public GTreePanel() {\r
+ try {\r
+ jbInit();\r
+ this.setJMenuBar(jMenuBar1);\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception {\r
+ this.getContentPane().setLayout(borderLayout1);\r
+ this.setBackground(Color.white);\r
+ this.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ scrollPane.setOpaque(false);\r
+ jMenu1.setText("File");\r
+ saveAsNewick.setText("Newick Format");\r
+ saveAsNewick.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ saveAsNewick_actionPerformed(e);\r
+ }\r
+ });\r
+ printMenu.setText("Print");\r
+ printMenu.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ printMenu_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu2.setText("View");\r
+ fontSize.setText("Font Size - 12");\r
+ fontSize.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fontSize_actionPerformed(e);\r
+ }\r
+ });\r
+ bootstrapMenu.setText("Show Bootstrap Values");\r
+ bootstrapMenu.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ bootstrapMenu_actionPerformed(e);\r
+ }\r
+ });\r
+ distanceMenu.setText("Show Distances");\r
+ distanceMenu.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ distanceMenu_actionPerformed(e);\r
+ }\r
+ });\r
+ fitToWindow.setSelected(true);\r
+ fitToWindow.setText("Fit To Window");\r
+ fitToWindow.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fitToWindow_actionPerformed(e);\r
+ }\r
+ });\r
+ epsTree.setText("EPS");\r
+ epsTree.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ epsTree_actionPerformed(e);\r
+ }\r
+ });\r
+ pngTree.setText("PNG");\r
+ pngTree.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pngTree_actionPerformed(e);\r
+ }\r
+ });\r
+ saveAsMenu.setText("Save as");\r
+ placeholdersMenu.setToolTipText(\r
+ "Marks leaves of tree not associated with a sequence");\r
+ placeholdersMenu.setText("Mark Unlinked Leaves");\r
+ placeholdersMenu.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ placeholdersMenu_actionPerformed(e);\r
+ }\r
+ });\r
+ textbox.setText("Output to Textbox...");\r
+ textbox.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ textbox_actionPerformed(e);\r
+ }\r
+ });\r
+ this.getContentPane().add(scrollPane, BorderLayout.CENTER);\r
+ jMenuBar1.add(jMenu1);\r
+ jMenuBar1.add(jMenu2);\r
+ jMenu1.add(saveAsMenu);\r
+ jMenu1.add(textbox);\r
+ jMenu1.add(printMenu);\r
+ jMenu2.add(fitToWindow);\r
+ jMenu2.add(fontSize);\r
+ jMenu2.add(distanceMenu);\r
+ jMenu2.add(bootstrapMenu);\r
+ jMenu2.add(placeholdersMenu);\r
+ saveAsMenu.add(saveAsNewick);\r
+ saveAsMenu.add(epsTree);\r
+ saveAsMenu.add(pngTree);\r
+ }\r
+\r
+ protected void printMenu_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void fontSize_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void distanceMenu_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void bootstrapMenu_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void fitToWindow_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void pngTree_actionPerformed(ActionEvent e) {\r
+ }\r
+\r
+ protected void epsTree_actionPerformed(ActionEvent e) {\r
}\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
+\r
+ protected void saveAsNewick_actionPerformed(ActionEvent e) {\r
}\r
\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- this.getContentPane().setLayout(borderLayout1);\r
- this.setBackground(Color.white);\r
- this.setFont(new java.awt.Font("Verdana", 0, 12));\r
- scrollPane.setOpaque(false);\r
- jMenu1.setText("File");\r
- saveAsNewick.setText("Newick Format");\r
- saveAsNewick.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveAsNewick_actionPerformed(e);\r
- }\r
- });\r
- printMenu.setText("Print");\r
- printMenu.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- printMenu_actionPerformed(e);\r
- }\r
- });\r
- jMenu2.setText("View");\r
- fontSize.setText("Font Size - 12");\r
- fontSize.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fontSize_actionPerformed(e);\r
- }\r
- });\r
- bootstrapMenu.setText("Show Bootstrap Values");\r
- bootstrapMenu.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- bootstrapMenu_actionPerformed(e);\r
- }\r
- });\r
- distanceMenu.setText("Show Distances");\r
- distanceMenu.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- distanceMenu_actionPerformed(e);\r
- }\r
- });\r
- fitToWindow.setSelected(true);\r
- fitToWindow.setText("Fit To Window");\r
- fitToWindow.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fitToWindow_actionPerformed(e);\r
- }\r
- });\r
- epsTree.setText("EPS");\r
- epsTree.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- epsTree_actionPerformed(e);\r
- }\r
- });\r
- pngTree.setText("PNG");\r
- pngTree.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pngTree_actionPerformed(e);\r
- }\r
- });\r
- saveAsMenu.setText("Save as");\r
- placeholdersMenu.setToolTipText(\r
- "Marks leaves of tree not associated with a sequence");\r
- placeholdersMenu.setText("Mark Unlinked Leaves");\r
- placeholdersMenu.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- placeholdersMenu_actionPerformed(e);\r
- }\r
- });\r
- textbox.setText("Output to Textbox...");\r
- textbox.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- textbox_actionPerformed(e);\r
- }\r
- });\r
- this.getContentPane().add(scrollPane, BorderLayout.CENTER);\r
- jMenuBar1.add(jMenu1);\r
- jMenuBar1.add(jMenu2);\r
- jMenu1.add(saveAsMenu);\r
- jMenu1.add(textbox);\r
- jMenu1.add(printMenu);\r
- jMenu2.add(fitToWindow);\r
- jMenu2.add(fontSize);\r
- jMenu2.add(distanceMenu);\r
- jMenu2.add(bootstrapMenu);\r
- jMenu2.add(placeholdersMenu);\r
- saveAsMenu.add(saveAsNewick);\r
- saveAsMenu.add(epsTree);\r
- saveAsMenu.add(pngTree);\r
- }\r
-\r
-\r
- protected void printMenu_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void fontSize_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void distanceMenu_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void pngTree_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void epsTree_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void saveAsNewick_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void textbox_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
+ protected void placeholdersMenu_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ public void textbox_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
+import javax.swing.*;\r
\r
-public class GUserDefinedColours extends JPanel\r
-{\r
- protected JColorChooser colorChooser = new JColorChooser();\r
- protected JPanel buttonPanel = new JPanel();\r
- protected GridLayout gridLayout = new GridLayout();\r
- JPanel jPanel2 = new JPanel();\r
- protected JButton okButton = new JButton();\r
- protected JButton applyButton = new JButton();\r
- protected JButton loadbutton = new JButton();\r
- protected JButton savebutton = new JButton();\r
- protected JButton cancelButton = new JButton();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
\r
- public GUserDefinedColours()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
+public class GUserDefinedColours extends JPanel {\r
+ protected JColorChooser colorChooser = new JColorChooser();\r
+ protected JPanel buttonPanel = new JPanel();\r
+ protected GridLayout gridLayout = new GridLayout();\r
+ JPanel jPanel2 = new JPanel();\r
+ protected JButton okButton = new JButton();\r
+ protected JButton applyButton = new JButton();\r
+ protected JButton loadbutton = new JButton();\r
+ protected JButton savebutton = new JButton();\r
+ protected JButton cancelButton = new JButton();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+\r
+ public GUserDefinedColours() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
}\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- this.setLayout(flowLayout1);\r
- buttonPanel.setLayout(gridLayout);\r
- gridLayout.setColumns(6);\r
- gridLayout.setRows(4);\r
- okButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- okButton.setText("OK");\r
- okButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- okButton_actionPerformed(e);\r
- }\r
- });\r
- applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- applyButton.setText("Apply");\r
- applyButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- applyButton_actionPerformed(e);\r
- }\r
- });\r
- loadbutton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- loadbutton.setText("Load scheme");\r
- loadbutton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- loadbutton_actionPerformed(e);\r
- }\r
- });\r
- savebutton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- savebutton.setText("Save scheme");\r
- savebutton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- savebutton_actionPerformed(e);\r
- }\r
- });\r
- cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- cancelButton.setText("Cancel");\r
- cancelButton.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancelButton_actionPerformed(e);\r
- }\r
- });\r
- this.setBackground(new Color(212, 208, 223));\r
- jPanel2.setOpaque(false);\r
- colorChooser.setOpaque(false);\r
- this.add(colorChooser, null);\r
- this.add(buttonPanel, null);\r
- this.add(jPanel2, null);\r
- jPanel2.add(okButton, null);\r
- jPanel2.add(applyButton, null);\r
- jPanel2.add(loadbutton, null);\r
- jPanel2.add(savebutton, null);\r
- jPanel2.add(cancelButton, null);\r
- }\r
-\r
-\r
- protected void okButton_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void applyButton_actionPerformed(ActionEvent e)\r
- {\r
\r
- }\r
-\r
- protected void loadbutton_actionPerformed(ActionEvent e)\r
- {\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(flowLayout1);\r
+ buttonPanel.setLayout(gridLayout);\r
+ gridLayout.setColumns(6);\r
+ gridLayout.setRows(4);\r
+ okButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ okButton.setText("OK");\r
+ okButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ okButton_actionPerformed(e);\r
+ }\r
+ });\r
+ applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ applyButton.setText("Apply");\r
+ applyButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ applyButton_actionPerformed(e);\r
+ }\r
+ });\r
+ loadbutton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ loadbutton.setText("Load scheme");\r
+ loadbutton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ loadbutton_actionPerformed(e);\r
+ }\r
+ });\r
+ savebutton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ savebutton.setText("Save scheme");\r
+ savebutton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ savebutton_actionPerformed(e);\r
+ }\r
+ });\r
+ cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ cancelButton.setText("Cancel");\r
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancelButton_actionPerformed(e);\r
+ }\r
+ });\r
+ this.setBackground(new Color(212, 208, 223));\r
+ jPanel2.setOpaque(false);\r
+ colorChooser.setOpaque(false);\r
+ this.add(colorChooser, null);\r
+ this.add(buttonPanel, null);\r
+ this.add(jPanel2, null);\r
+ jPanel2.add(okButton, null);\r
+ jPanel2.add(applyButton, null);\r
+ jPanel2.add(loadbutton, null);\r
+ jPanel2.add(savebutton, null);\r
+ jPanel2.add(cancelButton, null);\r
+ }\r
\r
- }\r
+ protected void okButton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void savebutton_actionPerformed(ActionEvent e)\r
- {\r
+ protected void applyButton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void loadbutton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void cancelButton_actionPerformed(ActionEvent e)\r
- {\r
+ protected void savebutton_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void cancelButton_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.jbgui;
-
-import java.awt.*;
-import javax.swing.*;
-import java.awt.event.*;
-
-public class GWebserviceInfo extends JPanel
-{
- protected JTextArea infoText = new JTextArea();
- JScrollPane jScrollPane1 = new JScrollPane();
- JScrollPane jScrollPane2 = new JScrollPane();
- protected JTextArea progressText = new JTextArea();
- JPanel jPanel1 = new JPanel();
- BorderLayout borderLayout1 = new BorderLayout();
- BorderLayout borderLayout2 = new BorderLayout();
- protected JPanel titlePanel = new JPanel();
- BorderLayout borderLayout3 = new BorderLayout();
- JPanel jPanel2 = new JPanel();
- protected JButton cancel = new JButton();
- GridBagLayout gridBagLayout1 = new GridBagLayout();
-
- public GWebserviceInfo()
- {
- try
- {
- jbInit();
- }
- catch(Exception e)
- {
- e.printStackTrace();
- }
- }
- private void jbInit() throws Exception
- {
- infoText.setFont(new java.awt.Font("Verdana", 0, 10));
- infoText.setBorder(null);
- infoText.setEditable(false);
- infoText.setText("");
- infoText.setLineWrap(true);
- infoText.setWrapStyleWord(true);
- this.setLayout(borderLayout1);
- progressText.setFont(new java.awt.Font("Verdana", 0, 10));
- progressText.setBorder(null);
- progressText.setEditable(false);
- progressText.setText("");
- progressText.setLineWrap(true);
- progressText.setWrapStyleWord(true);
- jPanel1.setLayout(borderLayout2);
- titlePanel.setBackground(Color.white);
- titlePanel.setPreferredSize(new Dimension(0, 60));
- titlePanel.setLayout(borderLayout3);
- jScrollPane2.setBorder(null);
- jScrollPane1.setBorder(null);
- jScrollPane1.setPreferredSize(new Dimension(400, 70));
- cancel.setFont(new java.awt.Font("Verdana", 0, 11));
- cancel.setText("Cancel");
- cancel.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
- jPanel2.setLayout(gridBagLayout1);
- jPanel2.setOpaque(false);
- this.add(jScrollPane2, BorderLayout.CENTER);
- this.add(jPanel1, BorderLayout.NORTH);
- jPanel1.add(jScrollPane1, BorderLayout.CENTER);
- jScrollPane1.getViewport().add(infoText, null);
- jScrollPane2.getViewport().add(progressText, null);
- jPanel1.add(titlePanel, BorderLayout.NORTH);
- titlePanel.add(jPanel2, BorderLayout.EAST);
- jPanel2.add(cancel, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0
- ,GridBagConstraints.SOUTH, GridBagConstraints.NONE, new Insets(24, 5, 21, 5), 0, 0));
- }
-
- protected void cancel_actionPerformed(ActionEvent e)
- {
-
- }
-}
+*/\r
+package jalview.jbgui;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+\r
+\r
+public class GWebserviceInfo extends JPanel {\r
+ protected JTextArea infoText = new JTextArea();\r
+ JScrollPane jScrollPane1 = new JScrollPane();\r
+ JScrollPane jScrollPane2 = new JScrollPane();\r
+ protected JTextArea progressText = new JTextArea();\r
+ JPanel jPanel1 = new JPanel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ protected JPanel titlePanel = new JPanel();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ JPanel jPanel2 = new JPanel();\r
+ protected JButton cancel = new JButton();\r
+ GridBagLayout gridBagLayout1 = new GridBagLayout();\r
+\r
+ public GWebserviceInfo() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception {\r
+ infoText.setFont(new java.awt.Font("Verdana", 0, 10));\r
+ infoText.setBorder(null);\r
+ infoText.setEditable(false);\r
+ infoText.setText("");\r
+ infoText.setLineWrap(true);\r
+ infoText.setWrapStyleWord(true);\r
+ this.setLayout(borderLayout1);\r
+ progressText.setFont(new java.awt.Font("Verdana", 0, 10));\r
+ progressText.setBorder(null);\r
+ progressText.setEditable(false);\r
+ progressText.setText("");\r
+ progressText.setLineWrap(true);\r
+ progressText.setWrapStyleWord(true);\r
+ jPanel1.setLayout(borderLayout2);\r
+ titlePanel.setBackground(Color.white);\r
+ titlePanel.setPreferredSize(new Dimension(0, 60));\r
+ titlePanel.setLayout(borderLayout3);\r
+ jScrollPane2.setBorder(null);\r
+ jScrollPane1.setBorder(null);\r
+ jScrollPane1.setPreferredSize(new Dimension(400, 70));\r
+ cancel.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ cancel.setText("Cancel");\r
+ cancel.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancel_actionPerformed(e);\r
+ }\r
+ });\r
+ jPanel2.setLayout(gridBagLayout1);\r
+ jPanel2.setOpaque(false);\r
+ this.add(jScrollPane2, BorderLayout.CENTER);\r
+ this.add(jPanel1, BorderLayout.NORTH);\r
+ jPanel1.add(jScrollPane1, BorderLayout.CENTER);\r
+ jScrollPane1.getViewport().add(infoText, null);\r
+ jScrollPane2.getViewport().add(progressText, null);\r
+ jPanel1.add(titlePanel, BorderLayout.NORTH);\r
+ titlePanel.add(jPanel2, BorderLayout.EAST);\r
+ jPanel2.add(cancel,\r
+ new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,\r
+ GridBagConstraints.SOUTH, GridBagConstraints.NONE,\r
+ new Insets(24, 5, 21, 5), 0, 0));\r
+ }\r
+\r
+ protected void cancel_actionPerformed(ActionEvent e) {\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.math;\r
\r
import jalview.util.*;\r
\r
import java.io.*;\r
\r
-public class Matrix {\r
-\r
- /**\r
- * SMJSPUBLIC\r
- */\r
- public double[][] value;\r
- public int rows;\r
- public int cols;\r
- public double[] d; // Diagonal\r
- public double[] e; // off diagonal\r
-\r
- public Matrix(double[][] value, int rows, int cols) {\r
- this.rows = rows;\r
- this.cols = cols;\r
- this.value = value;\r
- }\r
-\r
- public Matrix transpose() {\r
- double[][] out = new double[cols][rows];\r
-\r
- for (int i = 0; i < cols; i++) {\r
- for (int j = 0; j < rows ; j++) {\r
- out[i][j] = value[j][i];\r
- }\r
- }\r
- return new Matrix(out,cols,rows);\r
- }\r
-\r
- public void print(PrintStream ps) {\r
\r
- for (int i = 0; i < rows; i++) {\r
- for (int j = 0; j < cols; j++) {\r
- Format.print(ps,"%8.2f",value[i][j]);\r
- }\r
- ps.println();\r
+public class Matrix {\r
+ /**\r
+ * SMJSPUBLIC\r
+ */\r
+ public double[][] value;\r
+ public int rows;\r
+ public int cols;\r
+ public double[] d; // Diagonal\r
+ public double[] e; // off diagonal\r
+\r
+ public Matrix(double[][] value, int rows, int cols) {\r
+ this.rows = rows;\r
+ this.cols = cols;\r
+ this.value = value;\r
}\r
- }\r
\r
+ public Matrix transpose() {\r
+ double[][] out = new double[cols][rows];\r
\r
- public Matrix preMultiply(Matrix in) {\r
- double[][] tmp = new double[in.rows][this.cols];\r
-\r
- for (int i = 0; i < in.rows; i++) {\r
- for (int j = 0; j < this.cols; j++ ) {\r
- tmp[i][j] = 0.0;\r
-\r
- for (int k = 0; k < in.cols; k++) {\r
- tmp[i][j] += in.value[i][k]*this.value[k][j];\r
+ for (int i = 0; i < cols; i++) {\r
+ for (int j = 0; j < rows; j++) {\r
+ out[i][j] = value[j][i];\r
+ }\r
}\r
\r
- }\r
+ return new Matrix(out, cols, rows);\r
}\r
\r
- return new Matrix(tmp,in.rows,this.cols);\r
- }\r
+ public void print(PrintStream ps) {\r
+ for (int i = 0; i < rows; i++) {\r
+ for (int j = 0; j < cols; j++) {\r
+ Format.print(ps, "%8.2f", value[i][j]);\r
+ }\r
\r
- public double[] vectorPostMultiply(double[] in) {\r
- double[] out = new double[in.length];\r
- for (int i = 0; i < in.length; i++) {\r
- out[i] = 0.0;\r
- for (int k=0; k < in.length; k++) {\r
- out[i] += value[i][k] * in[k];\r
- }\r
+ ps.println();\r
+ }\r
}\r
- return out;\r
- }\r
- public Matrix postMultiply(Matrix in) {\r
\r
- double[][] out = new double[this.rows][in.cols];\r
- for (int i = 0; i < this.rows; i++) {\r
- for (int j = 0; j < in.cols; j++ ) {\r
+ public Matrix preMultiply(Matrix in) {\r
+ double[][] tmp = new double[in.rows][this.cols];\r
\r
- out[i][j] = 0.0;\r
+ for (int i = 0; i < in.rows; i++) {\r
+ for (int j = 0; j < this.cols; j++) {\r
+ tmp[i][j] = 0.0;\r
\r
- for (int k = 0; k < rows; k++) {\r
- out[i][j] = out[i][j] + value[i][k]*in.value[k][j];\r
+ for (int k = 0; k < in.cols; k++) {\r
+ tmp[i][j] += (in.value[i][k] * this.value[k][j]);\r
+ }\r
+ }\r
}\r
\r
- }\r
+ return new Matrix(tmp, in.rows, this.cols);\r
}\r
- return new Matrix(out,this.cols,in.rows);\r
- }\r
\r
- public Matrix copy() {\r
- double[][] newmat = new double[rows][cols];\r
+ public double[] vectorPostMultiply(double[] in) {\r
+ double[] out = new double[in.length];\r
\r
- for (int i = 0; i < rows; i++) {\r
- for (int j = 0; j < cols; j++) {\r
- newmat[i][j] = value[i][j];\r
- }\r
- }\r
- return new Matrix(newmat,rows,cols);\r
- }\r
-\r
- public void tred() {\r
- int n = rows;\r
- int l;\r
- int k;\r
- int j;\r
- int i;\r
-\r
- double scale;\r
- double hh;\r
- double h;\r
- double g;\r
- double f;\r
-\r
- this.d = new double[rows];\r
- this.e = new double[rows];\r
-\r
- for (i=n; i >= 2;i--) {\r
- l=i-1;\r
- h = 0.0;\r
- scale = 0.0;\r
-\r
- if (l > 1) {\r
- for (k=1;k<=l;k++) {\r
- scale += Math.abs(value[i-1][k-1]);\r
- }\r
- if (scale == 0.0) {\r
- e[i-1] = value[i-1][l-1];\r
- } else {\r
- for (k=1; k <= l; k++) {\r
- value[i-1][k-1] /= scale;\r
- h += value[i-1][k-1]*value[i-1][k-1];\r
- }\r
- f = value[i-1][l-1];\r
- if (f>0) {\r
- g = -1.0*Math.sqrt(h);\r
- } else {\r
- g = Math.sqrt(h);\r
- }\r
- e[i-1] = scale*g;\r
- h -= f*g;\r
- value[i-1][l-1] = f-g;\r
- f=0.0;\r
- for (j=1; j <= l; j++) {\r
- value[j-1][i-1] = value[i-1][j-1]/h;\r
- g=0.0;\r
- for (k= 1; k <= j; k++) {\r
- g += value[j-1][k-1]*value[i-1][k-1];\r
- }\r
- for (k=j+1; k<=l;k++) {\r
- g+= value[k-1][j-1]*value[i-1][k-1];\r
- }\r
- e[j-1] = g/h;\r
- f+=e[j-1]*value[i-1][j-1];\r
- }\r
- hh=f/(h+h);\r
- for (j=1;j<=l;j++) {\r
- f=value[i-1][j-1];\r
- g = e[j-1] - hh*f;\r
- e[j-1] = g;\r
- for (k=1;k<=j;k++) {\r
- value[j-1][k-1] -= (f*e[k-1]+g*value[i-1][k-1]);\r
- }\r
- }\r
- }\r
- } else {\r
- e[i-1] = value[i-1][l-1];\r
- }\r
- d[i-1] = h;\r
- }\r
- d[0] = 0.0;\r
- e[0] = 0.0;\r
- for (i=1;i<=n;i++) {\r
- l=i-1;\r
- if (d[i-1] != 0.0) {\r
- for (j=1;j<=l;j++) {\r
- g=0.0;\r
- for (k=1;k<=l;k++) {\r
- g+= value[i-1][k-1]*value[k-1][j-1];\r
- }\r
- for (k=1;k<=l;k++) {\r
- value[k-1][j-1] -= g*value[k-1][i-1];\r
- }\r
- }\r
- }\r
- d[i-1] = value[i-1][i-1];\r
- value[i-1][i-1] = 1.0;\r
- for (j=1;j<=l;j++) {\r
- value[j-1][i-1] = 0.0;\r
- value[i-1][j-1] = 0.0;\r
- }\r
- }\r
- }\r
-\r
- public void tqli() {\r
- int n = rows;\r
-\r
- int m;\r
- int l;\r
- int iter;\r
- int i;\r
- int k;\r
- double s;\r
- double r;\r
- double p;\r
- ;\r
- double g;\r
- double f;\r
- double dd;\r
- double c;\r
- double b;\r
-\r
- for (i=2;i<=n;i++) {\r
- e[i-2] = e[i-1];\r
- }\r
- e[n-1] = 0.0;\r
- for (l=1;l<=n;l++) {\r
- iter=0;\r
- do {\r
- for (m=l;m<=(n-1);m++) {\r
- dd=Math.abs(d[m-1]) + Math.abs(d[m]);\r
- if (Math.abs(e[m-1]) + dd == dd)\r
- break;\r
- }\r
- if (m != l) {\r
- iter++;\r
- if (iter == 30) {\r
- System.err.print("Too many iterations in tqli");\r
- System.exit(0); // JBPNote - should this really be here ???\r
- } else {\r
- // System.out.println("Iteration " + iter);\r
- }\r
- g=(d[l]-d[l-1])/(2.0*e[l-1]);\r
- r = Math.sqrt((g*g) + 1.0);\r
- g=d[m-1]-d[l-1]+e[l-1]/(g + sign(r,g));\r
- c = 1.0;\r
- s = c;\r
- p=0.0;\r
- for (i=m-1;i>=l;i--) {\r
- f = s*e[i-1];\r
- b = c*e[i-1];\r
- if (Math.abs(f) >= Math.abs(g)) {\r
- c=g/f;\r
- r = Math.sqrt((c*c)+1.0);\r
- e[i] = f*r;\r
- s = 1.0/r;\r
- c *= s;\r
- } else {\r
- s=f/g;\r
- r = Math.sqrt((s*s)+1.0);\r
- e[i] = g*r;\r
- c = 1.0/r;\r
- s *= c;\r
- }\r
- g=d[i] -p;\r
- r=(d[i-1]-g)*s + 2.0*c*b;\r
- p=s*r;\r
- d[i] = g + p;\r
- g = c * r - b;\r
- for (k=1; k <= n; k++) {\r
- f=value[k-1][i];\r
- value[k-1][i] = s*value[k-1][i-1] + c*f;\r
- value[k-1][i-1] = c*value[k-1][i-1] - s*f;\r
- }\r
- }\r
- d[l-1] = d[l-1] - p;\r
- e[l-1] = g;\r
- e[m-1] = 0.0;\r
- }\r
- } while ( m != l);\r
- }\r
- }\r
- public void tred2() {\r
- int n = rows;\r
- int l;\r
- int k;\r
- int j;\r
- int i;\r
-\r
- double scale;\r
- double hh;\r
- double h;\r
- double g;\r
- double f;\r
-\r
- this.d = new double[rows];\r
- this.e = new double[rows];\r
-\r
- for (i=n-1; i >= 1;i--) {\r
- l=i-1;\r
- h = 0.0;\r
- scale = 0.0;\r
-\r
- if (l > 0) {\r
- for (k=0;k<l;k++) {\r
- scale += Math.abs(value[i][k]);\r
- }\r
- if (scale == 0.0) {\r
- e[i] = value[i][l];\r
- } else {\r
- for (k=0; k < l; k++) {\r
- value[i][k] /= scale;\r
- h += value[i][k]*value[i][k];\r
- }\r
- f = value[i][l];\r
- if (f>0) {\r
- g = -1.0*Math.sqrt(h);\r
- } else {\r
- g = Math.sqrt(h);\r
- }\r
- e[i] = scale*g;\r
- h -= f*g;\r
- value[i][l] = f-g;\r
- f=0.0;\r
- for (j=0; j < l; j++) {\r
- value[j][i] = value[i][j]/h;\r
- g=0.0;\r
- for (k= 0; k < j; k++) {\r
- g += value[j][k]*value[i][k];\r
- }\r
- for (k=j; k<l;k++) {\r
- g+= value[k][j]*value[i][k];\r
- }\r
- e[j] = g/h;\r
- f+=e[j]*value[i][j];\r
- }\r
- hh=f/(h+h);\r
- for (j=0;j<l;j++) {\r
- f=value[i][j];\r
- g = e[j] - hh*f;\r
- e[j] = g;\r
- for (k=0;k<j;k++) {\r
- value[j][k] -= (f*e[k]+g*value[i][k]);\r
- }\r
- }\r
- }\r
- } else {\r
- e[i] = value[i][l];\r
- }\r
- d[i] = h;\r
- }\r
- d[0] = 0.0;\r
- e[0] = 0.0;\r
- for (i=0;i<n;i++) {\r
- l=i-1;\r
- if (d[i] != 0.0) {\r
- for (j=0;j<l;j++) {\r
- g=0.0;\r
- for (k=0;k<l;k++) {\r
- g+= value[i][k]*value[k][j];\r
- }\r
- for (k=0;k<l;k++) {\r
- value[k][j] -= g*value[k][i];\r
- }\r
- }\r
- }\r
- d[i] = value[i][i];\r
- value[i][i] = 1.0;\r
- for (j=0;j<l;j++) {\r
- value[j][i] = 0.0;\r
- value[i][j] = 0.0;\r
- }\r
- }\r
- }\r
-\r
- public void tqli2() {\r
- int n = rows;\r
-\r
- int m;\r
- int l;\r
- int iter;\r
- int i;\r
- int k;\r
- double s;\r
- double r;\r
- double p;\r
- ;\r
- double g;\r
- double f;\r
- double dd;\r
- double c;\r
- double b;\r
-\r
- for (i=2;i<=n;i++) {\r
- e[i-2] = e[i-1];\r
- }\r
- e[n-1] = 0.0;\r
- for (l=1;l<=n;l++) {\r
- iter=0;\r
- do {\r
- for (m=l;m<=(n-1);m++) {\r
- dd=Math.abs(d[m-1]) + Math.abs(d[m]);\r
- if (Math.abs(e[m-1]) + dd == dd)\r
- break;\r
- }\r
- if (m != l) {\r
- iter++;\r
- if (iter == 30) {\r
- System.err.print("Too many iterations in tqli");\r
- System.exit(0); // JBPNote - same as above - not a graceful exit!\r
- } else {\r
- // System.out.println("Iteration " + iter);\r
- }\r
- g=(d[l]-d[l-1])/(2.0*e[l-1]);\r
- r = Math.sqrt((g*g) + 1.0);\r
- g=d[m-1]-d[l-1]+e[l-1]/(g + sign(r,g));\r
- c = 1.0;\r
- s = c;\r
- p=0.0;\r
- for (i=m-1;i>=l;i--) {\r
- f = s*e[i-1];\r
- b = c*e[i-1];\r
- if (Math.abs(f) >= Math.abs(g)) {\r
- c=g/f;\r
- r = Math.sqrt((c*c)+1.0);\r
- e[i] = f*r;\r
- s = 1.0/r;\r
- c *= s;\r
- } else {\r
- s=f/g;\r
- r = Math.sqrt((s*s)+1.0);\r
- e[i] = g*r;\r
- c = 1.0/r;\r
- s *= c;\r
- }\r
- g=d[i] -p;\r
- r=(d[i-1]-g)*s + 2.0*c*b;\r
- p=s*r;\r
- d[i] = g + p;\r
- g = c * r - b;\r
- for (k=1; k <= n; k++) {\r
- f=value[k-1][i];\r
- value[k-1][i] = s*value[k-1][i-1] + c*f;\r
- value[k-1][i-1] = c*value[k-1][i-1] - s*f;\r
+ for (int i = 0; i < in.length; i++) {\r
+ out[i] = 0.0;\r
+\r
+ for (int k = 0; k < in.length; k++) {\r
+ out[i] += (value[i][k] * in[k]);\r
}\r
- }\r
- d[l-1] = d[l-1] - p;\r
- e[l-1] = g;\r
- e[m-1] = 0.0;\r
}\r
- } while ( m != l);\r
- }\r
- }\r
\r
- public double sign(double a, double b) {\r
- if (b < 0) {\r
- return -Math.abs(a);\r
- } else {\r
- return Math.abs(a);\r
+ return out;\r
}\r
- }\r
\r
- public double[] getColumn(int n) {\r
- double[] out = new double[rows];\r
- for (int i=0;i<rows;i++) {\r
- out[i] = value[i][n];\r
- }\r
- return out;\r
- }\r
+ public Matrix postMultiply(Matrix in) {\r
+ double[][] out = new double[this.rows][in.cols];\r
\r
+ for (int i = 0; i < this.rows; i++) {\r
+ for (int j = 0; j < in.cols; j++) {\r
+ out[i][j] = 0.0;\r
\r
- public void printD(PrintStream ps) {\r
+ for (int k = 0; k < rows; k++) {\r
+ out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);\r
+ }\r
+ }\r
+ }\r
\r
- for (int j = 0; j < rows;j++) {\r
- Format.print(ps,"%15.4e",d[j]);\r
+ return new Matrix(out, this.cols, in.rows);\r
}\r
- }\r
- public void printE(PrintStream ps) {\r
\r
- for (int j = 0; j < rows;j++) {\r
- Format.print(ps,"%15.4e",e[j]);\r
- }\r
- }\r
+ public Matrix copy() {\r
+ double[][] newmat = new double[rows][cols];\r
\r
- public static void main(String[] args) {\r
- int n = Integer.parseInt(args[0]);\r
- double[][] in = new double[n][n];\r
+ for (int i = 0; i < rows; i++) {\r
+ for (int j = 0; j < cols; j++) {\r
+ newmat[i][j] = value[i][j];\r
+ }\r
+ }\r
\r
- for (int i = 0;i < n;i++) {\r
- for (int j = 0; j < n; j++) {\r
- in[i][j] = (double)Math.random();\r
- }\r
+ return new Matrix(newmat, rows, cols);\r
}\r
\r
- Matrix origmat = new Matrix(in,n,n);\r
- // System.out.println(" --- Original matrix ---- ");\r
- /// origmat.print(System.out);\r
- //System.out.println();\r
-\r
- //System.out.println(" --- transpose matrix ---- ");\r
- Matrix trans = origmat.transpose();\r
- //trans.print(System.out);\r
- //System.out.println();\r
-\r
- //System.out.println(" --- OrigT * Orig ---- ");\r
-\r
- Matrix symm = trans.postMultiply(origmat);\r
- //symm.print(System.out);\r
- //System.out.println();\r
-\r
- // Copy the symmetric matrix for later\r
- Matrix origsymm = symm.copy();\r
+ public void tred() {\r
+ int n = rows;\r
+ int l;\r
+ int k;\r
+ int j;\r
+ int i;\r
+\r
+ double scale;\r
+ double hh;\r
+ double h;\r
+ double g;\r
+ double f;\r
+\r
+ this.d = new double[rows];\r
+ this.e = new double[rows];\r
+\r
+ for (i = n; i >= 2; i--) {\r
+ l = i - 1;\r
+ h = 0.0;\r
+ scale = 0.0;\r
+\r
+ if (l > 1) {\r
+ for (k = 1; k <= l; k++) {\r
+ scale += Math.abs(value[i - 1][k - 1]);\r
+ }\r
+\r
+ if (scale == 0.0) {\r
+ e[i - 1] = value[i - 1][l - 1];\r
+ } else {\r
+ for (k = 1; k <= l; k++) {\r
+ value[i - 1][k - 1] /= scale;\r
+ h += (value[i - 1][k - 1] * value[i - 1][k - 1]);\r
+ }\r
+\r
+ f = value[i - 1][l - 1];\r
+\r
+ if (f > 0) {\r
+ g = -1.0 * Math.sqrt(h);\r
+ } else {\r
+ g = Math.sqrt(h);\r
+ }\r
+\r
+ e[i - 1] = scale * g;\r
+ h -= (f * g);\r
+ value[i - 1][l - 1] = f - g;\r
+ f = 0.0;\r
+\r
+ for (j = 1; j <= l; j++) {\r
+ value[j - 1][i - 1] = value[i - 1][j - 1] / h;\r
+ g = 0.0;\r
+\r
+ for (k = 1; k <= j; k++) {\r
+ g += (value[j - 1][k - 1] * value[i - 1][k - 1]);\r
+ }\r
+\r
+ for (k = j + 1; k <= l; k++) {\r
+ g += (value[k - 1][j - 1] * value[i - 1][k - 1]);\r
+ }\r
+\r
+ e[j - 1] = g / h;\r
+ f += (e[j - 1] * value[i - 1][j - 1]);\r
+ }\r
+\r
+ hh = f / (h + h);\r
+\r
+ for (j = 1; j <= l; j++) {\r
+ f = value[i - 1][j - 1];\r
+ g = e[j - 1] - (hh * f);\r
+ e[j - 1] = g;\r
+\r
+ for (k = 1; k <= j; k++) {\r
+ value[j - 1][k - 1] -= ((f * e[k - 1]) +\r
+ (g * value[i - 1][k - 1]));\r
+ }\r
+ }\r
+ }\r
+ } else {\r
+ e[i - 1] = value[i - 1][l - 1];\r
+ }\r
\r
+ d[i - 1] = h;\r
+ }\r
\r
- // This produces the tridiagonal transformation matrix\r
- long tstart = System.currentTimeMillis();\r
- symm.tred();\r
- long tend = System.currentTimeMillis();\r
- //System.out.println("Time take for tred = " + (tend-tstart) + "ms");\r
- //System.out.println(" ---Tridiag transform matrix ---");\r
- //symm.print(System.out);\r
- //System.out.println();\r
+ d[0] = 0.0;\r
+ e[0] = 0.0;\r
\r
- //System.out.println(" --- D vector ---");\r
- //symm.printD(System.out);\r
- //System.out.println();\r
- //System.out.println(" --- E vector ---");\r
- //symm.printE(System.out);\r
- //System.out.println();\r
+ for (i = 1; i <= n; i++) {\r
+ l = i - 1;\r
\r
+ if (d[i - 1] != 0.0) {\r
+ for (j = 1; j <= l; j++) {\r
+ g = 0.0;\r
\r
- // Now produce the diagonalization matrix\r
- tstart = System.currentTimeMillis();\r
- symm.tqli();\r
- tend = System.currentTimeMillis();\r
- //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");\r
+ for (k = 1; k <= l; k++) {\r
+ g += (value[i - 1][k - 1] * value[k - 1][j - 1]);\r
+ }\r
\r
- //System.out.println(" --- New diagonalization matrix ---");\r
- //symm.print(System.out);\r
- //System.out.println();\r
+ for (k = 1; k <= l; k++) {\r
+ value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);\r
+ }\r
+ }\r
+ }\r
\r
- //System.out.println(" --- D vector ---");\r
- //symm.printD(System.out);\r
- //System.out.println();\r
- //System.out.println(" --- E vector ---");\r
- //symm.printE(System.out);\r
- //System.out.println();\r
+ d[i - 1] = value[i - 1][i - 1];\r
+ value[i - 1][i - 1] = 1.0;\r
\r
- //System.out.println(" --- First eigenvector --- ");\r
- //double[] eigenv = symm.getColumn(0);\r
- //for (int i=0; i < eigenv.length;i++) {\r
- // Format.print(System.out,"%15.4f",eigenv[i]);\r
- // }\r
- //System.out.println();\r
+ for (j = 1; j <= l; j++) {\r
+ value[j - 1][i - 1] = 0.0;\r
+ value[i - 1][j - 1] = 0.0;\r
+ }\r
+ }\r
+ }\r
\r
- //double[] neigenv = origsymm.vectorPostMultiply(eigenv);\r
+ public void tqli() {\r
+ int n = rows;\r
+\r
+ int m;\r
+ int l;\r
+ int iter;\r
+ int i;\r
+ int k;\r
+ double s;\r
+ double r;\r
+ double p;\r
+ ;\r
+\r
+ double g;\r
+ double f;\r
+ double dd;\r
+ double c;\r
+ double b;\r
+\r
+ for (i = 2; i <= n; i++) {\r
+ e[i - 2] = e[i - 1];\r
+ }\r
\r
- //for (int i=0; i < neigenv.length;i++) {\r
- // Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]);\r
- //}\r
+ e[n - 1] = 0.0;\r
+\r
+ for (l = 1; l <= n; l++) {\r
+ iter = 0;\r
+\r
+ do {\r
+ for (m = l; m <= (n - 1); m++) {\r
+ dd = Math.abs(d[m - 1]) + Math.abs(d[m]);\r
+\r
+ if ((Math.abs(e[m - 1]) + dd) == dd) {\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (m != l) {\r
+ iter++;\r
+\r
+ if (iter == 30) {\r
+ System.err.print("Too many iterations in tqli");\r
+ System.exit(0); // JBPNote - should this really be here ???\r
+ } else {\r
+ // System.out.println("Iteration " + iter);\r
+ }\r
+\r
+ g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);\r
+ r = Math.sqrt((g * g) + 1.0);\r
+ g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g)));\r
+ c = 1.0;\r
+ s = c;\r
+ p = 0.0;\r
+\r
+ for (i = m - 1; i >= l; i--) {\r
+ f = s * e[i - 1];\r
+ b = c * e[i - 1];\r
+\r
+ if (Math.abs(f) >= Math.abs(g)) {\r
+ c = g / f;\r
+ r = Math.sqrt((c * c) + 1.0);\r
+ e[i] = f * r;\r
+ s = 1.0 / r;\r
+ c *= s;\r
+ } else {\r
+ s = f / g;\r
+ r = Math.sqrt((s * s) + 1.0);\r
+ e[i] = g * r;\r
+ c = 1.0 / r;\r
+ s *= c;\r
+ }\r
+\r
+ g = d[i] - p;\r
+ r = ((d[i - 1] - g) * s) + (2.0 * c * b);\r
+ p = s * r;\r
+ d[i] = g + p;\r
+ g = (c * r) - b;\r
+\r
+ for (k = 1; k <= n; k++) {\r
+ f = value[k - 1][i];\r
+ value[k - 1][i] = (s * value[k - 1][i - 1]) +\r
+ (c * f);\r
+ value[k - 1][i - 1] = (c * value[k - 1][i - 1]) -\r
+ (s * f);\r
+ }\r
+ }\r
+\r
+ d[l - 1] = d[l - 1] - p;\r
+ e[l - 1] = g;\r
+ e[m - 1] = 0.0;\r
+ }\r
+ } while (m != l);\r
+ }\r
+ }\r
\r
- //System.out.println();\r
- }\r
+ public void tred2() {\r
+ int n = rows;\r
+ int l;\r
+ int k;\r
+ int j;\r
+ int i;\r
+\r
+ double scale;\r
+ double hh;\r
+ double h;\r
+ double g;\r
+ double f;\r
+\r
+ this.d = new double[rows];\r
+ this.e = new double[rows];\r
+\r
+ for (i = n - 1; i >= 1; i--) {\r
+ l = i - 1;\r
+ h = 0.0;\r
+ scale = 0.0;\r
+\r
+ if (l > 0) {\r
+ for (k = 0; k < l; k++) {\r
+ scale += Math.abs(value[i][k]);\r
+ }\r
+\r
+ if (scale == 0.0) {\r
+ e[i] = value[i][l];\r
+ } else {\r
+ for (k = 0; k < l; k++) {\r
+ value[i][k] /= scale;\r
+ h += (value[i][k] * value[i][k]);\r
+ }\r
+\r
+ f = value[i][l];\r
+\r
+ if (f > 0) {\r
+ g = -1.0 * Math.sqrt(h);\r
+ } else {\r
+ g = Math.sqrt(h);\r
+ }\r
+\r
+ e[i] = scale * g;\r
+ h -= (f * g);\r
+ value[i][l] = f - g;\r
+ f = 0.0;\r
+\r
+ for (j = 0; j < l; j++) {\r
+ value[j][i] = value[i][j] / h;\r
+ g = 0.0;\r
+\r
+ for (k = 0; k < j; k++) {\r
+ g += (value[j][k] * value[i][k]);\r
+ }\r
+\r
+ for (k = j; k < l; k++) {\r
+ g += (value[k][j] * value[i][k]);\r
+ }\r
+\r
+ e[j] = g / h;\r
+ f += (e[j] * value[i][j]);\r
+ }\r
+\r
+ hh = f / (h + h);\r
+\r
+ for (j = 0; j < l; j++) {\r
+ f = value[i][j];\r
+ g = e[j] - (hh * f);\r
+ e[j] = g;\r
+\r
+ for (k = 0; k < j; k++) {\r
+ value[j][k] -= ((f * e[k]) + (g * value[i][k]));\r
+ }\r
+ }\r
+ }\r
+ } else {\r
+ e[i] = value[i][l];\r
+ }\r
\r
-}\r
+ d[i] = h;\r
+ }\r
\r
+ d[0] = 0.0;\r
+ e[0] = 0.0;\r
\r
+ for (i = 0; i < n; i++) {\r
+ l = i - 1;\r
\r
+ if (d[i] != 0.0) {\r
+ for (j = 0; j < l; j++) {\r
+ g = 0.0;\r
\r
+ for (k = 0; k < l; k++) {\r
+ g += (value[i][k] * value[k][j]);\r
+ }\r
\r
+ for (k = 0; k < l; k++) {\r
+ value[k][j] -= (g * value[k][i]);\r
+ }\r
+ }\r
+ }\r
\r
+ d[i] = value[i][i];\r
+ value[i][i] = 1.0;\r
\r
+ for (j = 0; j < l; j++) {\r
+ value[j][i] = 0.0;\r
+ value[i][j] = 0.0;\r
+ }\r
+ }\r
+ }\r
\r
+ public void tqli2() {\r
+ int n = rows;\r
+\r
+ int m;\r
+ int l;\r
+ int iter;\r
+ int i;\r
+ int k;\r
+ double s;\r
+ double r;\r
+ double p;\r
+ ;\r
+\r
+ double g;\r
+ double f;\r
+ double dd;\r
+ double c;\r
+ double b;\r
+\r
+ for (i = 2; i <= n; i++) {\r
+ e[i - 2] = e[i - 1];\r
+ }\r
\r
+ e[n - 1] = 0.0;\r
+\r
+ for (l = 1; l <= n; l++) {\r
+ iter = 0;\r
+\r
+ do {\r
+ for (m = l; m <= (n - 1); m++) {\r
+ dd = Math.abs(d[m - 1]) + Math.abs(d[m]);\r
+\r
+ if ((Math.abs(e[m - 1]) + dd) == dd) {\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (m != l) {\r
+ iter++;\r
+\r
+ if (iter == 30) {\r
+ System.err.print("Too many iterations in tqli");\r
+ System.exit(0); // JBPNote - same as above - not a graceful exit!\r
+ } else {\r
+ // System.out.println("Iteration " + iter);\r
+ }\r
+\r
+ g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);\r
+ r = Math.sqrt((g * g) + 1.0);\r
+ g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g)));\r
+ c = 1.0;\r
+ s = c;\r
+ p = 0.0;\r
+\r
+ for (i = m - 1; i >= l; i--) {\r
+ f = s * e[i - 1];\r
+ b = c * e[i - 1];\r
+\r
+ if (Math.abs(f) >= Math.abs(g)) {\r
+ c = g / f;\r
+ r = Math.sqrt((c * c) + 1.0);\r
+ e[i] = f * r;\r
+ s = 1.0 / r;\r
+ c *= s;\r
+ } else {\r
+ s = f / g;\r
+ r = Math.sqrt((s * s) + 1.0);\r
+ e[i] = g * r;\r
+ c = 1.0 / r;\r
+ s *= c;\r
+ }\r
+\r
+ g = d[i] - p;\r
+ r = ((d[i - 1] - g) * s) + (2.0 * c * b);\r
+ p = s * r;\r
+ d[i] = g + p;\r
+ g = (c * r) - b;\r
+\r
+ for (k = 1; k <= n; k++) {\r
+ f = value[k - 1][i];\r
+ value[k - 1][i] = (s * value[k - 1][i - 1]) +\r
+ (c * f);\r
+ value[k - 1][i - 1] = (c * value[k - 1][i - 1]) -\r
+ (s * f);\r
+ }\r
+ }\r
+\r
+ d[l - 1] = d[l - 1] - p;\r
+ e[l - 1] = g;\r
+ e[m - 1] = 0.0;\r
+ }\r
+ } while (m != l);\r
+ }\r
+ }\r
\r
+ public double sign(double a, double b) {\r
+ if (b < 0) {\r
+ return -Math.abs(a);\r
+ } else {\r
+ return Math.abs(a);\r
+ }\r
+ }\r
\r
+ public double[] getColumn(int n) {\r
+ double[] out = new double[rows];\r
\r
+ for (int i = 0; i < rows; i++) {\r
+ out[i] = value[i][n];\r
+ }\r
\r
+ return out;\r
+ }\r
\r
+ public void printD(PrintStream ps) {\r
+ for (int j = 0; j < rows; j++) {\r
+ Format.print(ps, "%15.4e", d[j]);\r
+ }\r
+ }\r
\r
+ public void printE(PrintStream ps) {\r
+ for (int j = 0; j < rows; j++) {\r
+ Format.print(ps, "%15.4e", e[j]);\r
+ }\r
+ }\r
\r
+ public static void main(String[] args) {\r
+ int n = Integer.parseInt(args[0]);\r
+ double[][] in = new double[n][n];\r
\r
+ for (int i = 0; i < n; i++) {\r
+ for (int j = 0; j < n; j++) {\r
+ in[i][j] = (double) Math.random();\r
+ }\r
+ }\r
\r
+ Matrix origmat = new Matrix(in, n, n);\r
+\r
+ // System.out.println(" --- Original matrix ---- ");\r
+ /// origmat.print(System.out);\r
+ //System.out.println();\r
+ //System.out.println(" --- transpose matrix ---- ");\r
+ Matrix trans = origmat.transpose();\r
+\r
+ //trans.print(System.out);\r
+ //System.out.println();\r
+ //System.out.println(" --- OrigT * Orig ---- ");\r
+ Matrix symm = trans.postMultiply(origmat);\r
+\r
+ //symm.print(System.out);\r
+ //System.out.println();\r
+ // Copy the symmetric matrix for later\r
+ Matrix origsymm = symm.copy();\r
+\r
+ // This produces the tridiagonal transformation matrix\r
+ long tstart = System.currentTimeMillis();\r
+ symm.tred();\r
+\r
+ long tend = System.currentTimeMillis();\r
+\r
+ //System.out.println("Time take for tred = " + (tend-tstart) + "ms");\r
+ //System.out.println(" ---Tridiag transform matrix ---");\r
+ //symm.print(System.out);\r
+ //System.out.println();\r
+ //System.out.println(" --- D vector ---");\r
+ //symm.printD(System.out);\r
+ //System.out.println();\r
+ //System.out.println(" --- E vector ---");\r
+ //symm.printE(System.out);\r
+ //System.out.println();\r
+ // Now produce the diagonalization matrix\r
+ tstart = System.currentTimeMillis();\r
+ symm.tqli();\r
+ tend = System.currentTimeMillis();\r
+\r
+ //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");\r
+ //System.out.println(" --- New diagonalization matrix ---");\r
+ //symm.print(System.out);\r
+ //System.out.println();\r
+ //System.out.println(" --- D vector ---");\r
+ //symm.printD(System.out);\r
+ //System.out.println();\r
+ //System.out.println(" --- E vector ---");\r
+ //symm.printE(System.out);\r
+ //System.out.println();\r
+ //System.out.println(" --- First eigenvector --- ");\r
+ //double[] eigenv = symm.getColumn(0);\r
+ //for (int i=0; i < eigenv.length;i++) {\r
+ // Format.print(System.out,"%15.4f",eigenv[i]);\r
+ // }\r
+ //System.out.println();\r
+ //double[] neigenv = origsymm.vectorPostMultiply(eigenv);\r
+ //for (int i=0; i < neigenv.length;i++) {\r
+ // Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]);\r
+ //}\r
+ //System.out.println();\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.math;\r
\r
-\r
-\r
public class RotatableMatrix {\r
+ float[][] matrix;\r
+ float[] temp;\r
+ float[][] rot;\r
\r
- float matrix[][];\r
-\r
- float[] temp;\r
-\r
- float[][] rot;\r
-\r
-\r
-\r
- public RotatableMatrix(int rows, int cols) {\r
-\r
- matrix = new float[rows][cols];\r
-\r
- temp = new float[3];\r
-\r
- rot = new float[3][3];\r
-\r
- }\r
-\r
-\r
-\r
- public void addElement(int i, int j, float value) {\r
-\r
- matrix[i][j] = value;\r
-\r
- }\r
-\r
-\r
-\r
- public void print() {\r
-\r
- System.out.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);\r
-\r
- System.out.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);\r
-\r
- System.out.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);\r
-\r
- }\r
-\r
-\r
-\r
- public void rotate (float degrees, char axis) {\r
-\r
-\r
-\r
- float costheta = (float)Math.cos(degrees*Math.PI/(float)180.0);\r
-\r
- float sintheta = (float)Math.sin(degrees*Math.PI/(float)180.0);\r
-\r
-\r
-\r
- if (axis == 'z') {\r
-\r
-\r
+ public RotatableMatrix(int rows, int cols) {\r
+ matrix = new float[rows][cols];\r
\r
- rot[0][0] = (float)costheta;\r
-\r
- rot[0][1] = (float)-sintheta;\r
-\r
- rot[0][2] = (float)0.0;\r
-\r
-\r
-\r
- rot[1][0] = (float)sintheta;\r
-\r
- rot[1][1] = (float)costheta;\r
-\r
- rot[1][2] = (float)0.0;\r
-\r
-\r
-\r
- rot[2][0] = (float)0.0;\r
-\r
- rot[2][1] = (float)0.0;\r
-\r
- rot[2][2] = (float)1.0;\r
-\r
-\r
-\r
- preMultiply(rot);\r
+ temp = new float[3];\r
\r
+ rot = new float[3][3];\r
}\r
\r
- if (axis == 'x') {\r
-\r
- rot[0][0] = (float)1.0;\r
-\r
- rot[0][1] = (float)0.0;\r
-\r
- rot[0][2] = (float)0.0;\r
-\r
-\r
-\r
- rot[1][0] = (float)0.0;\r
-\r
- rot[1][1] = (float)costheta;\r
-\r
- rot[1][2] = (float)sintheta;\r
-\r
-\r
-\r
- rot[2][0] = (float)0.0;\r
-\r
- rot[2][1] = (float)-sintheta;\r
-\r
- rot[2][2] = (float)costheta;\r
-\r
-\r
-\r
- preMultiply(rot);\r
-\r
-\r
-\r
+ public void addElement(int i, int j, float value) {\r
+ matrix[i][j] = value;\r
}\r
\r
- if (axis == 'y') {\r
-\r
- rot[0][0] = (float)costheta;\r
-\r
- rot[0][1] = (float)0.0;\r
-\r
- rot[0][2] = (float)-sintheta;\r
-\r
-\r
-\r
- rot[1][0] = (float)0.0;\r
-\r
- rot[1][1] = (float)1.0;\r
-\r
- rot[1][2] = (float)0.0;\r
-\r
-\r
-\r
- rot[2][0] = (float)sintheta;\r
-\r
- rot[2][1] = (float)0.0;\r
-\r
- rot[2][2] = (float)costheta;\r
-\r
-\r
-\r
- preMultiply(rot);\r
-\r
+ public void print() {\r
+ System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +\r
+ matrix[0][2]);\r
\r
+ System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +\r
+ matrix[1][2]);\r
\r
+ System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +\r
+ matrix[2][2]);\r
}\r
\r
+ public void rotate(float degrees, char axis) {\r
+ float costheta = (float) Math.cos((degrees * Math.PI) / (float) 180.0);\r
\r
+ float sintheta = (float) Math.sin((degrees * Math.PI) / (float) 180.0);\r
\r
- }\r
-\r
-\r
-\r
- public float[] vectorMultiply(float[] vect) {\r
+ if (axis == 'z') {\r
+ rot[0][0] = (float) costheta;\r
\r
- temp[0] = vect[0];\r
+ rot[0][1] = (float) -sintheta;\r
\r
- temp[1] = vect[1];\r
+ rot[0][2] = (float) 0.0;\r
\r
- temp[2] = vect[2];\r
+ rot[1][0] = (float) sintheta;\r
\r
+ rot[1][1] = (float) costheta;\r
\r
+ rot[1][2] = (float) 0.0;\r
\r
- for (int i = 0; i < 3; i++) {\r
+ rot[2][0] = (float) 0.0;\r
\r
- temp[i] = matrix[i][0]*vect[0] + matrix[i][1]*vect[1] + matrix[i][2]*vect[2];\r
+ rot[2][1] = (float) 0.0;\r
\r
- }\r
-\r
-\r
-\r
- vect[0] = temp[0];\r
-\r
- vect[1] = temp[1];\r
-\r
- vect[2] = temp[2];\r
-\r
-\r
-\r
- return vect;\r
+ rot[2][2] = (float) 1.0;\r
\r
- }\r
+ preMultiply(rot);\r
+ }\r
\r
+ if (axis == 'x') {\r
+ rot[0][0] = (float) 1.0;\r
\r
+ rot[0][1] = (float) 0.0;\r
\r
- public void preMultiply(float mat[][]) {\r
+ rot[0][2] = (float) 0.0;\r
\r
- float tmp[][] = new float[3][3];\r
+ rot[1][0] = (float) 0.0;\r
\r
+ rot[1][1] = (float) costheta;\r
\r
+ rot[1][2] = (float) sintheta;\r
\r
- for (int i = 0; i < 3 ; i++) {\r
+ rot[2][0] = (float) 0.0;\r
\r
- for (int j = 0; j < 3; j++ ) {\r
+ rot[2][1] = (float) -sintheta;\r
\r
- tmp[i][j] = mat[i][0]*matrix[0][j] +\r
+ rot[2][2] = (float) costheta;\r
\r
- mat[i][1]*matrix[1][j] +\r
+ preMultiply(rot);\r
+ }\r
\r
- mat[i][2]*matrix[2][j];\r
+ if (axis == 'y') {\r
+ rot[0][0] = (float) costheta;\r
\r
- }\r
+ rot[0][1] = (float) 0.0;\r
\r
- }\r
+ rot[0][2] = (float) -sintheta;\r
\r
+ rot[1][0] = (float) 0.0;\r
\r
+ rot[1][1] = (float) 1.0;\r
\r
- for (int i = 0; i < 3 ; i++) {\r
+ rot[1][2] = (float) 0.0;\r
\r
- for (int j = 0; j < 3; j++ ) {\r
+ rot[2][0] = (float) sintheta;\r
\r
- matrix[i][j] = tmp[i][j];\r
+ rot[2][1] = (float) 0.0;\r
\r
- }\r
+ rot[2][2] = (float) costheta;\r
\r
+ preMultiply(rot);\r
+ }\r
}\r
\r
- }\r
-\r
-\r
-\r
- public void postMultiply(float mat[][]) {\r
-\r
- float tmp[][] = new float[3][3];\r
+ public float[] vectorMultiply(float[] vect) {\r
+ temp[0] = vect[0];\r
\r
+ temp[1] = vect[1];\r
\r
+ temp[2] = vect[2];\r
\r
- for (int i = 0; i < 3 ; i++) {\r
+ for (int i = 0; i < 3; i++) {\r
+ temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +\r
+ (matrix[i][2] * vect[2]);\r
+ }\r
\r
- for (int j = 0; j < 3; j++ ) {\r
+ vect[0] = temp[0];\r
\r
- tmp[i][j] = matrix[i][0]*mat[0][j] +\r
+ vect[1] = temp[1];\r
\r
- matrix[i][1]*mat[1][j] +\r
-\r
- matrix[i][2]*mat[2][j];\r
-\r
- }\r
+ vect[2] = temp[2];\r
\r
+ return vect;\r
}\r
\r
-\r
-\r
- for (int i = 0; i < 3 ; i++) {\r
-\r
- for (int j = 0; j < 3; j++ ) {\r
-\r
- matrix[i][j] = tmp[i][j];\r
-\r
- }\r
-\r
+ public void preMultiply(float[][] mat) {\r
+ float[][] tmp = new float[3][3];\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ tmp[i][j] = (mat[i][0] * matrix[0][j]) +\r
+ (mat[i][1] * matrix[1][j]) + (mat[i][2] * matrix[2][j]);\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ matrix[i][j] = tmp[i][j];\r
+ }\r
+ }\r
}\r
\r
- }\r
-\r
-\r
-\r
- public static void main(String[] args) {\r
-\r
-\r
-\r
- RotatableMatrix m = new RotatableMatrix(3,3);\r
-\r
- m.addElement(0,0,1);\r
-\r
- m.addElement(0,1,0);\r
-\r
- m.addElement(0,2,0);\r
-\r
- m.addElement(1,0,0);\r
-\r
- m.addElement(1,1,2);\r
-\r
- m.addElement(1,2,0);\r
-\r
- m.addElement(2,0,0);\r
-\r
- m.addElement(2,1,0);\r
-\r
- m.addElement(2,2,1);\r
-\r
-\r
-\r
- m.print();\r
-\r
-\r
-\r
- RotatableMatrix n = new RotatableMatrix(3,3);\r
-\r
- n.addElement(0,0,2);\r
-\r
- n.addElement(0,1,1);\r
-\r
- n.addElement(0,2,1);\r
-\r
- n.addElement(1,0,2);\r
-\r
- n.addElement(1,1,1);\r
+ public void postMultiply(float[][] mat) {\r
+ float[][] tmp = new float[3][3];\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ tmp[i][j] = (matrix[i][0] * mat[0][j]) +\r
+ (matrix[i][1] * mat[1][j]) + (matrix[i][2] * mat[2][j]);\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3; j++) {\r
+ matrix[i][j] = tmp[i][j];\r
+ }\r
+ }\r
+ }\r
\r
- n.addElement(1,2,1);\r
+ public static void main(String[] args) {\r
+ RotatableMatrix m = new RotatableMatrix(3, 3);\r
\r
- n.addElement(2,0,2);\r
+ m.addElement(0, 0, 1);\r
\r
- n.addElement(2,1,1);\r
+ m.addElement(0, 1, 0);\r
\r
- n.addElement(2,2,1);\r
+ m.addElement(0, 2, 0);\r
\r
+ m.addElement(1, 0, 0);\r
\r
+ m.addElement(1, 1, 2);\r
\r
- n.print();\r
+ m.addElement(1, 2, 0);\r
\r
+ m.addElement(2, 0, 0);\r
\r
+ m.addElement(2, 1, 0);\r
\r
- //m.postMultiply(n.matrix);\r
+ m.addElement(2, 2, 1);\r
\r
- //m.print();\r
+ m.print();\r
\r
- // m.rotate(45,'z',new RotatableMatrix(3,3));\r
+ RotatableMatrix n = new RotatableMatrix(3, 3);\r
\r
+ n.addElement(0, 0, 2);\r
\r
+ n.addElement(0, 1, 1);\r
\r
- float vect[] = new float[3];\r
+ n.addElement(0, 2, 1);\r
\r
- vect[0] = 2;\r
+ n.addElement(1, 0, 2);\r
\r
- vect[1] = 4;\r
+ n.addElement(1, 1, 1);\r
\r
- vect[2] = 6;\r
+ n.addElement(1, 2, 1);\r
\r
+ n.addElement(2, 0, 2);\r
\r
+ n.addElement(2, 1, 1);\r
\r
- vect = m.vectorMultiply(vect);\r
+ n.addElement(2, 2, 1);\r
\r
- System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);\r
+ n.print();\r
\r
+ //m.postMultiply(n.matrix);\r
+ //m.print();\r
+ // m.rotate(45,'z',new RotatableMatrix(3,3));\r
+ float[] vect = new float[3];\r
\r
+ vect[0] = 2;\r
\r
- }\r
+ vect[1] = 4;\r
\r
- public void setIdentity() {\r
+ vect[2] = 6;\r
\r
- matrix[0][0] = (float)1.0;\r
+ vect = m.vectorMultiply(vect);\r
\r
- matrix[1][1] = (float)1.0;\r
+ System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);\r
+ }\r
\r
- matrix[2][2] = (float)1.0;\r
+ public void setIdentity() {\r
+ matrix[0][0] = (float) 1.0;\r
\r
- matrix[0][1] = (float)0.0;\r
+ matrix[1][1] = (float) 1.0;\r
\r
- matrix[0][2] = (float)0.0;\r
+ matrix[2][2] = (float) 1.0;\r
\r
- matrix[1][0] = (float)0.0;\r
+ matrix[0][1] = (float) 0.0;\r
\r
- matrix[1][2] = (float) 0.0;\r
+ matrix[0][2] = (float) 0.0;\r
\r
- matrix[2][0] = (float)0.0;\r
+ matrix[1][0] = (float) 0.0;\r
\r
- matrix[2][1] = (float)0.0;\r
+ matrix[1][2] = (float) 0.0;\r
\r
- }\r
+ matrix[2][0] = (float) 0.0;\r
\r
+ matrix[2][1] = (float) 0.0;\r
+ }\r
}\r
-\r
-\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
-\r
-import java.util.*;\r
import java.awt.*;\r
\r
-public class Blosum62ColourScheme extends ResidueColourScheme\r
-{\r
-\r
- public Blosum62ColourScheme()\r
- {\r
- super();\r
- }\r
-\r
- public Color findColour(String s, int j)\r
- {\r
- if( threshold!=0 && !aboveThreshold(s,j))\r
- return Color.white;\r
-\r
- Hashtable hash = (Hashtable)consensus.elementAt(j);\r
-\r
- if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
- {\r
- String max = (String)hash.get("maxResidue");\r
-\r
- if (max.indexOf(s)>-1)\r
- return new Color(154, 154, 255);\r
- else {\r
+import java.util.*;\r
\r
- int c = 0,\r
- max_aa=0,\r
- n=max.length();\r
- do {\r
- c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);\r
- } while (++max_aa<n);\r
\r
- if (c>0)\r
- return new Color(204, 204, 255);\r
- else\r
- return Color.white;\r
- }\r
+public class Blosum62ColourScheme extends ResidueColourScheme {\r
+ public Blosum62ColourScheme() {\r
+ super();\r
}\r
- else\r
- return Color.white;\r
-\r
- }\r
-\r
\r
+ public Color findColour(String s, int j) {\r
+ if ((threshold != 0) && !aboveThreshold(s, j)) {\r
+ return Color.white;\r
+ }\r
+\r
+ Hashtable hash = (Hashtable) consensus.elementAt(j);\r
+\r
+ if (!jalview.util.Comparison.isGap((s.charAt(0)))) {\r
+ String max = (String) hash.get("maxResidue");\r
+\r
+ if (max.indexOf(s) > -1) {\r
+ return new Color(154, 154, 255);\r
+ } else {\r
+ int c = 0;\r
+ int max_aa = 0;\r
+ int n = max.length();\r
+\r
+ do {\r
+ c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
+ max_aa + 1), s);\r
+ } while (++max_aa < n);\r
+\r
+ if (c > 0) {\r
+ return new Color(204, 204, 255);\r
+ } else {\r
+ return Color.white;\r
+ }\r
+ }\r
+ } else {\r
+ return Color.white;\r
+ }\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
\r
-public class BuriedColourScheme extends ScoreColourScheme {\r
\r
- public BuriedColourScheme() {\r
- super(ResidueProperties.buried,ResidueProperties.buriedmin,ResidueProperties.buriedmax);\r
- }\r
+public class BuriedColourScheme extends ScoreColourScheme {\r
+ public BuriedColourScheme() {\r
+ super(ResidueProperties.buried, ResidueProperties.buriedmin,\r
+ ResidueProperties.buriedmax);\r
+ }\r
\r
- public Color makeColour(float c) {\r
- return new Color(0,(float)(1.0-c),c);\r
- }\r
+ public Color makeColour(float c) {\r
+ return new Color(0, (float) (1.0 - c), c);\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import jalview.datamodel.*;\r
-import java.util.*;\r
+\r
import java.awt.*;\r
\r
-public class ClustalxColourScheme extends ResidueColourScheme\r
-{\r
- Hashtable[] cons;\r
- int[][] cons2;\r
- ConsensusColour[] colours;\r
- ConsensusColour[] ResidueColour;\r
- int size;\r
- Consensus[] conses = new Consensus[32];\r
+import java.util.*;\r
+\r
+\r
+public class ClustalxColourScheme extends ResidueColourScheme {\r
public static Hashtable colhash = new Hashtable();\r
+ Hashtable[] cons;\r
+ int[][] cons2;\r
+ ConsensusColour[] colours;\r
+ ConsensusColour[] ResidueColour;\r
+ int size;\r
+ Consensus[] conses = new Consensus[32];\r
+ Vector colourTable = new Vector();\r
\r
{\r
- colhash.put("RED",new Color((float)0.9,(float)0.2,(float)0.1));\r
- colhash.put("BLUE",new Color((float)0.5,(float)0.7,(float)0.9));\r
- colhash.put("GREEN",new Color((float)0.1,(float)0.8,(float)0.1));\r
- colhash.put("ORANGE",new Color((float)0.9,(float)0.6,(float)0.3));\r
- colhash.put("CYAN",new Color((float)0.1,(float)0.7,(float)0.7));\r
- colhash.put("PINK",new Color((float)0.9,(float)0.5,(float)0.5));\r
- colhash.put("MAGENTA",new Color((float)0.8,(float)0.3,(float)0.8));\r
- colhash.put("YELLOW",new Color((float)0.8,(float)0.8,(float)0.0));\r
-\r
+ colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));\r
+ colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));\r
+ colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));\r
+ colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));\r
+ colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));\r
+ colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));\r
+ colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));\r
+ colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));\r
}\r
- Vector colourTable = new Vector();\r
-\r
- public ClustalxColourScheme(Vector seqs, int maxWidth)\r
- {\r
- resetClustalX(seqs, maxWidth);\r
- }\r
-\r
- public void resetClustalX(Vector seqs, int maxWidth)\r
- {\r
- cons2 = new int[maxWidth][24];\r
- int start = 0;\r
-\r
- // Initialize the array\r
- for (int j=0;j<24;j++)\r
- for (int i=0; i < maxWidth;i++)\r
- cons2[i][j] = 0;\r
-\r
- int res,i, j = 0;\r
- String seq;\r
- while(j < seqs.size())\r
- {\r
- seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
- int end_j = seq.length()-1;\r
- for (i = start; i <= end_j; i++)\r
- {\r
- if(seq.length()-1<i)\r
- res = 23;\r
- else\r
- res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();\r
- cons2[i][res]++;\r
- }\r
- j++;\r
- }\r
-\r
- this.size = seqs.size();\r
- makeColours();\r
- }\r
- public void makeColours() {\r
- conses[0] = new Consensus("WLVIMAFCYHP",60);\r
- conses[1] = new Consensus("WLVIMAFCYHP",80);\r
- conses[2] = new Consensus("ED",50);\r
- conses[3] = new Consensus("KR",60);\r
- conses[4] = new Consensus("G",50);\r
- conses[5] = new Consensus("N",50);\r
- conses[6] = new Consensus("QE",50);\r
- conses[7] = new Consensus("P",50);\r
- conses[8] = new Consensus("TS",50);\r
-\r
- conses[26] = new Consensus("A",85);\r
- conses[27] = new Consensus("C",85);\r
- conses[10] = new Consensus("E",85);\r
- conses[11] = new Consensus("F",85);\r
- conses[12] = new Consensus("G",85);\r
- conses[13] = new Consensus("H",85);\r
- conses[14] = new Consensus("I",85);\r
- conses[15] = new Consensus("L",85);\r
- conses[16] = new Consensus("M",85);\r
- conses[17] = new Consensus("N",85);\r
- conses[18] = new Consensus("P",85);\r
- conses[19] = new Consensus("Q",85);\r
- conses[20] = new Consensus("R",85);\r
- conses[21] = new Consensus("S",85);\r
- conses[22] = new Consensus("T",85);\r
- conses[23] = new Consensus("V",85);\r
- conses[24] = new Consensus("W",85);\r
- conses[25] = new Consensus("Y",85);\r
- conses[28] = new Consensus("K",85);\r
- conses[29] = new Consensus("D",85);\r
-\r
- conses[30] = new Consensus("G",0);\r
- conses[31] = new Consensus("P",0);\r
-\r
- // We now construct the colours\r
- colours = new ConsensusColour[11];\r
-\r
-\r
- Consensus[] tmp8 = new Consensus[1];\r
- tmp8[0] = conses[30];//G\r
- colours[7] =new ConsensusColour((Color)colhash.get("ORANGE"),tmp8);\r
-\r
- Consensus[] tmp9 = new Consensus[1];\r
- tmp9[0] = conses[31];//P\r
- colours[8] =new ConsensusColour((Color)colhash.get("YELLOW"),tmp9);\r
-\r
- Consensus[] tmp10 = new Consensus[1];\r
- tmp10[0] = conses[27];//C\r
- colours[9] =new ConsensusColour((Color)colhash.get("PINK"),tmp8);\r
-\r
- Consensus[] tmp1 = new Consensus[14];\r
- tmp1[0] = conses[0]; //%\r
- tmp1[1] = conses[1]; //#\r
- tmp1[2] = conses[26]; //A\r
- tmp1[3] = conses[27]; //C\r
- tmp1[4] = conses[11]; //F\r
- tmp1[5] = conses[13]; //H\r
- tmp1[6] = conses[14]; //I\r
- tmp1[7] = conses[15]; //L\r
- tmp1[8] = conses[16]; //M\r
- tmp1[9] = conses[23]; //V\r
- tmp1[10] = conses[24]; //W\r
- tmp1[11] = conses[25]; //Y\r
- tmp1[12] = conses[18]; //P\r
- tmp1[13] = conses[19]; //p\r
- colours[0] = new ConsensusColour((Color)colhash.get("BLUE"),tmp1);\r
-\r
- colours[10] = new ConsensusColour((Color)colhash.get("CYAN"),tmp1);\r
-\r
- Consensus[] tmp2 = new Consensus[5];\r
- tmp2[0] = conses[8]; //t\r
- tmp2[1] = conses[21]; //S\r
- tmp2[2] = conses[22]; //T\r
- tmp2[3] = conses[0]; //%\r
- tmp2[4] = conses[1]; //#\r
- colours[1] = new ConsensusColour((Color)colhash.get("GREEN"),tmp2);\r
-\r
- Consensus[] tmp3 = new Consensus[3];\r
-\r
- tmp3[0] = conses[17]; //N\r
- tmp3[1] = conses[29]; //D\r
- tmp3[2] = conses[5]; //n\r
- colours[2] = new ConsensusColour((Color)colhash.get("GREEN"),tmp3);\r
-\r
- Consensus[] tmp4 = new Consensus[6];\r
- tmp4[0] = conses[6]; // q = QE\r
- tmp4[1] = conses[19]; //Q\r
- tmp4[2] = conses[22]; //E\r
- tmp4[3] = conses[3]; //+\r
- tmp4[4] = conses[28]; //K\r
- tmp4[5] = conses[20]; //R\r
- colours[3] = new ConsensusColour((Color)colhash.get("GREEN"),tmp4);\r
- Consensus[] tmp5 = new Consensus[4];\r
- tmp5[0] = conses[3]; //+\r
- tmp5[1] = conses[28]; //K\r
- tmp5[2] = conses[20]; //R\r
- tmp5[3] = conses[19]; //Q\r
- colours[4] = new ConsensusColour((Color)colhash.get("RED"),tmp5);\r
- Consensus[] tmp6 = new Consensus[5];\r
- tmp6[0] = conses[3]; //-\r
- tmp6[1] = conses[29]; //D\r
- tmp6[2] = conses[10]; //E\r
- tmp6[3] = conses[6]; //q\r
- tmp6[4] = conses[19]; //Q\r
- colours[5] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp6);\r
-\r
- Consensus[] tmp7 = new Consensus[5];\r
- tmp7[0] = conses[3]; //-\r
- tmp7[1] = conses[29]; //D\r
- tmp7[2] = conses[10]; //E\r
- tmp7[3] = conses[17]; //N\r
- tmp7[4] = conses[2]; //DE\r
- colours[6] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp7);\r
-\r
- // Now attach the ConsensusColours to the residue letters\r
- ResidueColour = new ConsensusColour[20];\r
- ResidueColour[0] = colours[0]; // A\r
- ResidueColour[1] = colours[4]; // R\r
- ResidueColour[2] = colours[2]; // N\r
- ResidueColour[3] = colours[6]; // D\r
- ResidueColour[4] = colours[0]; // C\r
- ResidueColour[5] = colours[3]; // Q\r
- ResidueColour[6] = colours[5]; // E\r
- ResidueColour[7] = colours[7]; // G\r
- ResidueColour[8] = colours[10]; // H\r
- ResidueColour[9] = colours[0]; // I\r
- ResidueColour[10] = colours[0]; // L\r
- ResidueColour[11] = colours[4]; // K\r
- ResidueColour[12] = colours[0]; // M\r
- ResidueColour[13] = colours[0]; // F\r
- ResidueColour[14] = colours[8]; // P\r
- ResidueColour[15] = colours[1]; // S\r
- ResidueColour[16] = colours[1]; // T\r
- ResidueColour[17] = colours[0]; // W\r
- ResidueColour[18] = colours[10]; // Y\r
- ResidueColour[19] = colours[0]; // V\r
- }\r
-\r
- public Color findColour(String s)\r
- {\r
- return Color.pink;\r
- }\r
-\r
- public Color findColour(String s, int j)\r
- {\r
- if( threshold!=0 && !aboveThreshold(s,j))\r
- return Color.white;\r
-\r
-\r
- int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();\r
-\r
- Color c = Color.white;\r
-\r
- if(i>19)\r
- return c;\r
-\r
- for (int k=0; k < ResidueColour[i].conses.length ; k++)\r
- if (ResidueColour[i].conses[k].isConserved(cons2,j,size))\r
- c = ResidueColour[i].c;\r
-\r
- if (i == 4)\r
- {\r
- if (conses[27].isConserved(cons2, j, size))\r
- c = (Color) colhash.get("PINK");\r
+\r
+ public ClustalxColourScheme(Vector seqs, int maxWidth) {\r
+ resetClustalX(seqs, maxWidth);\r
}\r
\r
+ public void resetClustalX(Vector seqs, int maxWidth) {\r
+ cons2 = new int[maxWidth][24];\r
\r
- return c;\r
+ int start = 0;\r
\r
- }\r
-}\r
+ // Initialize the array\r
+ for (int j = 0; j < 24; j++)\r
+ for (int i = 0; i < maxWidth; i++)\r
+ cons2[i][j] = 0;\r
\r
-class ConsensusColour {\r
+ int res;\r
+ int i;\r
+ int j = 0;\r
+ String seq;\r
\r
- Consensus[] conses;\r
- Color c;\r
+ while (j < seqs.size()) {\r
+ seq = ((SequenceI) seqs.elementAt(j)).getSequence();\r
\r
- public ConsensusColour(Color c,Consensus[] conses) {\r
- this.conses = conses;\r
- // this.list = list;\r
- this.c = c;\r
- }\r
-}\r
+ int end_j = seq.length() - 1;\r
\r
+ for (i = start; i <= end_j; i++) {\r
+ if ((seq.length() - 1) < i) {\r
+ res = 23;\r
+ } else {\r
+ res = ((Integer) ResidueProperties.aaHash.get(seq.charAt(i) +\r
+ "")).intValue();\r
+ }\r
\r
+ cons2[i][res]++;\r
+ }\r
\r
+ j++;\r
+ }\r
+\r
+ this.size = seqs.size();\r
+ makeColours();\r
+ }\r
\r
+ public void makeColours() {\r
+ conses[0] = new Consensus("WLVIMAFCYHP", 60);\r
+ conses[1] = new Consensus("WLVIMAFCYHP", 80);\r
+ conses[2] = new Consensus("ED", 50);\r
+ conses[3] = new Consensus("KR", 60);\r
+ conses[4] = new Consensus("G", 50);\r
+ conses[5] = new Consensus("N", 50);\r
+ conses[6] = new Consensus("QE", 50);\r
+ conses[7] = new Consensus("P", 50);\r
+ conses[8] = new Consensus("TS", 50);\r
+\r
+ conses[26] = new Consensus("A", 85);\r
+ conses[27] = new Consensus("C", 85);\r
+ conses[10] = new Consensus("E", 85);\r
+ conses[11] = new Consensus("F", 85);\r
+ conses[12] = new Consensus("G", 85);\r
+ conses[13] = new Consensus("H", 85);\r
+ conses[14] = new Consensus("I", 85);\r
+ conses[15] = new Consensus("L", 85);\r
+ conses[16] = new Consensus("M", 85);\r
+ conses[17] = new Consensus("N", 85);\r
+ conses[18] = new Consensus("P", 85);\r
+ conses[19] = new Consensus("Q", 85);\r
+ conses[20] = new Consensus("R", 85);\r
+ conses[21] = new Consensus("S", 85);\r
+ conses[22] = new Consensus("T", 85);\r
+ conses[23] = new Consensus("V", 85);\r
+ conses[24] = new Consensus("W", 85);\r
+ conses[25] = new Consensus("Y", 85);\r
+ conses[28] = new Consensus("K", 85);\r
+ conses[29] = new Consensus("D", 85);\r
+\r
+ conses[30] = new Consensus("G", 0);\r
+ conses[31] = new Consensus("P", 0);\r
+\r
+ // We now construct the colours\r
+ colours = new ConsensusColour[11];\r
+\r
+ Consensus[] tmp8 = new Consensus[1];\r
+ tmp8[0] = conses[30]; //G\r
+ colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);\r
+\r
+ Consensus[] tmp9 = new Consensus[1];\r
+ tmp9[0] = conses[31]; //P\r
+ colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);\r
+\r
+ Consensus[] tmp10 = new Consensus[1];\r
+ tmp10[0] = conses[27]; //C\r
+ colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);\r
+\r
+ Consensus[] tmp1 = new Consensus[14];\r
+ tmp1[0] = conses[0]; //%\r
+ tmp1[1] = conses[1]; //#\r
+ tmp1[2] = conses[26]; //A\r
+ tmp1[3] = conses[27]; //C\r
+ tmp1[4] = conses[11]; //F\r
+ tmp1[5] = conses[13]; //H\r
+ tmp1[6] = conses[14]; //I\r
+ tmp1[7] = conses[15]; //L\r
+ tmp1[8] = conses[16]; //M\r
+ tmp1[9] = conses[23]; //V\r
+ tmp1[10] = conses[24]; //W\r
+ tmp1[11] = conses[25]; //Y\r
+ tmp1[12] = conses[18]; //P\r
+ tmp1[13] = conses[19]; //p\r
+ colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);\r
+\r
+ colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);\r
+\r
+ Consensus[] tmp2 = new Consensus[5];\r
+ tmp2[0] = conses[8]; //t\r
+ tmp2[1] = conses[21]; //S\r
+ tmp2[2] = conses[22]; //T\r
+ tmp2[3] = conses[0]; //%\r
+ tmp2[4] = conses[1]; //#\r
+ colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);\r
+\r
+ Consensus[] tmp3 = new Consensus[3];\r
+\r
+ tmp3[0] = conses[17]; //N\r
+ tmp3[1] = conses[29]; //D\r
+ tmp3[2] = conses[5]; //n\r
+ colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);\r
+\r
+ Consensus[] tmp4 = new Consensus[6];\r
+ tmp4[0] = conses[6]; // q = QE\r
+ tmp4[1] = conses[19]; //Q\r
+ tmp4[2] = conses[22]; //E\r
+ tmp4[3] = conses[3]; //+\r
+ tmp4[4] = conses[28]; //K\r
+ tmp4[5] = conses[20]; //R\r
+ colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);\r
+\r
+ Consensus[] tmp5 = new Consensus[4];\r
+ tmp5[0] = conses[3]; //+\r
+ tmp5[1] = conses[28]; //K\r
+ tmp5[2] = conses[20]; //R\r
+ tmp5[3] = conses[19]; //Q\r
+ colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);\r
+\r
+ Consensus[] tmp6 = new Consensus[5];\r
+ tmp6[0] = conses[3]; //-\r
+ tmp6[1] = conses[29]; //D\r
+ tmp6[2] = conses[10]; //E\r
+ tmp6[3] = conses[6]; //q\r
+ tmp6[4] = conses[19]; //Q\r
+ colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);\r
+\r
+ Consensus[] tmp7 = new Consensus[5];\r
+ tmp7[0] = conses[3]; //-\r
+ tmp7[1] = conses[29]; //D\r
+ tmp7[2] = conses[10]; //E\r
+ tmp7[3] = conses[17]; //N\r
+ tmp7[4] = conses[2]; //DE\r
+ colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);\r
+\r
+ // Now attach the ConsensusColours to the residue letters\r
+ ResidueColour = new ConsensusColour[20];\r
+ ResidueColour[0] = colours[0]; // A\r
+ ResidueColour[1] = colours[4]; // R\r
+ ResidueColour[2] = colours[2]; // N\r
+ ResidueColour[3] = colours[6]; // D\r
+ ResidueColour[4] = colours[0]; // C\r
+ ResidueColour[5] = colours[3]; // Q\r
+ ResidueColour[6] = colours[5]; // E\r
+ ResidueColour[7] = colours[7]; // G\r
+ ResidueColour[8] = colours[10]; // H\r
+ ResidueColour[9] = colours[0]; // I\r
+ ResidueColour[10] = colours[0]; // L\r
+ ResidueColour[11] = colours[4]; // K\r
+ ResidueColour[12] = colours[0]; // M\r
+ ResidueColour[13] = colours[0]; // F\r
+ ResidueColour[14] = colours[8]; // P\r
+ ResidueColour[15] = colours[1]; // S\r
+ ResidueColour[16] = colours[1]; // T\r
+ ResidueColour[17] = colours[0]; // W\r
+ ResidueColour[18] = colours[10]; // Y\r
+ ResidueColour[19] = colours[0]; // V\r
+ }\r
\r
+ public Color findColour(String s) {\r
+ return Color.pink;\r
+ }\r
+\r
+ public Color findColour(String s, int j) {\r
+ if ((threshold != 0) && !aboveThreshold(s, j)) {\r
+ return Color.white;\r
+ }\r
\r
+ int i = ((Integer) ResidueProperties.aaHash.get(s)).intValue();\r
\r
+ Color c = Color.white;\r
\r
+ if (i > 19) {\r
+ return c;\r
+ }\r
\r
+ for (int k = 0; k < ResidueColour[i].conses.length; k++)\r
+ if (ResidueColour[i].conses[k].isConserved(cons2, j, size)) {\r
+ c = ResidueColour[i].c;\r
+ }\r
\r
+ if (i == 4) {\r
+ if (conses[27].isConserved(cons2, j, size)) {\r
+ c = (Color) colhash.get("PINK");\r
+ }\r
+ }\r
\r
+ return c;\r
+ }\r
+}\r
\r
\r
+class ConsensusColour {\r
+ Consensus[] conses;\r
+ Color c;\r
\r
+ public ConsensusColour(Color c, Consensus[] conses) {\r
+ this.conses = conses;\r
\r
+ // this.list = list;\r
+ this.c = c;\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
+\r
import java.util.*;\r
\r
-public interface ColourSchemeI\r
-{\r
- public Color findColour(String aa);\r
- public Color findColour(String s,int j);\r
- public void setConsensus(Vector v);\r
+\r
+public interface ColourSchemeI {\r
+ public Color findColour(String aa);\r
+\r
+ public Color findColour(String s, int j);\r
+\r
+ public void setConsensus(Vector v);\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
-public class ColourSchemeProperty\r
-{\r
- public static final int CLUSTAL = 0;\r
- public static final int BLOSUM = 1;\r
- public static final int PID = 2;\r
- public static final int ZAPPO = 3;\r
- public static final int HYDROPHOBIC=4;\r
- public static final int HELIX=5;\r
- public static final int STRAND=6;\r
- public static final int TURN = 7;\r
- public static final int BURIED = 8;\r
- public static final int NUCLEOTIDE = 9;\r
- public static final int USER_DEFINED = 10;\r
- public static final int NONE = 11;\r
-\r
- public static int getColourIndexFromName(String name)\r
- {\r
- int ret=11;\r
- if(name.equalsIgnoreCase("Clustal"))\r
- ret = CLUSTAL;\r
- else if(name.equalsIgnoreCase("Blosum62"))\r
- ret = BLOSUM;\r
- else if(name.equalsIgnoreCase("% Identity"))\r
- ret = PID;\r
- else if(name.equalsIgnoreCase("Zappo"))\r
- ret = ZAPPO;\r
- else if(name.equalsIgnoreCase("Hydrophobic"))\r
- ret = HYDROPHOBIC;\r
- else if(name.equalsIgnoreCase("Helix Propensity"))\r
- ret = HELIX;\r
- else if(name.equalsIgnoreCase("Strand Propensity"))\r
- ret = STRAND;\r
- else if(name.equalsIgnoreCase("Turn Propensity"))\r
- ret = TURN;\r
- else if(name.equalsIgnoreCase("Buried Index"))\r
- ret = BURIED;\r
- else if(name.equalsIgnoreCase("Nucleotide"))\r
- ret = NUCLEOTIDE;\r
- else if(name.equalsIgnoreCase("User Defined"))\r
- ret = USER_DEFINED;\r
-\r
- return ret;\r
- }\r
-\r
- public static String getColourName(ColourSchemeI cs)\r
- {\r
- if(cs instanceof ConservationColourScheme)\r
- cs = ((ConservationColourScheme)cs).cs;\r
-\r
-\r
- int index = 11;\r
- if(cs instanceof ClustalxColourScheme)\r
- index = CLUSTAL;\r
- else if(cs instanceof Blosum62ColourScheme)\r
- index = BLOSUM;\r
- else if(cs instanceof PIDColourScheme)\r
- index = PID;\r
- else if(cs instanceof ZappoColourScheme)\r
- index = ZAPPO;\r
- else if(cs instanceof HydrophobicColourScheme)\r
- index = HYDROPHOBIC;\r
- else if(cs instanceof HelixColourScheme)\r
- index = HELIX;\r
- else if(cs instanceof StrandColourScheme)\r
- index = STRAND;\r
- else if(cs instanceof TurnColourScheme)\r
- index = TURN;\r
- else if(cs instanceof BuriedColourScheme)\r
- index = BURIED;\r
- else if(cs instanceof NucleotideColourScheme)\r
- index = NUCLEOTIDE;\r
- else if(cs instanceof UserColourScheme)\r
- index = USER_DEFINED;\r
-\r
- return getColourName(index);\r
- }\r
-\r
- public static String getColourName(int index)\r
- {\r
- String ret=null;\r
- switch(index)\r
- {\r
- case CLUSTAL: ret = "Clustal"; break;\r
- case BLOSUM: ret = "Blosum62"; break;\r
- case PID: ret = "% Identity"; break;\r
- case ZAPPO: ret = "Zappo"; break;\r
- case HYDROPHOBIC: ret="Hydrophobic";break;\r
- case HELIX: ret="Helix Propensity";break;\r
- case STRAND: ret="Strand Propensity";break;\r
- case TURN: ret="Turn Propensity";break;\r
- case BURIED: ret="Buried Index";break;\r
- case NUCLEOTIDE:ret="Nucleotide"; break;\r
- case USER_DEFINED:ret="User Defined";break;\r
- default: ret = "None"; break;\r
+public class ColourSchemeProperty {\r
+ public static final int CLUSTAL = 0;\r
+ public static final int BLOSUM = 1;\r
+ public static final int PID = 2;\r
+ public static final int ZAPPO = 3;\r
+ public static final int HYDROPHOBIC = 4;\r
+ public static final int HELIX = 5;\r
+ public static final int STRAND = 6;\r
+ public static final int TURN = 7;\r
+ public static final int BURIED = 8;\r
+ public static final int NUCLEOTIDE = 9;\r
+ public static final int USER_DEFINED = 10;\r
+ public static final int NONE = 11;\r
+\r
+ public static int getColourIndexFromName(String name) {\r
+ int ret = 11;\r
+\r
+ if (name.equalsIgnoreCase("Clustal")) {\r
+ ret = CLUSTAL;\r
+ } else if (name.equalsIgnoreCase("Blosum62")) {\r
+ ret = BLOSUM;\r
+ } else if (name.equalsIgnoreCase("% Identity")) {\r
+ ret = PID;\r
+ } else if (name.equalsIgnoreCase("Zappo")) {\r
+ ret = ZAPPO;\r
+ } else if (name.equalsIgnoreCase("Hydrophobic")) {\r
+ ret = HYDROPHOBIC;\r
+ } else if (name.equalsIgnoreCase("Helix Propensity")) {\r
+ ret = HELIX;\r
+ } else if (name.equalsIgnoreCase("Strand Propensity")) {\r
+ ret = STRAND;\r
+ } else if (name.equalsIgnoreCase("Turn Propensity")) {\r
+ ret = TURN;\r
+ } else if (name.equalsIgnoreCase("Buried Index")) {\r
+ ret = BURIED;\r
+ } else if (name.equalsIgnoreCase("Nucleotide")) {\r
+ ret = NUCLEOTIDE;\r
+ } else if (name.equalsIgnoreCase("User Defined")) {\r
+ ret = USER_DEFINED;\r
+ }\r
+\r
+ return ret;\r
+ }\r
+\r
+ public static String getColourName(ColourSchemeI cs) {\r
+ if (cs instanceof ConservationColourScheme) {\r
+ cs = ((ConservationColourScheme) cs).cs;\r
+ }\r
+\r
+ int index = 11;\r
+\r
+ if (cs instanceof ClustalxColourScheme) {\r
+ index = CLUSTAL;\r
+ } else if (cs instanceof Blosum62ColourScheme) {\r
+ index = BLOSUM;\r
+ } else if (cs instanceof PIDColourScheme) {\r
+ index = PID;\r
+ } else if (cs instanceof ZappoColourScheme) {\r
+ index = ZAPPO;\r
+ } else if (cs instanceof HydrophobicColourScheme) {\r
+ index = HYDROPHOBIC;\r
+ } else if (cs instanceof HelixColourScheme) {\r
+ index = HELIX;\r
+ } else if (cs instanceof StrandColourScheme) {\r
+ index = STRAND;\r
+ } else if (cs instanceof TurnColourScheme) {\r
+ index = TURN;\r
+ } else if (cs instanceof BuriedColourScheme) {\r
+ index = BURIED;\r
+ } else if (cs instanceof NucleotideColourScheme) {\r
+ index = NUCLEOTIDE;\r
+ } else if (cs instanceof UserColourScheme) {\r
+ index = USER_DEFINED;\r
+ }\r
+\r
+ return getColourName(index);\r
+ }\r
+\r
+ public static String getColourName(int index) {\r
+ String ret = null;\r
+\r
+ switch (index) {\r
+ case CLUSTAL:\r
+ ret = "Clustal";\r
+\r
+ break;\r
+\r
+ case BLOSUM:\r
+ ret = "Blosum62";\r
+\r
+ break;\r
+\r
+ case PID:\r
+ ret = "% Identity";\r
+\r
+ break;\r
+\r
+ case ZAPPO:\r
+ ret = "Zappo";\r
+\r
+ break;\r
+\r
+ case HYDROPHOBIC:\r
+ ret = "Hydrophobic";\r
+\r
+ break;\r
+\r
+ case HELIX:\r
+ ret = "Helix Propensity";\r
+\r
+ break;\r
+\r
+ case STRAND:\r
+ ret = "Strand Propensity";\r
+\r
+ break;\r
+\r
+ case TURN:\r
+ ret = "Turn Propensity";\r
+\r
+ break;\r
+\r
+ case BURIED:\r
+ ret = "Buried Index";\r
+\r
+ break;\r
+\r
+ case NUCLEOTIDE:\r
+ ret = "Nucleotide";\r
+\r
+ break;\r
+\r
+ case USER_DEFINED:\r
+ ret = "User Defined";\r
+\r
+ break;\r
+\r
+ default:\r
+ ret = "None";\r
+\r
+ break;\r
+ }\r
+\r
+ return ret;\r
}\r
- return ret;\r
- }\r
-\r
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)\r
- {\r
- return getColour(al, getColourIndexFromName(name));\r
- }\r
-\r
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)\r
- {\r
- ColourSchemeI cs = null;\r
- switch(index)\r
- {\r
- case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;\r
- case BLOSUM: cs = new Blosum62ColourScheme(); break;\r
- case PID: cs = new PIDColourScheme(); break;\r
- case ZAPPO: cs = new ZappoColourScheme(); break;\r
- case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;\r
- case HELIX: cs = new HelixColourScheme(); break;\r
- case STRAND: cs = new StrandColourScheme(); break;\r
- case TURN: cs = new TurnColourScheme(); break;\r
- case BURIED: cs = new BuriedColourScheme(); break;\r
- case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;\r
- case USER_DEFINED: cs = new UserColourScheme(null);\r
- break;\r
-\r
- default: break;\r
+\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,\r
+ String name) {\r
+ return getColour(al, getColourIndexFromName(name));\r
}\r
\r
- return cs;\r
- }\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,\r
+ int index) {\r
+ ColourSchemeI cs = null;\r
+\r
+ switch (index) {\r
+ case CLUSTAL:\r
+ cs = new ClustalxColourScheme(al.getSequences(), al.getWidth());\r
+\r
+ break;\r
+\r
+ case BLOSUM:\r
+ cs = new Blosum62ColourScheme();\r
+\r
+ break;\r
+\r
+ case PID:\r
+ cs = new PIDColourScheme();\r
+\r
+ break;\r
+\r
+ case ZAPPO:\r
+ cs = new ZappoColourScheme();\r
+\r
+ break;\r
+\r
+ case HYDROPHOBIC:\r
+ cs = new HydrophobicColourScheme();\r
+\r
+ break;\r
+\r
+ case HELIX:\r
+ cs = new HelixColourScheme();\r
+\r
+ break;\r
+\r
+ case STRAND:\r
+ cs = new StrandColourScheme();\r
+\r
+ break;\r
+\r
+ case TURN:\r
+ cs = new TurnColourScheme();\r
+\r
+ break;\r
+\r
+ case BURIED:\r
+ cs = new BuriedColourScheme();\r
+\r
+ break;\r
+\r
+ case NUCLEOTIDE:\r
+ cs = new NucleotideColourScheme();\r
+\r
+ break;\r
+\r
+ case USER_DEFINED:\r
+ cs = new UserColourScheme(null);\r
+\r
+ break;\r
+\r
+ default:\r
+ break;\r
+ }\r
+\r
+ return cs;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
+\r
////////////////////////////////////////////\r
// This does nothing at all at the moment!!!!!!!!!!\r
// AW 15th Dec 2004\r
/////////////////////////////////////////\r
public class Consensus {\r
+ int[] mask;\r
+ double threshold;\r
+ String maskstr;\r
\r
- int[] mask;\r
- double threshold;\r
- String maskstr;\r
-\r
- public Consensus(String mask, double threshold) {\r
- // this.id = id;\r
- // this.mask = mask;\r
+ public Consensus(String mask, double threshold) {\r
+ // this.id = id;\r
+ // this.mask = mask;\r
this.maskstr = mask;\r
- setMask(mask);\r
- this.threshold = threshold;\r
- }\r
+ setMask(mask);\r
+ this.threshold = threshold;\r
+ }\r
\r
- public void setMask(String s) {\r
- this.mask = setNums(s);\r
- // for (int i=0; i < mask.length; i++) {\r
- // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
- // }\r
- }\r
+ public void setMask(String s) {\r
+ this.mask = setNums(s);\r
\r
- public boolean isConserved(int[][] cons2,int col ,int size) {\r
- int tot = 0;\r
- for (int i = 0; i < mask.length; i++)\r
- tot += cons2[col][mask[i]];\r
+ // for (int i=0; i < mask.length; i++) {\r
+ // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
+ // }\r
+ }\r
\r
- if ( (double) tot > threshold * size / 100)\r
- return true;\r
+ public boolean isConserved(int[][] cons2, int col, int size) {\r
+ int tot = 0;\r
\r
- return false;\r
- }\r
+ for (int i = 0; i < mask.length; i++)\r
+ tot += cons2[col][mask[i]];\r
\r
- int[] setNums(String s)\r
- {\r
- int [] out = new int[s.length()];\r
- int i = 0;\r
- while (i < s.length())\r
- {\r
- out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();\r
- i++;\r
+ if ((double) tot > ((threshold * size) / 100)) {\r
+ return true;\r
+ }\r
\r
+ return false;\r
}\r
\r
- return out;\r
- }\r
+ int[] setNums(String s) {\r
+ int[] out = new int[s.length()];\r
+ int i = 0;\r
\r
+ while (i < s.length()) {\r
+ out[i] = ((Integer) ResidueProperties.aaHash.get(s.substring(i,\r
+ i + 1))).intValue();\r
+ i++;\r
+ }\r
\r
+ return out;\r
+ }\r
}\r
-\r
-\r
-\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
-import java.awt.*;\r
+\r
import jalview.analysis.*;\r
+\r
+import java.awt.*;\r
+\r
import java.util.Vector;\r
\r
+\r
public class ConservationColourScheme extends ResidueColourScheme {\r
- public Conservation conserve;\r
- public ColourSchemeI cs;\r
- public int inc = 30;\r
-\r
- public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
- {\r
- super();\r
- conserve = cons;\r
- cs = oldcs;\r
- }\r
-\r
- public void setConsensus(Vector consensus)\r
- {\r
- this.consensus = consensus;\r
- if(cs!=null)\r
- cs.setConsensus(consensus);\r
- }\r
-\r
- public Color findColour(String s, int i)\r
- {\r
- Color c = Color.white;\r
- if (cs == null)\r
- return c;\r
-\r
- char ch = conserve.getConsSequence().getSequence().charAt(i);\r
- if (ch == '*' || ch == '+')\r
- {\r
- c = cs.findColour(s, i);\r
- }\r
- else\r
- {\r
- int tmp = 10;\r
- int t = 0;\r
- if (!jalview.util.Comparison.isGap(ch))\r
- t = Integer.parseInt(ch + "");\r
-\r
- c = cs.findColour(s, i);\r
-\r
- while (tmp >= t)\r
- {\r
- c = lighter(c, inc);\r
- tmp--;\r
- }\r
-\r
- }\r
-\r
- return c;\r
- }\r
-\r
-\r
- public Color lighter(Color c, int inc) {\r
- int red = c.getRed();\r
- int blue = c.getBlue();\r
- int green = c.getGreen();\r
-\r
- if (red < 255-inc) { red = red +inc;} else {red = 255;}\r
- if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}\r
- if (green < 255-inc) { green = green +inc;} else {green = 255;}\r
-\r
- return new Color(red,green,blue);\r
- }\r
+ public Conservation conserve;\r
+ public ColourSchemeI cs;\r
+ public int inc = 30;\r
+\r
+ public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs) {\r
+ super();\r
+ conserve = cons;\r
+ cs = oldcs;\r
+ }\r
+\r
+ public void setConsensus(Vector consensus) {\r
+ this.consensus = consensus;\r
+\r
+ if (cs != null) {\r
+ cs.setConsensus(consensus);\r
+ }\r
+ }\r
+\r
+ public Color findColour(String s, int i) {\r
+ Color c = Color.white;\r
+\r
+ if (cs == null) {\r
+ return c;\r
+ }\r
+\r
+ char ch = conserve.getConsSequence().getSequence().charAt(i);\r
+\r
+ if ((ch == '*') || (ch == '+')) {\r
+ c = cs.findColour(s, i);\r
+ } else {\r
+ int tmp = 10;\r
+ int t = 0;\r
+\r
+ if (!jalview.util.Comparison.isGap(ch)) {\r
+ t = Integer.parseInt(ch + "");\r
+ }\r
+\r
+ c = cs.findColour(s, i);\r
+\r
+ while (tmp >= t) {\r
+ c = lighter(c, inc);\r
+ tmp--;\r
+ }\r
+ }\r
+\r
+ return c;\r
+ }\r
+\r
+ public Color lighter(Color c, int inc) {\r
+ int red = c.getRed();\r
+ int blue = c.getBlue();\r
+ int green = c.getGreen();\r
+\r
+ if (red < (255 - inc)) {\r
+ red = red + inc;\r
+ } else {\r
+ red = 255;\r
+ }\r
+\r
+ if (blue < (255 - inc)) {\r
+ blue = blue + inc;\r
+ } else {\r
+ blue = 255;\r
+ }\r
+\r
+ if (green < (255 - inc)) {\r
+ green = green + inc;\r
+ } else {\r
+ green = 255;\r
+ }\r
\r
+ return new Color(red, green, blue);\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
\r
-public class HelixColourScheme extends ScoreColourScheme {\r
-\r
\r
- public HelixColourScheme() {\r
- super(ResidueProperties.helix,ResidueProperties.helixmin,ResidueProperties.helixmax);\r
- }\r
+public class HelixColourScheme extends ScoreColourScheme {\r
+ public HelixColourScheme() {\r
+ super(ResidueProperties.helix, ResidueProperties.helixmin,\r
+ ResidueProperties.helixmax);\r
+ }\r
\r
- public Color makeColour(float c) {\r
- return new Color(c,(float)1.0-c,c);\r
- }\r
+ public Color makeColour(float c) {\r
+ return new Color(c, (float) 1.0 - c, c);\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
\r
-public class HydrophobicColourScheme extends ScoreColourScheme {\r
\r
- public HydrophobicColourScheme() {\r
- super(ResidueProperties.hyd,ResidueProperties.hydmin,ResidueProperties.hydmax);\r
- }\r
+public class HydrophobicColourScheme extends ScoreColourScheme {\r
+ public HydrophobicColourScheme() {\r
+ super(ResidueProperties.hyd, ResidueProperties.hydmin,\r
+ ResidueProperties.hydmax);\r
+ }\r
\r
- public Color makeColour(float c) {\r
- return new Color(c,(float)0.0,(float)1.0-c);\r
- }\r
+ public Color makeColour(float c) {\r
+ return new Color(c, (float) 0.0, (float) 1.0 - c);\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
\r
-public class NucleotideColourScheme extends ResidueColourScheme\r
-{\r
- public NucleotideColourScheme() {\r
- super(ResidueProperties.nucleotide,0);\r
- }\r
-\r
-\r
- public Color findColour(String n)\r
- {\r
- // System.out.println("called"); log.debug\r
- return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];\r
- }\r
-\r
-\r
- public Color findColour(String n, int j) {\r
-\r
- if (threshold == 0 || aboveThreshold( n, j))\r
- try\r
- {\r
- return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
- }\r
- catch (Exception ex)\r
- {\r
- return Color.white;\r
- }\r
- else\r
- return Color.white;\r
-\r
- }\r
\r
+public class NucleotideColourScheme extends ResidueColourScheme {\r
+ public NucleotideColourScheme() {\r
+ super(ResidueProperties.nucleotide, 0);\r
+ }\r
+\r
+ public Color findColour(String n) {\r
+ // System.out.println("called"); log.debug\r
+ return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+ }\r
+\r
+ public Color findColour(String n, int j) {\r
+ if ((threshold == 0) || aboveThreshold(n, j)) {\r
+ try {\r
+ return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+ } catch (Exception ex) {\r
+ return Color.white;\r
+ }\r
+ } else {\r
+ return Color.white;\r
+ }\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import jalview.datamodel.*;\r
-import java.util.*;\r
+\r
import java.awt.*;\r
\r
+import java.util.*;\r
+\r
+\r
public class PIDColourScheme extends ResidueColourScheme {\r
public Color[] pidColours;\r
public float[] thresholds;\r
-\r
SequenceGroup group;\r
\r
public PIDColourScheme() {\r
- this.pidColours = ResidueProperties.pidColours;\r
- this.thresholds = ResidueProperties.pidThresholds;\r
+ this.pidColours = ResidueProperties.pidColours;\r
+ this.thresholds = ResidueProperties.pidThresholds;\r
}\r
\r
+ public Color findColour(String s, int j) {\r
+ if ((threshold != 0) && !aboveThreshold(s, j)) {\r
+ return Color.white;\r
+ }\r
\r
+ Color c = Color.white;\r
+ Hashtable hash = (Hashtable) consensus.elementAt(j);\r
\r
- public Color findColour(String s, int j) {\r
+ double sc = 0;\r
\r
- if( threshold!=0 && !aboveThreshold(s,j))\r
- return Color.white;\r
+ if ((Integer.parseInt(hash.get("maxCount").toString()) != -1) &&\r
+ hash.contains(s)) {\r
+ sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(\r
+ "size")).intValue();\r
\r
- Color c = Color.white;\r
- Hashtable hash = (Hashtable)consensus.elementAt(j);\r
+ // MC Should be isGap\r
+ if (!jalview.util.Comparison.isGap((s.charAt(0)))) {\r
+ for (int i = 0; i < thresholds.length; i++) {\r
+ if (sc > thresholds[i]) {\r
+ c = pidColours[i];\r
\r
- double sc = 0;\r
- if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
- {\r
- sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;\r
- // MC Should be isGap\r
- if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
- {\r
- for (int i = 0; i < thresholds.length; i++)\r
- {\r
- if (sc > thresholds[i])\r
- {\r
- c = pidColours[i];\r
- break;\r
+ break;\r
+ }\r
+ }\r
}\r
- }\r
}\r
\r
- }\r
- return c;\r
- }\r
+ return c;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
-import java.util.*;\r
import java.awt.*;\r
\r
-public class ResidueColourScheme implements ColourSchemeI{\r
- Color [] colors;\r
- int threshold = 0;\r
- public Vector consensus;\r
+import java.util.*;\r
+\r
+\r
+public class ResidueColourScheme implements ColourSchemeI {\r
+ Color[] colors;\r
+ int threshold = 0;\r
+ public Vector consensus;\r
\r
public ResidueColourScheme(Color[] colors, int threshold) {\r
- this.colors = colors;\r
- this.threshold = threshold;\r
+ this.colors = colors;\r
+ this.threshold = threshold;\r
}\r
\r
- public ResidueColourScheme()\r
- { }\r
+ public ResidueColourScheme() {\r
+ }\r
\r
- public void setConsensus(Vector consensus)\r
- {\r
- this.consensus = consensus;\r
+ public void setConsensus(Vector consensus) {\r
+ this.consensus = consensus;\r
}\r
\r
- public Color findColour(String aa)\r
- {\r
- return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
+ public Color findColour(String aa) {\r
+ return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
}\r
\r
public Color findColour(String s, int j) {\r
-\r
- if( threshold==0 || aboveThreshold(s,j))\r
- return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
- else\r
- return Color.white;\r
-\r
+ if ((threshold == 0) || aboveThreshold(s, j)) {\r
+ return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];\r
+ } else {\r
+ return Color.white;\r
+ }\r
}\r
\r
public int getThreshold() {\r
- return threshold;\r
+ return threshold;\r
}\r
\r
public void setThreshold(int ct) {\r
- threshold = ct;\r
+ threshold = ct;\r
}\r
\r
- public boolean aboveThreshold(String s, int j)\r
- {\r
- Hashtable hash = (Hashtable)consensus.elementAt(j);\r
-\r
- if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))\r
- {\r
- //// resCount//////////////////// ///////////////seq count////////////\r
- double sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ( (Integer) hash.get("size")).intValue();\r
+ public boolean aboveThreshold(String s, int j) {\r
+ Hashtable hash = (Hashtable) consensus.elementAt(j);\r
\r
- if (sc >= threshold)\r
- return true;\r
+ if ((((Integer) hash.get("maxCount")).intValue() != -1) &&\r
+ hash.contains(s)) {\r
+ //// resCount//////////////////// ///////////////seq count////////////\r
+ double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(\r
+ "size")).intValue();\r
\r
+ if (sc >= threshold) {\r
+ return true;\r
+ }\r
}\r
\r
- return false;\r
+ return false;\r
}\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.Color;\r
+\r
import java.util.*;\r
\r
+\r
public class ResidueProperties {\r
+ //Stores residue codes/names and colours and other things\r
+ public static Hashtable aaHash = new Hashtable(); // stores the number value of the aa\r
+ public static Hashtable aa3Hash = new Hashtable();\r
+ public static Hashtable aa2Triplet = new Hashtable();\r
+ public static Hashtable nucleotideHash = new Hashtable();\r
+\r
+ static {\r
+ aaHash.put("A", new Integer(0));\r
+ aaHash.put("R", new Integer(1));\r
+ aaHash.put("N", new Integer(2));\r
+ aaHash.put("D", new Integer(3));\r
+ aaHash.put("C", new Integer(4));\r
+ aaHash.put("Q", new Integer(5));\r
+ aaHash.put("E", new Integer(6));\r
+ aaHash.put("G", new Integer(7));\r
+ aaHash.put("H", new Integer(8));\r
+ aaHash.put("I", new Integer(9));\r
+ aaHash.put("L", new Integer(10));\r
+ aaHash.put("K", new Integer(11));\r
+ aaHash.put("M", new Integer(12));\r
+ aaHash.put("F", new Integer(13));\r
+ aaHash.put("P", new Integer(14));\r
+ aaHash.put("S", new Integer(15));\r
+ aaHash.put("T", new Integer(16));\r
+ aaHash.put("W", new Integer(17));\r
+ aaHash.put("Y", new Integer(18));\r
+ aaHash.put("V", new Integer(19));\r
+ aaHash.put("B", new Integer(20));\r
+ aaHash.put("Z", new Integer(21));\r
+ aaHash.put("X", new Integer(22));\r
+ aaHash.put("a", new Integer(0));\r
+ aaHash.put("r", new Integer(1));\r
+ aaHash.put("n", new Integer(2));\r
+ aaHash.put("d", new Integer(3));\r
+ aaHash.put("c", new Integer(4));\r
+ aaHash.put("q", new Integer(5));\r
+ aaHash.put("e", new Integer(6));\r
+ aaHash.put("g", new Integer(7));\r
+ aaHash.put("h", new Integer(8));\r
+ aaHash.put("i", new Integer(9));\r
+ aaHash.put("l", new Integer(10));\r
+ aaHash.put("k", new Integer(11));\r
+ aaHash.put("m", new Integer(12));\r
+ aaHash.put("f", new Integer(13));\r
+ aaHash.put("p", new Integer(14));\r
+ aaHash.put("s", new Integer(15));\r
+ aaHash.put("t", new Integer(16));\r
+ aaHash.put("w", new Integer(17));\r
+ aaHash.put("y", new Integer(18));\r
+ aaHash.put("v", new Integer(19));\r
+ aaHash.put("b", new Integer(20));\r
+ aaHash.put("z", new Integer(21));\r
+ aaHash.put("x", new Integer(22));\r
+ aaHash.put("-", new Integer(23));\r
+ aaHash.put("*", new Integer(23));\r
+ aaHash.put(".", new Integer(23));\r
+ aaHash.put(" ", new Integer(23));\r
+ }\r
+\r
+ static {\r
+ nucleotideHash.put("A", new Integer(0));\r
+ nucleotideHash.put("C", new Integer(1));\r
+ nucleotideHash.put("G", new Integer(2));\r
+ nucleotideHash.put("T", new Integer(3));\r
+ nucleotideHash.put("U", new Integer(4));\r
+ }\r
+\r
+ // These numbers should correspond to the indices in the Color hashes\r
+ public static Hashtable aaSpecialsHash = new Hashtable();\r
+\r
+ static {\r
+ aaSpecialsHash.put("-", new Integer(23));\r
+ aaSpecialsHash.put("*", new Integer(24));\r
+ aaSpecialsHash.put(".", new Integer(25));\r
+ aaSpecialsHash.put(" ", new Integer(26));\r
+ }\r
+\r
+ static {\r
+ aa3Hash.put("ALA", new Integer(0));\r
+ aa3Hash.put("ARG", new Integer(1));\r
+ aa3Hash.put("ASN", new Integer(2));\r
+ aa3Hash.put("ASP", new Integer(3)); //D\r
+ aa3Hash.put("CYS", new Integer(4));\r
+ aa3Hash.put("GLN", new Integer(5)); //Q\r
+ aa3Hash.put("GLU", new Integer(6)); // E\r
+ aa3Hash.put("GLY", new Integer(7));\r
+ aa3Hash.put("HIS", new Integer(8));\r
+ aa3Hash.put("ILE", new Integer(9));\r
+ aa3Hash.put("LEU", new Integer(10));\r
+ aa3Hash.put("LYS", new Integer(11));\r
+ aa3Hash.put("MET", new Integer(12));\r
+ aa3Hash.put("PHE", new Integer(13));\r
+ aa3Hash.put("PRO", new Integer(14));\r
+ aa3Hash.put("SER", new Integer(15));\r
+ aa3Hash.put("THR", new Integer(16));\r
+ aa3Hash.put("TRP", new Integer(17));\r
+ aa3Hash.put("TYR", new Integer(18));\r
+ aa3Hash.put("VAL", new Integer(19));\r
+ aa3Hash.put("B", new Integer(20));\r
+ aa3Hash.put("Z", new Integer(21));\r
+ aa3Hash.put("X", new Integer(22));\r
+ aa3Hash.put("-", new Integer(23));\r
+ aa3Hash.put("*", new Integer(23));\r
+ aa3Hash.put(".", new Integer(23));\r
+ aa3Hash.put(" ", new Integer(23));\r
+ }\r
+\r
+ static {\r
+ aa2Triplet.put("A", "ALA");\r
+ aa2Triplet.put("R", "ARG");\r
+ aa2Triplet.put("N", "ASN");\r
+ aa2Triplet.put("D", "ASP");\r
+ aa2Triplet.put("C", "CYS");\r
+ aa2Triplet.put("Q", "GLN");\r
+ aa2Triplet.put("E", "GLU");\r
+ aa2Triplet.put("G", "GLY");\r
+ aa2Triplet.put("H", "HIS");\r
+ aa2Triplet.put("I", "ILE");\r
+ aa2Triplet.put("L", "LEU");\r
+ aa2Triplet.put("K", "LYS");\r
+ aa2Triplet.put("M", "MET");\r
+ aa2Triplet.put("F", "PHE");\r
+ aa2Triplet.put("P", "PRO");\r
+ aa2Triplet.put("S", "SER");\r
+ aa2Triplet.put("T", "THR");\r
+ aa2Triplet.put("W", "TRP");\r
+ aa2Triplet.put("Y", "TYR");\r
+ aa2Triplet.put("V", "VAL");\r
+ }\r
+\r
+ public static String[] aa = {\r
+ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",\r
+ "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "\r
+ };\r
+ public static Color midBlue = new Color(100, 100, 255);\r
+ public static Vector scaleColours = new Vector();\r
+\r
+ static {\r
+ scaleColours.addElement(new Color(114, 0, 147));\r
+ scaleColours.addElement(new Color(156, 0, 98));\r
+ scaleColours.addElement(new Color(190, 0, 0));\r
+ scaleColours.addElement(Color.red);\r
+ scaleColours.addElement(new Color(255, 125, 0));\r
+ scaleColours.addElement(Color.orange);\r
+ scaleColours.addElement(new Color(255, 194, 85));\r
+ scaleColours.addElement(Color.yellow);\r
+ scaleColours.addElement(new Color(255, 255, 181));\r
+ scaleColours.addElement(Color.white);\r
+ }\r
+\r
+ public static Color[] taylor = {\r
+ new Color(204, 255, 0), // A Greenish-yellowy-yellow\r
+ new Color(0, 0, 255), // R Blueish-bluey-blue\r
+ new Color(204, 0, 255), // N Blueish-reddy-blue\r
+ new Color(255, 0, 0), // D Reddish-reddy-red\r
+ new Color(255, 255, 0), // C Yellowish-yellowy-yellow\r
+ new Color(255, 0, 204), // Q Reddish-bluey-red\r
+ new Color(255, 0, 102), // E Blueish-reddy-red\r
+ new Color(255, 153, 0), // G Yellowy-reddy-yellow\r
+ new Color(0, 102, 255), // H Greenish-bluey-blue\r
+ new Color(102, 255, 0), // I Greenish-yellowy-green\r
+ new Color(51, 255, 0), // L Yellowish-greeny-green\r
+ new Color(102, 0, 255), // K Reddish-bluey-blue\r
+ new Color(0, 255, 0), // M Greenish-greeny-green\r
+ new Color(0, 255, 102), // F Blueish-greeny-green\r
+ new Color(255, 204, 0), // P Reddish-yellowy-yellow\r
+ new Color(255, 51, 0), // S Yellowish-reddy-red\r
+ new Color(255, 102, 0), // T Reddish-yellowy-red\r
+ new Color(0, 204, 255), // W Blueish-greeny-green\r
+ new Color(0, 255, 204), // Y Greenish-bluey-green\r
+ new Color(153, 255, 0), // V Yellowish-greeny-yellow\r
+ Color.white, // B\r
+ Color.white, // Z\r
+ Color.white, // X\r
+ Color.white, // -\r
+ Color.white, // *\r
+ Color.white // .\r
+ };\r
+ public static Color[] nucleotide = {\r
+ new Color(100, 247, 63), // A\r
+ new Color(255, 179, 64), // C\r
+ new Color(235, 65, 60), // G\r
+ new Color(60, 136, 238), // T\r
+ new Color(60, 136, 238) // U\r
+ };\r
+ public static Color[] color = {\r
+ Color.pink, // A\r
+ midBlue, // R\r
+ Color.green, // N\r
+ Color.red, // D\r
+ Color.yellow, // C\r
+ Color.green, // Q\r
+ Color.red, // E\r
+ Color.magenta, // G\r
+ Color.red, // H\r
+ Color.pink, // I\r
+ Color.pink, // L\r
+ midBlue, // K\r
+ Color.pink, // M\r
+ Color.orange, // F\r
+ Color.magenta, // P\r
+ Color.green, // S\r
+ Color.green, // T\r
+ Color.orange, // W\r
+ Color.orange, // Y\r
+ Color.pink, // V\r
+ Color.white, // B\r
+ Color.white, // Z\r
+ Color.white, // X\r
+ Color.white, // -\r
+ Color.white, // *\r
+ Color.white, // .\r
+ Color.white // ' '\r
+ };\r
+\r
+ // Dunno where I got these numbers from\r
+ public static double[] hyd2 = {\r
+ 0.62, //A\r
+ 0.29, //R\r
+ -0.90, //N\r
+ -0.74, //D\r
+ 1.19, //C\r
+ 0.48, //Q\r
+ -0.40, //E\r
+ 1.38, //G\r
+ -1.50, //H\r
+ 1.06, //I\r
+ 0.64, //L\r
+ -0.78, //K\r
+ 0.12, //M\r
+ -0.85, //F\r
+ -2.53, //P\r
+ -0.18, //S\r
+ -0.05, //T\r
+ 1.08, //W\r
+ 0.81, //Y\r
+ 0.0, //V\r
+ 0.26, //B\r
+ 0.0, //Z\r
+ 0.0 //X\r
+ };\r
+ public static double[] helix = {\r
+ 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,\r
+ 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0\r
+ };\r
+ public static double helixmin = 0.57;\r
+ public static double helixmax = 1.51;\r
+ public static double[] strand = {\r
+ 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,\r
+ 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0\r
+ };\r
+ public static double strandmin = 0.37;\r
+ public static double strandmax = 1.7;\r
+ public static double[] turn = {\r
+ 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,\r
+ 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0\r
+ };\r
+ public static double turnmin = 0.47;\r
+ public static double turnmax = 1.56;\r
+ public static double[] buried = {\r
+ 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,\r
+ 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00\r
+ };\r
+ public static double buriedmin = 0.05;\r
+ public static double buriedmax = 4.6;\r
+\r
+ // This is hydropathy index\r
+ // Kyte, J., and Doolittle, R.F., J. Mol. Biol.\r
+ // 1157, 105-132, 1982\r
+ public static double[] hyd = {\r
+ 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9,\r
+ 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0\r
+ };\r
+ public static final double hydmax = 4.5;\r
+ public static final double hydmin = -3.9;\r
+\r
+ //public static final double hydmax = 1.38;\r
+ //public static final double hydmin = -2.53;\r
+ static final int[][] BLOSUM62 = {\r
+ {\r
+ 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,\r
+ -2, 0, -2, -1, 0, -4\r
+ },\r
+ {\r
+ -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,\r
+ -3, -1, 0, -1, -4\r
+ },\r
+ {\r
+ -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,\r
+ 3, 0, -1, -4\r
+ },\r
+ {\r
+ -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,\r
+ -3, -3, 4, 1, -1, -4\r
+ },\r
+ {\r
+ 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,\r
+ -2, -1, -3, -3, -2, -4\r
+ },\r
+ {\r
+ -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,\r
+ -2, 0, 3, -1, -4\r
+ },\r
+ {\r
+ -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,\r
+ -2, 1, 4, -1, -4\r
+ },\r
+ {\r
+ 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,\r
+ -3, -3, -1, -2, -1, -4\r
+ },\r
+ {\r
+ -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,\r
+ -3, 0, 0, -1, -4\r
+ },\r
+ {\r
+ -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,\r
+ -1, 3, -3, -3, -1, -4\r
+ },\r
+ {\r
+ -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,\r
+ -1, 1, -4, -3, -1, -4\r
+ },\r
+ {\r
+ -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,\r
+ -2, 0, 1, -1, -4\r
+ },\r
+ {\r
+ -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,\r
+ -1, 1, -3, -1, -1, -4\r
+ },\r
+ {\r
+ -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,\r
+ -1, -3, -3, -1, -4\r
+ },\r
+ {\r
+ -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,\r
+ -4, -3, -2, -2, -1, -2, -4\r
+ },\r
+ {\r
+ 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,\r
+ -2, 0, 0, 0, -4\r
+ },\r
+ {\r
+ 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,\r
+ -2, 0, -1, -1, 0, -4\r
+ },\r
+ {\r
+ -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,\r
+ 11, 2, -3, -4, -3, -2, -4\r
+ },\r
+ {\r
+ -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,\r
+ 7, -1, -3, -2, -1, -4\r
+ },\r
+ {\r
+ 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,\r
+ -1, 4, -3, -2, -1, -4\r
+ },\r
+ {\r
+ -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,\r
+ -3, 4, 1, -1, -4\r
+ },\r
+ {\r
+ -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,\r
+ -2, 1, 4, -1, -4\r
+ },\r
+ {\r
+ 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,\r
+ -1, -1, -1, -1, -1, -4\r
+ },\r
+ {\r
+ -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,\r
+ -4, -4, -4, -4, -4, -4, 1\r
+ },\r
+ };\r
+ static final int[][] PAM250 = {\r
+ {\r
+ 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,\r
+ 0, 0, 0, -8\r
+ },\r
+ {\r
+ -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,\r
+ -2, -1, 0, -1, -8\r
+ },\r
+ {\r
+ 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,\r
+ 2, 1, 0, -8\r
+ },\r
+ {\r
+ 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,\r
+ 3, 3, -1, -8\r
+ },\r
+ {\r
+ -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,\r
+ -8, 0, -2, -4, -5, -3, -8\r
+ },\r
+ {\r
+ 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,\r
+ -2, 1, 3, -1, -8\r
+ },\r
+ {\r
+ 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,\r
+ 3, 3, -1, -8\r
+ },\r
+ {\r
+ 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,\r
+ -1, 0, 0, -1, -8\r
+ },\r
+ {\r
+ -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,\r
+ -2, 1, 2, -1, -8\r
+ },\r
+ {\r
+ -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,\r
+ -1, 4, -2, -2, -1, -8\r
+ },\r
+ {\r
+ -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,\r
+ -1, 2, -3, -3, -1, -8\r
+ },\r
+ {\r
+ -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,\r
+ 1, 0, -1, -8\r
+ },\r
+ {\r
+ -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,\r
+ 2, -2, -2, -1, -8\r
+ },\r
+ {\r
+ -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,\r
+ -1, -4, -5, -2, -8\r
+ },\r
+ {\r
+ 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,\r
+ -1, -1, 0, -1, -8\r
+ },\r
+ {\r
+ 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,\r
+ 0, 0, 0, -8\r
+ },\r
+ {\r
+ 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,\r
+ 0, -1, 0, -8\r
+ },\r
+ {\r
+ -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,\r
+ 0, -6, -5, -6, -4, -8\r
+ },\r
+ {\r
+ -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,\r
+ 10, -2, -3, -4, -2, -8\r
+ },\r
+ {\r
+ 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,\r
+ -2, 4, -2, -2, -1, -8\r
+ },\r
+ {\r
+ 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,\r
+ 3, 2, -1, -8\r
+ },\r
+ {\r
+ 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,\r
+ 2, 3, -1, -8\r
+ },\r
+ {\r
+ 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,\r
+ -2, -1, -1, -1, -1, -8\r
+ },\r
+ {\r
+ -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,\r
+ -8, -8, -8, -8, -8, -8, 1\r
+ },\r
+ };\r
+ public static Hashtable ssHash = new Hashtable(); // stores the number value of the aa\r
+\r
+ static {\r
+ ssHash.put("H", Color.magenta);\r
+ ssHash.put("E", Color.yellow);\r
+ ssHash.put("-", Color.white);\r
+ ssHash.put(".", Color.white);\r
+ ssHash.put("S", Color.cyan);\r
+ ssHash.put("T", Color.blue);\r
+ ssHash.put("G", Color.pink);\r
+ ssHash.put("I", Color.pink);\r
+ ssHash.put("B", Color.yellow);\r
+ }\r
+\r
+ static final int[][] DNA = {\r
+ { 5, -4, -4, -4, 1 }, // C\r
+ { -4, 5, -4, -4, 1 }, // T\r
+ { -4, -4, 5, -4, 1 }, // A\r
+ { -4, -4, -4, 5, 1 }, // G\r
+ { 1, 1, 1, 1, 1 }, // -\r
+ };\r
+ public static Color[] pidColours = {\r
+ midBlue, new Color(153, 153, 255), \r
+ // Color.lightGray,\r
+ new Color(204, 204, 255),\r
+ };\r
+ public static float[] pidThresholds = { 80, 60, 40, };\r
+ public static Hashtable codonHash = new Hashtable();\r
+ public static Vector Lys = new Vector();\r
+ public static Vector Asn = new Vector();\r
+ public static Vector Gln = new Vector();\r
+ public static Vector His = new Vector();\r
+ public static Vector Glu = new Vector();\r
+ public static Vector Asp = new Vector();\r
+ public static Vector Tyr = new Vector();\r
+ public static Vector Thr = new Vector();\r
+ public static Vector Pro = new Vector();\r
+ public static Vector Ala = new Vector();\r
+ public static Vector Ser = new Vector();\r
+ public static Vector Arg = new Vector();\r
+ public static Vector Gly = new Vector();\r
+ public static Vector Trp = new Vector();\r
+ public static Vector Cys = new Vector();\r
+ public static Vector Ile = new Vector();\r
+ public static Vector Met = new Vector();\r
+ public static Vector Leu = new Vector();\r
+ public static Vector Val = new Vector();\r
+ public static Vector Phe = new Vector();\r
+ public static Vector STOP = new Vector();\r
+\r
+ static {\r
+ codonHash.put("K", Lys);\r
+ codonHash.put("N", Asn);\r
+ codonHash.put("Q", Gln);\r
+ codonHash.put("H", His);\r
+ codonHash.put("E", Glu);\r
+ codonHash.put("D", Asp);\r
+ codonHash.put("Y", Tyr);\r
+ codonHash.put("T", Thr);\r
+ codonHash.put("P", Pro);\r
+ codonHash.put("A", Ala);\r
+ codonHash.put("S", Ser);\r
+ codonHash.put("R", Arg);\r
+ codonHash.put("G", Gly);\r
+ codonHash.put("W", Trp);\r
+ codonHash.put("C", Cys);\r
+ codonHash.put("I", Ile);\r
+ codonHash.put("M", Met);\r
+ codonHash.put("L", Leu);\r
+ codonHash.put("V", Val);\r
+ codonHash.put("F", Phe);\r
+ codonHash.put("STOP", STOP);\r
+ }\r
+\r
+ public static Hashtable codonHash2 = new Hashtable();\r
+\r
+ static {\r
+ codonHash2.put("AAA", "K");\r
+ codonHash2.put("AAG", "K");\r
+ codonHash2.put("AAC", "N");\r
+ codonHash2.put("AAT", "N");\r
+\r
+ codonHash2.put("CAA", "E");\r
+ codonHash2.put("CAG", "E");\r
+ codonHash2.put("CAC", "H");\r
+ codonHash2.put("CAT", "H");\r
+\r
+ codonHash2.put("GAA", "Q");\r
+ codonHash2.put("GAG", "Q");\r
+ codonHash2.put("GAC", "D");\r
+ codonHash2.put("GAT", "D");\r
+\r
+ codonHash2.put("TAC", "Y");\r
+ codonHash2.put("TAT", "Y");\r
+\r
+ codonHash2.put("ACA", "T");\r
+ codonHash2.put("AAG", "T");\r
+ codonHash2.put("ACC", "T");\r
+ codonHash2.put("ACT", "T");\r
+\r
+ codonHash2.put("CCA", "P");\r
+ codonHash2.put("CCG", "P");\r
+ codonHash2.put("CCC", "P");\r
+ codonHash2.put("CCT", "P");\r
+\r
+ codonHash2.put("GCA", "A");\r
+ codonHash2.put("GCG", "A");\r
+ codonHash2.put("GCC", "A");\r
+ codonHash2.put("GCT", "A");\r
+\r
+ codonHash2.put("TCA", "S");\r
+ codonHash2.put("TCG", "S");\r
+ codonHash2.put("TCC", "S");\r
+ codonHash2.put("TCT", "S");\r
+ codonHash2.put("AGC", "S");\r
+ codonHash2.put("AGT", "S");\r
+\r
+ codonHash2.put("AGA", "R");\r
+ codonHash2.put("AGG", "R");\r
+ codonHash2.put("CGA", "R");\r
+ codonHash2.put("CGG", "R");\r
+ codonHash2.put("CGC", "R");\r
+ codonHash2.put("CGT", "R");\r
+\r
+ codonHash2.put("GGA", "G");\r
+ codonHash2.put("GGG", "G");\r
+ codonHash2.put("GGC", "G");\r
+ codonHash2.put("GGT", "G");\r
+\r
+ codonHash2.put("TGA", "*");\r
+ codonHash2.put("TAA", "*");\r
+ codonHash2.put("TAG", "*");\r
+\r
+ codonHash2.put("TGG", "W");\r
+\r
+ codonHash2.put("TGC", "C");\r
+ codonHash2.put("TGT", "C");\r
+\r
+ codonHash2.put("ATA", "I");\r
+ codonHash2.put("ATC", "I");\r
+ codonHash2.put("ATT", "I");\r
+\r
+ codonHash2.put("ATG", "M");\r
+\r
+ codonHash2.put("CTA", "L");\r
+ codonHash2.put("CTG", "L");\r
+ codonHash2.put("CTC", "L");\r
+ codonHash2.put("CTT", "L");\r
+ codonHash2.put("TTA", "L");\r
+ codonHash2.put("TTG", "L");\r
+\r
+ codonHash2.put("GTA", "V");\r
+ codonHash2.put("GTG", "V");\r
+ codonHash2.put("GTC", "V");\r
+ codonHash2.put("GTT", "V");\r
+\r
+ codonHash2.put("TTC", "F");\r
+ codonHash2.put("TTT", "F");\r
+ }\r
+\r
+ static {\r
+ Lys.addElement("AAA");\r
+ Lys.addElement("AAG");\r
+ Asn.addElement("AAC");\r
+ Asn.addElement("AAT");\r
+\r
+ Gln.addElement("CAA");\r
+ Gln.addElement("CAG");\r
+ His.addElement("CAC");\r
+ His.addElement("CAT");\r
+\r
+ Glu.addElement("GAA");\r
+ Glu.addElement("GAG");\r
+ Asp.addElement("GAC");\r
+ Asp.addElement("GAT");\r
+\r
+ Tyr.addElement("TAC");\r
+ Tyr.addElement("TAT");\r
+\r
+ Thr.addElement("ACA");\r
+ Thr.addElement("ACG");\r
+ Thr.addElement("ACC");\r
+ Thr.addElement("ACT");\r
+\r
+ Pro.addElement("CCA");\r
+ Pro.addElement("CCG");\r
+ Pro.addElement("CCC");\r
+ Pro.addElement("CCT");\r
+\r
+ Ala.addElement("GCA");\r
+ Ala.addElement("GCG");\r
+ Ala.addElement("GCC");\r
+ Ala.addElement("GCT");\r
+\r
+ Ser.addElement("TCA");\r
+ Ser.addElement("TCG");\r
+ Ser.addElement("TCC");\r
+ Ser.addElement("TCT");\r
+ Ser.addElement("AGC");\r
+ Ser.addElement("AGT");\r
+\r
+ Arg.addElement("AGA");\r
+ Arg.addElement("AGG");\r
+ Arg.addElement("CGA");\r
+ Arg.addElement("CGG");\r
+ Arg.addElement("CGC");\r
+ Arg.addElement("CGT");\r
+\r
+ Gly.addElement("GGA");\r
+ Gly.addElement("GGG");\r
+ Gly.addElement("GGC");\r
+ Gly.addElement("GGT");\r
+\r
+ STOP.addElement("TGA");\r
+ STOP.addElement("TAA");\r
+ STOP.addElement("TAG");\r
+\r
+ Trp.addElement("TGG");\r
+\r
+ Cys.addElement("TGC");\r
+ Cys.addElement("TGT");\r
+\r
+ Ile.addElement("ATA");\r
+ Ile.addElement("ATC");\r
+ Ile.addElement("ATT");\r
+\r
+ Met.addElement("ATG");\r
+\r
+ Leu.addElement("CTA");\r
+ Leu.addElement("CTG");\r
+ Leu.addElement("CTC");\r
+ Leu.addElement("CTT");\r
+ Leu.addElement("TTA");\r
+ Leu.addElement("TTG");\r
+\r
+ Val.addElement("GTA");\r
+ Val.addElement("GTG");\r
+ Val.addElement("GTC");\r
+ Val.addElement("GTT");\r
+\r
+ Phe.addElement("TTC");\r
+ Phe.addElement("TTT");\r
+ }\r
+\r
+ public static Color[][] groupColors = {\r
+ { Color.red, Color.red.brighter(), Color.red.brighter().brighter() },\r
+ {\r
+ Color.orange, Color.orange.brighter(),\r
+ Color.orange.brighter().brighter()\r
+ },\r
+ { Color.green, Color.green.brighter(), Color.green.brighter().brighter() },\r
+ { Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter() },\r
+ {\r
+ Color.magenta, Color.magenta.brighter(),\r
+ Color.magenta.brighter().brighter()\r
+ },\r
+ { Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter() },\r
+ { Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter() },\r
+ };\r
+\r
+ //Stores residue codes/names and colours and other things\r
+ public static Hashtable propHash = new Hashtable();\r
+ public static Hashtable hydrophobic = new Hashtable();\r
+ public static Hashtable polar = new Hashtable();\r
+ public static Hashtable small = new Hashtable();\r
+ public static Hashtable positive = new Hashtable();\r
+ public static Hashtable negative = new Hashtable();\r
+ public static Hashtable charged = new Hashtable();\r
+ public static Hashtable aromatic = new Hashtable();\r
+ public static Hashtable aliphatic = new Hashtable();\r
+ public static Hashtable tiny = new Hashtable();\r
+ public static Hashtable proline = new Hashtable();\r
+\r
+ static {\r
+ hydrophobic.put("I", new Integer(1));\r
+ hydrophobic.put("L", new Integer(1));\r
+ hydrophobic.put("V", new Integer(1));\r
+ hydrophobic.put("C", new Integer(1));\r
+ hydrophobic.put("A", new Integer(1));\r
+ hydrophobic.put("G", new Integer(1));\r
+ hydrophobic.put("M", new Integer(1));\r
+ hydrophobic.put("F", new Integer(1));\r
+ hydrophobic.put("Y", new Integer(1));\r
+ hydrophobic.put("W", new Integer(1));\r
+ hydrophobic.put("H", new Integer(1));\r
+ hydrophobic.put("K", new Integer(1));\r
+ hydrophobic.put("X", new Integer(1));\r
+ hydrophobic.put("-", new Integer(1));\r
+ hydrophobic.put("*", new Integer(1));\r
+ hydrophobic.put("R", new Integer(0));\r
+ hydrophobic.put("E", new Integer(0));\r
+ hydrophobic.put("Q", new Integer(0));\r
+ hydrophobic.put("D", new Integer(0));\r
+ hydrophobic.put("N", new Integer(0));\r
+ hydrophobic.put("S", new Integer(0));\r
+ hydrophobic.put("T", new Integer(0));\r
+ hydrophobic.put("P", new Integer(0));\r
+ }\r
+\r
+ static {\r
+ polar.put("Y", new Integer(1));\r
+ polar.put("W", new Integer(1));\r
+ polar.put("H", new Integer(1));\r
+ polar.put("K", new Integer(1));\r
+ polar.put("R", new Integer(1));\r
+ polar.put("E", new Integer(1));\r
+ polar.put("Q", new Integer(1));\r
+ polar.put("D", new Integer(1));\r
+ polar.put("N", new Integer(1));\r
+ polar.put("S", new Integer(1));\r
+ polar.put("T", new Integer(1));\r
+ polar.put("X", new Integer(1));\r
+ polar.put("-", new Integer(1));\r
+ polar.put("*", new Integer(1));\r
+ polar.put("I", new Integer(0));\r
+ polar.put("L", new Integer(0));\r
+ polar.put("V", new Integer(0));\r
+ polar.put("C", new Integer(0));\r
+ polar.put("A", new Integer(0));\r
+ polar.put("G", new Integer(0));\r
+ polar.put("M", new Integer(0));\r
+ polar.put("F", new Integer(0));\r
+ polar.put("P", new Integer(0));\r
+ }\r
+\r
+ static {\r
+ small.put("I", new Integer(0));\r
+ small.put("L", new Integer(0));\r
+ small.put("V", new Integer(1));\r
+ small.put("C", new Integer(1));\r
+ small.put("A", new Integer(1));\r
+ small.put("G", new Integer(1));\r
+ small.put("M", new Integer(0));\r
+ small.put("F", new Integer(0));\r
+ small.put("Y", new Integer(0));\r
+ small.put("W", new Integer(0));\r
+ small.put("H", new Integer(0));\r
+ small.put("K", new Integer(0));\r
+ small.put("R", new Integer(0));\r
+ small.put("E", new Integer(0));\r
+ small.put("Q", new Integer(0));\r
+ small.put("D", new Integer(1));\r
+ small.put("N", new Integer(1));\r
+ small.put("S", new Integer(1));\r
+ small.put("T", new Integer(1));\r
+ small.put("P", new Integer(1));\r
+ small.put("-", new Integer(1));\r
+ small.put("*", new Integer(1));\r
+ }\r
+\r
+ static {\r
+ positive.put("I", new Integer(0));\r
+ positive.put("L", new Integer(0));\r
+ positive.put("V", new Integer(0));\r
+ positive.put("C", new Integer(0));\r
+ positive.put("A", new Integer(0));\r
+ positive.put("G", new Integer(0));\r
+ positive.put("M", new Integer(0));\r
+ positive.put("F", new Integer(0));\r
+ positive.put("Y", new Integer(0));\r
+ positive.put("W", new Integer(0));\r
+ positive.put("H", new Integer(1));\r
+ positive.put("K", new Integer(1));\r
+ positive.put("R", new Integer(1));\r
+ positive.put("E", new Integer(0));\r
+ positive.put("Q", new Integer(0));\r
+ positive.put("D", new Integer(0));\r
+ positive.put("N", new Integer(0));\r
+ positive.put("S", new Integer(0));\r
+ positive.put("T", new Integer(0));\r
+ positive.put("P", new Integer(0));\r
+ positive.put("-", new Integer(1));\r
+ positive.put("*", new Integer(1));\r
+ }\r
+\r
+ static {\r
+ negative.put("I", new Integer(0));\r
+ negative.put("L", new Integer(0));\r
+ negative.put("V", new Integer(0));\r
+ negative.put("C", new Integer(0));\r
+ negative.put("A", new Integer(0));\r
+ negative.put("G", new Integer(0));\r
+ negative.put("M", new Integer(0));\r
+ negative.put("F", new Integer(0));\r
+ negative.put("Y", new Integer(0));\r
+ negative.put("W", new Integer(0));\r
+ negative.put("H", new Integer(0));\r
+ negative.put("K", new Integer(0));\r
+ negative.put("R", new Integer(0));\r
+ negative.put("E", new Integer(1));\r
+ negative.put("Q", new Integer(0));\r
+ negative.put("D", new Integer(1));\r
+ negative.put("N", new Integer(0));\r
+ negative.put("S", new Integer(0));\r
+ negative.put("T", new Integer(0));\r
+ negative.put("P", new Integer(0));\r
+ negative.put("-", new Integer(1));\r
+ negative.put("*", new Integer(1));\r
+ }\r
+\r
+ static {\r
+ charged.put("I", new Integer(0));\r
+ charged.put("L", new Integer(0));\r
+ charged.put("V", new Integer(0));\r
+ charged.put("C", new Integer(0));\r
+ charged.put("A", new Integer(0));\r
+ charged.put("G", new Integer(0));\r
+ charged.put("M", new Integer(0));\r
+ charged.put("F", new Integer(0));\r
+ charged.put("Y", new Integer(0));\r
+ charged.put("W", new Integer(0));\r
+ charged.put("H", new Integer(1));\r
+ charged.put("K", new Integer(1));\r
+ charged.put("R", new Integer(1));\r
+ charged.put("E", new Integer(1));\r
+ charged.put("Q", new Integer(0));\r
+ charged.put("D", new Integer(1));\r
+ charged.put("N", new Integer(1));\r
+ charged.put("S", new Integer(0));\r
+ charged.put("T", new Integer(0));\r
+ charged.put("P", new Integer(0));\r
+ charged.put("-", new Integer(1));\r
+ charged.put("*", new Integer(1));\r
+ }\r
+\r
+ static {\r
+ aromatic.put("I", new Integer(0));\r
+ aromatic.put("L", new Integer(0));\r
+ aromatic.put("V", new Integer(0));\r
+ aromatic.put("C", new Integer(0));\r
+ aromatic.put("A", new Integer(0));\r
+ aromatic.put("G", new Integer(0));\r
+ aromatic.put("M", new Integer(0));\r
+ aromatic.put("F", new Integer(1));\r
+ aromatic.put("Y", new Integer(1));\r
+ aromatic.put("W", new Integer(1));\r
+ aromatic.put("H", new Integer(1));\r
+ aromatic.put("K", new Integer(0));\r
+ aromatic.put("R", new Integer(0));\r
+ aromatic.put("E", new Integer(0));\r
+ aromatic.put("Q", new Integer(0));\r
+ aromatic.put("D", new Integer(0));\r
+ aromatic.put("N", new Integer(0));\r
+ aromatic.put("S", new Integer(0));\r
+ aromatic.put("T", new Integer(0));\r
+ aromatic.put("P", new Integer(0));\r
+ aromatic.put("-", new Integer(1));\r
+ aromatic.put("*", new Integer(1));\r
+ }\r
+\r
+ static {\r
+ aliphatic.put("I", new Integer(1));\r
+ aliphatic.put("L", new Integer(1));\r
+ aliphatic.put("V", new Integer(1));\r
+ aliphatic.put("C", new Integer(0));\r
+ aliphatic.put("A", new Integer(0));\r
+ aliphatic.put("G", new Integer(0));\r
+ aliphatic.put("M", new Integer(0));\r
+ aliphatic.put("F", new Integer(0));\r
+ aliphatic.put("Y", new Integer(0));\r
+ aliphatic.put("W", new Integer(0));\r
+ aliphatic.put("H", new Integer(0));\r
+ aliphatic.put("K", new Integer(0));\r
+ aliphatic.put("R", new Integer(0));\r
+ aliphatic.put("E", new Integer(0));\r
+ aliphatic.put("Q", new Integer(0));\r
+ aliphatic.put("D", new Integer(0));\r
+ aliphatic.put("N", new Integer(0));\r
+ aliphatic.put("S", new Integer(0));\r
+ aliphatic.put("T", new Integer(0));\r
+ aliphatic.put("P", new Integer(0));\r
+ aliphatic.put("-", new Integer(1));\r
+ aliphatic.put("*", new Integer(1));\r
+ }\r
\r
- //Stores residue codes/names and colours and other things\r
- public static Hashtable aaHash = new Hashtable(); // stores the number value of the aa\r
- public static Hashtable aa3Hash = new Hashtable();\r
- public static Hashtable aa2Triplet = new Hashtable();\r
- public static Hashtable nucleotideHash = new Hashtable();\r
-\r
- static {\r
- aaHash.put("A", new Integer(0));\r
- aaHash.put("R", new Integer(1));\r
- aaHash.put("N", new Integer(2));\r
- aaHash.put("D", new Integer(3));\r
- aaHash.put("C", new Integer(4));\r
- aaHash.put("Q", new Integer(5));\r
- aaHash.put("E", new Integer(6));\r
- aaHash.put("G", new Integer(7));\r
- aaHash.put("H", new Integer(8));\r
- aaHash.put("I", new Integer(9));\r
- aaHash.put("L", new Integer(10));\r
- aaHash.put("K", new Integer(11));\r
- aaHash.put("M", new Integer(12));\r
- aaHash.put("F", new Integer(13));\r
- aaHash.put("P", new Integer(14));\r
- aaHash.put("S", new Integer(15));\r
- aaHash.put("T", new Integer(16));\r
- aaHash.put("W", new Integer(17));\r
- aaHash.put("Y", new Integer(18));\r
- aaHash.put("V", new Integer(19));\r
- aaHash.put("B", new Integer(20));\r
- aaHash.put("Z", new Integer(21));\r
- aaHash.put("X", new Integer(22));\r
- aaHash.put("a", new Integer(0));\r
- aaHash.put("r", new Integer(1));\r
- aaHash.put("n", new Integer(2));\r
- aaHash.put("d", new Integer(3));\r
- aaHash.put("c", new Integer(4));\r
- aaHash.put("q", new Integer(5));\r
- aaHash.put("e", new Integer(6));\r
- aaHash.put("g", new Integer(7));\r
- aaHash.put("h", new Integer(8));\r
- aaHash.put("i", new Integer(9));\r
- aaHash.put("l", new Integer(10));\r
- aaHash.put("k", new Integer(11));\r
- aaHash.put("m", new Integer(12));\r
- aaHash.put("f", new Integer(13));\r
- aaHash.put("p", new Integer(14));\r
- aaHash.put("s", new Integer(15));\r
- aaHash.put("t", new Integer(16));\r
- aaHash.put("w", new Integer(17));\r
- aaHash.put("y", new Integer(18));\r
- aaHash.put("v", new Integer(19));\r
- aaHash.put("b", new Integer(20));\r
- aaHash.put("z", new Integer(21));\r
- aaHash.put("x", new Integer(22));\r
- aaHash.put("-", new Integer(23));\r
- aaHash.put("*", new Integer(23));\r
- aaHash.put(".", new Integer(23));\r
- aaHash.put(" ", new Integer(23));\r
- }\r
-\r
- static {\r
- nucleotideHash.put("A", new Integer(0));\r
- nucleotideHash.put("C", new Integer(1));\r
- nucleotideHash.put("G", new Integer(2));\r
- nucleotideHash.put("T", new Integer(3));\r
- nucleotideHash.put("U", new Integer(4));\r
- }\r
-\r
- // These numbers should correspond to the indices in the Color hashes\r
- public static Hashtable aaSpecialsHash = new Hashtable();\r
- static {\r
- aaSpecialsHash.put("-", new Integer(23));\r
- aaSpecialsHash.put("*", new Integer(24));\r
- aaSpecialsHash.put(".", new Integer(25));\r
- aaSpecialsHash.put(" ", new Integer(26));\r
- }\r
-\r
- static {\r
- aa3Hash.put("ALA", new Integer(0));\r
- aa3Hash.put("ARG", new Integer(1));\r
- aa3Hash.put("ASN", new Integer(2));\r
- aa3Hash.put("ASP", new Integer(3)); //D\r
- aa3Hash.put("CYS", new Integer(4));\r
- aa3Hash.put("GLN", new Integer(5)); //Q\r
- aa3Hash.put("GLU", new Integer(6)); // E\r
- aa3Hash.put("GLY", new Integer(7));\r
- aa3Hash.put("HIS", new Integer(8));\r
- aa3Hash.put("ILE", new Integer(9));\r
- aa3Hash.put("LEU", new Integer(10));\r
- aa3Hash.put("LYS", new Integer(11));\r
- aa3Hash.put("MET", new Integer(12));\r
- aa3Hash.put("PHE", new Integer(13));\r
- aa3Hash.put("PRO", new Integer(14));\r
- aa3Hash.put("SER", new Integer(15));\r
- aa3Hash.put("THR", new Integer(16));\r
- aa3Hash.put("TRP", new Integer(17));\r
- aa3Hash.put("TYR", new Integer(18));\r
- aa3Hash.put("VAL", new Integer(19));\r
- aa3Hash.put("B", new Integer(20));\r
- aa3Hash.put("Z", new Integer(21));\r
- aa3Hash.put("X", new Integer(22));\r
- aa3Hash.put("-", new Integer(23));\r
- aa3Hash.put("*", new Integer(23));\r
- aa3Hash.put(".", new Integer(23));\r
- aa3Hash.put(" ", new Integer(23));\r
- }\r
-\r
- static{\r
- aa2Triplet.put("A", "ALA");\r
- aa2Triplet.put("R", "ARG");\r
- aa2Triplet.put("N", "ASN");\r
- aa2Triplet.put("D", "ASP");\r
- aa2Triplet.put("C", "CYS");\r
- aa2Triplet.put("Q", "GLN");\r
- aa2Triplet.put("E", "GLU");\r
- aa2Triplet.put("G", "GLY");\r
- aa2Triplet.put("H", "HIS");\r
- aa2Triplet.put("I", "ILE");\r
- aa2Triplet.put("L", "LEU");\r
- aa2Triplet.put("K", "LYS");\r
- aa2Triplet.put("M", "MET");\r
- aa2Triplet.put("F", "PHE");\r
- aa2Triplet.put("P", "PRO");\r
- aa2Triplet.put("S", "SER");\r
- aa2Triplet.put("T", "THR");\r
- aa2Triplet.put("W", "TRP");\r
- aa2Triplet.put("Y", "TYR");\r
- aa2Triplet.put("V", "VAL");\r
- }\r
-\r
- public static String aa[] = {\r
- "A","R","N","D","C","Q","E","G","H","I","L","K","M","F","P","S","T","W","Y","V","B","Z","X","_","*","."," "\r
- };\r
- public static Color midBlue = new Color(100,100,255);\r
- public static Vector scaleColours = new Vector();\r
- static {\r
- scaleColours.addElement(new Color(114,0,147));\r
- scaleColours.addElement(new Color(156,0,98));\r
- scaleColours.addElement(new Color(190,0,0));\r
- scaleColours.addElement(Color.red);\r
- scaleColours.addElement(new Color(255,125,0));\r
- scaleColours.addElement(Color.orange);\r
- scaleColours.addElement(new Color(255,194,85));\r
- scaleColours.addElement(Color.yellow);\r
- scaleColours.addElement(new Color(255,255,181));\r
- scaleColours.addElement(Color.white);\r
- }\r
-\r
- public static Color[] taylor = {\r
- new Color(204,255,0), // A Greenish-yellowy-yellow\r
- new Color(0,0,255), // R Blueish-bluey-blue\r
- new Color(204,0,255), // N Blueish-reddy-blue\r
- new Color(255,0,0), // D Reddish-reddy-red\r
- new Color(255,255,0), // C Yellowish-yellowy-yellow\r
- new Color(255,0,204), // Q Reddish-bluey-red\r
- new Color(255,0,102), // E Blueish-reddy-red\r
- new Color(255,153,0), // G Yellowy-reddy-yellow\r
- new Color(0,102,255), // H Greenish-bluey-blue\r
- new Color(102,255,0), // I Greenish-yellowy-green\r
- new Color(51,255,0), // L Yellowish-greeny-green\r
- new Color(102,0,255), // K Reddish-bluey-blue\r
- new Color(0,255,0), // M Greenish-greeny-green\r
- new Color(0,255,102), // F Blueish-greeny-green\r
- new Color(255,204,0), // P Reddish-yellowy-yellow\r
- new Color(255,51,0), // S Yellowish-reddy-red\r
- new Color(255,102,0), // T Reddish-yellowy-red\r
- new Color(0,204,255), // W Blueish-greeny-green\r
- new Color(0,255,204), // Y Greenish-bluey-green\r
- new Color(153,255,0), // V Yellowish-greeny-yellow\r
- Color.white, // B\r
- Color.white, // Z\r
- Color.white, // X\r
- Color.white, // -\r
- Color.white, // *\r
- Color.white // .\r
- };\r
-\r
- public static Color[] nucleotide = {\r
- new Color(100,247,63), // A\r
- new Color(255,179,64), // C\r
- new Color(235,65,60), // G\r
- new Color(60,136,238), // T\r
- new Color(60,136,238) // U\r
- };\r
-\r
- public static Color[] color = {\r
- Color.pink, // A\r
- midBlue, // R\r
- Color.green, // N\r
- Color.red, // D\r
- Color.yellow, // C\r
- Color.green, // Q\r
- Color.red, // E\r
- Color.magenta, // G\r
- Color.red, // H\r
- Color.pink, // I\r
- Color.pink, // L\r
- midBlue, // K\r
- Color.pink, // M\r
- Color.orange, // F\r
- Color.magenta, // P\r
- Color.green, // S\r
- Color.green, // T\r
- Color.orange, // W\r
- Color.orange, // Y\r
- Color.pink, // V\r
- Color.white, // B\r
- Color.white, // Z\r
- Color.white, // X\r
- Color.white, // -\r
- Color.white, // *\r
- Color.white, // .\r
- Color.white // ' '\r
- };\r
-\r
- // Dunno where I got these numbers from\r
- public static double[] hyd2 = {\r
- 0.62, //A\r
- 0.29, //R\r
- -0.90, //N\r
- -0.74, //D\r
- 1.19, //C\r
- 0.48, //Q\r
- -0.40, //E\r
- 1.38, //G\r
- -1.50, //H\r
- 1.06, //I\r
- 0.64, //L\r
- -0.78, //K\r
- 0.12, //M\r
- -0.85, //F\r
- -2.53, //P\r
- -0.18, //S\r
- -0.05, //T\r
- 1.08, //W\r
- 0.81, //Y\r
- 0.0, //V\r
- 0.26, //B\r
- 0.0, //Z\r
- 0.0 //X\r
- };\r
- public static double[] helix = {\r
- 1.42,\r
- 0.98,\r
- 0.67,\r
- 1.01,\r
- 0.70,\r
- 1.11,\r
- 1.51,\r
- 0.57,\r
- 1.00,\r
- 1.08,\r
- 1.21,\r
- 1.16,\r
- 1.45,\r
- 1.13,\r
- 0.57,\r
- 0.77,\r
- 0.83,\r
- 1.08,\r
- 0.69,\r
- 1.06,\r
- 0.84,\r
- 1.31,\r
- 1.00,\r
- 0.0\r
- };\r
- public static double helixmin = 0.57;\r
- public static double helixmax = 1.51;\r
-\r
- public static double[] strand = {\r
- 0.83,0.93,0.89,0.54,1.19,1.10,0.37,\r
- 0.75,0.87,1.60,1.30,0.74,1.05,1.38,0.55,\r
- 0.75,1.19,1.37,1.47,1.70,0.72,0.74,1.0,0.0};\r
-\r
- public static double strandmin = 0.37;\r
- public static double strandmax = 1.7;\r
-\r
- public static double[] turn = {\r
- 0.66,0.95,1.56,1.46,1.19,0.98,0.74,\r
- 1.56,0.95,0.47,0.59,1.01,0.60,0.60,1.52,\r
- 1.43,0.96,0.96,1.14,0.50,1.51,0.86,1.00,0,0};\r
-\r
- public static double turnmin = 0.47;\r
- public static double turnmax = 1.56;\r
-\r
- public static double[] buried = {\r
- 1.7,\r
- 0.1,\r
- 0.4,\r
- 0.4,\r
- 4.6,\r
- 0.3,\r
- 0.3,\r
- 1.8,\r
- 0.8,\r
- 3.1,\r
- 2.4,\r
- 0.05,\r
- 1.9,\r
- 2.2,\r
- 0.6,\r
- 0.8,0.7,1.6,0.5,2.9,0.4,0.3,\r
- 1.358,\r
- 0.00\r
- };\r
-\r
- public static double buriedmin = 0.05;\r
- public static double buriedmax = 4.6;\r
-\r
- // This is hydropathy index\r
- // Kyte, J., and Doolittle, R.F., J. Mol. Biol.\r
- // 1157, 105-132, 1982\r
-\r
- public static double hyd[] = {\r
- 1.8,\r
- -4.5,\r
- -3.5,\r
- -3.5,\r
- 2.5,\r
- -3.5,\r
- -3.5,\r
- -0.4,\r
- -3.2,\r
- 4.5,\r
- 3.8,\r
- -3.9,\r
- 1.9,\r
- 2.8,\r
- -1.6,\r
- -0.8,\r
- -0.7,\r
- -0.9,\r
- -1.3,\r
- 4.2,\r
- -3.5,\r
- -3.5,\r
- -0.49,\r
- 0.0\r
- };\r
-\r
- public static final double hydmax = 4.5;\r
- public static final double hydmin = -3.9;\r
-\r
- public static double getHydmax() {\r
- return hydmax;\r
- }\r
- public static double getHydmin() {\r
- return hydmin;\r
- }\r
- public static double[] getHyd() {\r
- return hyd;\r
- }\r
- //public static final double hydmax = 1.38;\r
- //public static final double hydmin = -2.53;\r
-\r
- static final int[][] BLOSUM62 = {\r
- //A R N D C Q E G H I L K M F P S T W Y V B Z X -\r
- { 4 ,-1, -2 ,-2 , 0 ,-1 ,-1 , 0 ,-2 ,-1 ,-1 ,-1 ,-1 ,-2 ,-1 , 1 , 0 ,-3 ,-2 , 0 ,-2, -1 , 0 ,-4},\r
- {-1 , 5 , 0 ,-2 ,-3 , 1 , 0 ,-2 , 0 ,-3 ,-2 , 2 ,-1 ,-3 ,-2 ,-1 ,-1 ,-3 ,-2 ,-3 ,-1 , 0 ,-1 ,-4 },\r
- {-2 , 0 , 6 , 1 ,-3 , 0 , 0 , 0 , 1 ,-3 ,-3 , 0 ,-2 ,-3 ,-2 , 1 , 0 ,-4 ,-2 ,-3 , 3 , 0 ,-1 ,-4 },\r
- {-2 ,-2 , 1 , 6 ,-3 , 0 , 2 ,-1 ,-1 ,-3 ,-4 ,-1 ,-3 ,-3 ,-1 , 0 ,-1 ,-4 ,-3 ,-3 , 4 , 1 ,-1 ,-4 },\r
- { 0 , 3 ,-3 ,-3 , 9 ,-3 ,-4 ,-3 ,-3 ,-1 ,-1 ,-3 ,-1 ,-2 ,-3 ,-1 ,-1 ,-2 ,-2 ,-1 ,-3 ,-3 ,-2 ,-4 },\r
- {-1 , 1 , 0 , 0 ,-3 , 5 , 2 ,-2 , 0 ,-3 ,-2 , 1 , 0 ,-3 ,-1 , 0 ,-1 ,-2 ,-1 ,-2 , 0 , 3 ,-1 ,-4 },\r
- {-1 , 0 , 0 , 2 ,-4 , 2 , 5 ,-2 , 0 ,-3 ,-3 , 1 ,-2 ,-3 ,-1 , 0 ,-1 ,-3 ,-2 ,-2 , 1 , 4 ,-1 ,-4 },\r
- { 0 ,-2 , 0 ,-1 ,-3 ,-2 ,-2 , 6 ,-2 ,-4 ,-4 ,-2 ,-3 ,-3 ,-2 , 0 ,-2 ,-2 ,-3 ,-3 ,-1 ,-2 ,-1 ,-4 },\r
- {-2 , 0 , 1 ,-1 ,-3 , 0 , 0 ,-2 , 8 ,-3 ,-3 ,-1 ,-2 ,-1 ,-2 ,-1 ,-2 ,-2 , 2 ,-3 , 0 , 0 ,-1 ,-4 },\r
- {-1 ,-3 ,-3 ,-3 ,-1 ,-3 ,-3 ,-4 ,-3 , 4 , 2 ,-3 , 1 , 0 ,-3 ,-2 ,-1 ,-3 ,-1 , 3 ,-3 ,-3 ,-1 ,-4 },\r
- {-1 ,-2 ,-3 ,-4 ,-1 ,-2 ,-3 ,-4 ,-3 , 2 , 4 ,-2 , 2 , 0 ,-3 ,-2 ,-1 ,-2 ,-1 , 1 ,-4 ,-3 ,-1 ,-4 },\r
- {-1 , 2 , 0 ,-1 ,-3 , 1 , 1 ,-2 ,-1 ,-3 ,-2 , 5 ,-1 ,-3 ,-1 , 0 ,-1 ,-3 ,-2 ,-2 , 0 , 1 ,-1 ,-4 },\r
- {-1 ,-1 ,-2 ,-3 ,-1 , 0 ,-2 ,-3 ,-2 , 1 , 2 ,-1 , 5 , 0 ,-2 ,-1 ,-1 ,-1 ,-1 , 1 ,-3 ,-1 ,-1 ,-4 },\r
- {-2 ,-3 ,-3 ,-3 ,-2 ,-3 ,-3 ,-3 ,-1 , 0 , 0 ,-3 , 0 , 6 ,-4 ,-2 ,-2 , 1 , 3 ,-1 ,-3 ,-3 ,-1 ,-4 },\r
- {-1 ,-2 ,-2 ,-1 ,-3 ,-1 ,-1 ,-2 ,-2 ,-3 ,-3 ,-1 ,-2 ,-4 , 7 ,-1 ,-1 ,-4 ,-3 ,-2 ,-2 ,-1 ,-2 ,-4 },\r
- { 1 ,-1 , 1 , 0 ,-1 , 0 , 0 , 0 ,-1 ,-2 ,-2 , 0 ,-1 ,-2 ,-1 , 4 , 1 ,-3 ,-2 ,-2 , 0 , 0 , 0 ,-4 },\r
- { 0 ,-1 , 0 ,-1 ,-1 ,-1 ,-1 ,-2 ,-2 ,-1 ,-1 ,-1 ,-1 ,-2 ,-1 , 1 , 5 ,-2 ,-2 , 0 ,-1 ,-1 , 0 ,-4 },\r
- {-3 ,-3 ,-4 ,-4 ,-2 ,-2 ,-3 ,-2 ,-2 ,-3 ,-2 ,-3 ,-1 , 1 ,-4 ,-3 ,-2 ,11 , 2 ,-3 ,-4 ,-3 ,-2 ,-4 },\r
- {-2 ,-2 ,-2 ,-3 ,-2 ,-1 ,-2 ,-3 , 2 ,-1 ,-1 ,-2 ,-1 , 3 ,-3 ,-2 ,-2 , 2 , 7 ,-1 ,-3 ,-2 ,-1 ,-4 },\r
- { 0 ,-3 ,-3 ,-3 ,-1 ,-2 ,-2 ,-3 ,-3 , 3 , 1 ,-2 , 1 ,-1 ,-2 ,-2 , 0 ,-3 ,-1 , 4 ,-3 ,-2 ,-1 ,-4 },\r
- {-2 ,-1 , 3 , 4 ,-3 , 0 , 1 ,-1 , 0 ,-3 ,-4 , 0 ,-3 ,-3 ,-2 , 0 ,-1 ,-4 ,-3 ,-3 , 4 , 1 ,-1 ,-4 },\r
- {-1 , 0 , 0 , 1 ,-3 , 3 , 4 ,-2 , 0 ,-3 ,-3 , 1 ,-1 ,-3 ,-1 , 0 ,-1 ,-3 ,-2 ,-2 , 1 , 4 ,-1 ,-4 },\r
- { 0 ,-1 ,-1 ,-1 ,-2 ,-1 ,-1 ,-1 ,-1 ,-1 ,-1 ,-1 ,-1 ,-1 ,-2 , 0 , 0 ,-2 ,-1 ,-1 ,-1 ,-1 ,-1 ,-4 },\r
- {-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 , 1 },\r
- };\r
- static final int[][] PAM250 = {\r
- { 2,-2 ,0 ,0,-2 ,0 ,0 ,1,-1,-1,-2,-1,-1,-3 ,1 ,1 ,1,-6,-3 ,0 ,0 ,0 ,0,-8},\r
- { -2 ,6 ,0,-1,-4 ,1,-1,-3 ,2,-2,-3 ,3 ,0,-4 ,0 ,0,-1 ,2,-4,-2,-1 ,0,-1,-8},\r
- { 0 ,0 ,2 ,2,-4 ,1 ,1 ,0 ,2,-2,-3 ,1,-2,-3 ,0 ,1 ,0,-4,-2,-2 ,2 ,1 ,0,-8},\r
- { 0,-1 ,2 ,4,-5 ,2 ,3 ,1 ,1,-2,-4 ,0,-3,-6,-1 ,0 ,0,-7,-4,-2 ,3 ,3,-1,-8},\r
- { -2,-4,-4,-5,12,-5,-5,-3,-3,-2,-6,-5,-5,-4,-3 ,0,-2,-8 ,0,-2,-4,-5,-3,-8},\r
- { 0 ,1 ,1 ,2,-5 ,4 ,2,-1 ,3,-2,-2 ,1,-1,-5 ,0,-1,-1,-5,-4,-2 ,1 ,3,-1,-8},\r
- { 0,-1 ,1 ,3,-5 ,2 ,4 ,0 ,1,-2,-3 ,0,-2,-5,-1 ,0 ,0,-7,-4,-2 ,3 ,3,-1,-8},\r
- { 1,-3 ,0 ,1,-3,-1 ,0 ,5,-2,-3,-4,-2,-3,-5 ,0 ,1 ,0,-7,-5,-1 ,0 ,0,-1,-8},\r
- { -1 ,2 ,2 ,1,-3 ,3 ,1,-2 ,6,-2,-2 ,0,-2,-2 ,0,-1,-1,-3 ,0,-2 ,1 ,2,-1,-8},\r
- { -1,-2,-2,-2,-2,-2,-2,-3,-2 ,5 ,2,-2 ,2 ,1,-2,-1 ,0,-5,-1 ,4,-2,-2,-1,-8},\r
- { -2,-3,-3,-4,-6,-2,-3,-4,-2 ,2 ,6,-3 ,4 ,2,-3,-3,-2,-2,-1 ,2,-3,-3,-1,-8},\r
- { -1 ,3 ,1 ,0,-5 ,1 ,0,-2 ,0,-2,-3 ,5 ,0,-5,-1 ,0 ,0,-3,-4,-2 ,1 ,0,-1,-8},\r
- { -1 ,0,-2,-3,-5,-1,-2,-3,-2 ,2 ,4 ,0 ,6 ,0,-2,-2,-1,-4,-2 ,2,-2,-2,-1,-8},\r
- { -3,-4,-3,-6,-4,-5,-5,-5,-2 ,1 ,2,-5 ,0 ,9,-5,-3,-3 ,0 ,7,-1,-4,-5,-2,-8},\r
- { 1 ,0 ,0,-1,-3 ,0,-1 ,0 ,0,-2,-3,-1,-2,-5 ,6 ,1 ,0,-6,-5,-1,-1 ,0,-1,-8},\r
- { 1 ,0 ,1 ,0 ,0,-1 ,0 ,1,-1,-1,-3 ,0,-2,-3 ,1 ,2 ,1,-2,-3,-1 ,0 ,0 ,0,-8},\r
- { 1,-1 ,0 ,0,-2,-1 ,0 ,0,-1 ,0,-2 ,0,-1,-3 ,0 ,1 ,3,-5,-3 ,0 ,0,-1 ,0,-8},\r
- { -6 ,2,-4,-7,-8,-5,-7,-7,-3,-5,-2,-3,-4 ,0,-6,-2,-5,17 ,0,-6,-5,-6,-4,-8},\r
- { -3,-4,-2,-4 ,0,-4,-4,-5 ,0,-1,-1,-4,-2 ,7,-5,-3,-3 ,0,10,-2,-3,-4,-2,-8},\r
- { 0,-2,-2,-2,-2,-2,-2,-1,-2 ,4 ,2,-2 ,2,-1,-1,-1 ,0,-6,-2 ,4,-2,-2,-1,-8},\r
- { 0,-1 ,2 ,3,-4 ,1 ,3 ,0 ,1,-2,-3 ,1,-2,-4,-1 ,0 ,0,-5,-3,-2 ,3 ,2,-1,-8},\r
- { 0 ,0 ,1 ,3,-5 ,3 ,3 ,0 ,2,-2,-3 ,0,-2,-5 ,0 ,0,-1,-6,-4,-2 ,2 ,3,-1,-8},\r
- { 0,-1 ,0,-1,-3,-1,-1,-1,-1,-1,-1,-1,-1,-2,-1 ,0 ,0,-4,-2,-1,-1,-1,-1,-8},\r
- { -8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8 ,1},\r
- };\r
-\r
- public static Hashtable ssHash = new Hashtable(); // stores the number value of the aa\r
-\r
- static {\r
- ssHash.put("H", Color.magenta);\r
- ssHash.put("E", Color.yellow);\r
- ssHash.put("-", Color.white);\r
- ssHash.put(".", Color.white);\r
- ssHash.put("S", Color.cyan);\r
- ssHash.put("T", Color.blue);\r
- ssHash.put("G", Color.pink);\r
- ssHash.put("I", Color.pink);\r
- ssHash.put("B", Color.yellow);\r
- }\r
- static final int[][] DNA = {\r
- // C T A G -\r
- { 5,-4,-4,-4, 1},// C\r
- {-4, 5,-4,-4, 1},// T\r
- {-4,-4, 5,-4, 1},// A\r
- {-4,-4,-4, 5, 1},// G\r
- { 1, 1, 1, 1, 1},// -\r
- };\r
- public static Hashtable getAAHash() {\r
- return aaHash;\r
- }\r
- public static Hashtable getAA3Hash() {\r
- return aa3Hash;\r
- }\r
- public static int[][] getDNA() {\r
- return ResidueProperties.DNA;\r
- }\r
- public static int[][] getBLOSUM62() {\r
- return ResidueProperties.BLOSUM62;\r
- }\r
- public static int getPAM250(String A1, String A2) {\r
- Integer pog1 = (Integer)aaHash.get(A1);\r
- Integer pog2 = (Integer)aaHash.get(A2);\r
- int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];\r
- return pog ;\r
- }\r
- public static int getBLOSUM62(String A1, String A2) {\r
- int pog = 0;\r
- try {\r
- Integer pog1 = (Integer)aaHash.get(A1);\r
- Integer pog2 = (Integer)aaHash.get(A2);\r
- pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];\r
- } catch (Exception e) {\r
- //System.out.println("Unknown residue in " + A1 + " " + A2);\r
+ static {\r
+ tiny.put("I", new Integer(0));\r
+ tiny.put("L", new Integer(0));\r
+ tiny.put("V", new Integer(0));\r
+ tiny.put("C", new Integer(0));\r
+ tiny.put("A", new Integer(1));\r
+ tiny.put("G", new Integer(1));\r
+ tiny.put("M", new Integer(0));\r
+ tiny.put("F", new Integer(0));\r
+ tiny.put("Y", new Integer(0));\r
+ tiny.put("W", new Integer(0));\r
+ tiny.put("H", new Integer(0));\r
+ tiny.put("K", new Integer(0));\r
+ tiny.put("R", new Integer(0));\r
+ tiny.put("E", new Integer(0));\r
+ tiny.put("Q", new Integer(0));\r
+ tiny.put("D", new Integer(0));\r
+ tiny.put("N", new Integer(0));\r
+ tiny.put("S", new Integer(1));\r
+ tiny.put("T", new Integer(0));\r
+ tiny.put("P", new Integer(0));\r
+ tiny.put("-", new Integer(1));\r
+ tiny.put("*", new Integer(1));\r
}\r
- return pog ;\r
- }\r
-\r
- public static Color[] pidColours = {\r
- midBlue,\r
- new Color(153,153,255),\r
- // Color.lightGray,\r
- new Color(204,204,255),\r
- };\r
- public static float[] pidThresholds = {\r
- 80,\r
- 60,\r
- 40,\r
- } ;\r
- private ResidueProperties() {}\r
-\r
- public static Hashtable codonHash = new Hashtable();\r
-\r
- public static Vector Lys = new Vector();\r
- public static Vector Asn = new Vector();\r
- public static Vector Gln = new Vector();\r
- public static Vector His = new Vector();\r
- public static Vector Glu = new Vector();\r
- public static Vector Asp = new Vector();\r
- public static Vector Tyr = new Vector();\r
- public static Vector Thr = new Vector();\r
- public static Vector Pro = new Vector();\r
- public static Vector Ala = new Vector();\r
- public static Vector Ser = new Vector();\r
- public static Vector Arg = new Vector();\r
- public static Vector Gly = new Vector();\r
- public static Vector Trp = new Vector();\r
- public static Vector Cys = new Vector();\r
- public static Vector Ile = new Vector();\r
- public static Vector Met = new Vector();\r
- public static Vector Leu = new Vector();\r
- public static Vector Val = new Vector();\r
- public static Vector Phe = new Vector();\r
- public static Vector STOP = new Vector();\r
-\r
- static {\r
- codonHash.put("K",Lys);\r
- codonHash.put("N",Asn);\r
- codonHash.put("Q",Gln);\r
- codonHash.put("H",His);\r
- codonHash.put("E",Glu);\r
- codonHash.put("D",Asp);\r
- codonHash.put("Y",Tyr);\r
- codonHash.put("T",Thr);\r
- codonHash.put("P",Pro);\r
- codonHash.put("A",Ala);\r
- codonHash.put("S",Ser);\r
- codonHash.put("R",Arg);\r
- codonHash.put("G",Gly);\r
- codonHash.put("W",Trp);\r
- codonHash.put("C",Cys);\r
- codonHash.put("I",Ile);\r
- codonHash.put("M",Met);\r
- codonHash.put("L",Leu);\r
- codonHash.put("V",Val);\r
- codonHash.put("F",Phe);\r
- codonHash.put("STOP",STOP);\r
- }\r
-\r
- public static Vector getCodons(String res) {\r
- if (codonHash.containsKey(res))\r
- return (Vector)codonHash.get(res);\r
- return null;\r
- }\r
-\r
- public static String codonTranslate(String codon) {\r
- Enumeration e = codonHash.keys();\r
- while (e.hasMoreElements()) {\r
- String key = (String)e.nextElement();\r
- Vector tmp = (Vector)codonHash.get(key);\r
- if (tmp.contains(codon)) {\r
- return key;\r
- }\r
+\r
+ static {\r
+ proline.put("I", new Integer(0));\r
+ proline.put("L", new Integer(0));\r
+ proline.put("V", new Integer(0));\r
+ proline.put("C", new Integer(0));\r
+ proline.put("A", new Integer(0));\r
+ proline.put("G", new Integer(0));\r
+ proline.put("M", new Integer(0));\r
+ proline.put("F", new Integer(0));\r
+ proline.put("Y", new Integer(0));\r
+ proline.put("W", new Integer(0));\r
+ proline.put("H", new Integer(0));\r
+ proline.put("K", new Integer(0));\r
+ proline.put("R", new Integer(0));\r
+ proline.put("E", new Integer(0));\r
+ proline.put("Q", new Integer(0));\r
+ proline.put("D", new Integer(0));\r
+ proline.put("N", new Integer(0));\r
+ proline.put("S", new Integer(0));\r
+ proline.put("T", new Integer(0));\r
+ proline.put("P", new Integer(1));\r
+ proline.put("-", new Integer(1));\r
+ proline.put("*", new Integer(1));\r
+ }\r
+\r
+ static {\r
+ propHash.put("hydrophobic", hydrophobic);\r
+ propHash.put("small", small);\r
+ propHash.put("positive", positive);\r
+ propHash.put("negative", negative);\r
+ propHash.put("charged", charged);\r
+ propHash.put("aromatic", aromatic);\r
+ propHash.put("aliphatic", aliphatic);\r
+ propHash.put("tiny", tiny);\r
+ propHash.put("proline", proline);\r
+ propHash.put("polar", polar);\r
+ }\r
+\r
+ public static Hashtable chainColours = new Hashtable();\r
+\r
+ static {\r
+ chainColours.put("A", Color.red);\r
+ chainColours.put("B", Color.orange);\r
+ chainColours.put("C", Color.yellow);\r
+ chainColours.put("D", Color.green);\r
+ chainColours.put("E", Color.cyan);\r
+ chainColours.put("F", Color.blue);\r
+ chainColours.put("G", Color.magenta);\r
+ chainColours.put("H", Color.pink);\r
+ }\r
+\r
+ private ResidueProperties() {\r
+ }\r
+\r
+ public static double getHydmax() {\r
+ return hydmax;\r
+ }\r
+\r
+ public static double getHydmin() {\r
+ return hydmin;\r
+ }\r
+\r
+ public static double[] getHyd() {\r
+ return hyd;\r
+ }\r
+\r
+ public static Hashtable getAAHash() {\r
+ return aaHash;\r
+ }\r
+\r
+ public static Hashtable getAA3Hash() {\r
+ return aa3Hash;\r
+ }\r
+\r
+ public static int[][] getDNA() {\r
+ return ResidueProperties.DNA;\r
+ }\r
+\r
+ public static int[][] getBLOSUM62() {\r
+ return ResidueProperties.BLOSUM62;\r
+ }\r
+\r
+ public static int getPAM250(String A1, String A2) {\r
+ Integer pog1 = (Integer) aaHash.get(A1);\r
+ Integer pog2 = (Integer) aaHash.get(A2);\r
+ int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];\r
+\r
+ return pog;\r
+ }\r
+\r
+ public static int getBLOSUM62(String A1, String A2) {\r
+ int pog = 0;\r
+\r
+ try {\r
+ Integer pog1 = (Integer) aaHash.get(A1);\r
+ Integer pog2 = (Integer) aaHash.get(A2);\r
+ pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];\r
+ } catch (Exception e) {\r
+ //System.out.println("Unknown residue in " + A1 + " " + A2);\r
+ }\r
+\r
+ return pog;\r
+ }\r
+\r
+ public static Vector getCodons(String res) {\r
+ if (codonHash.containsKey(res)) {\r
+ return (Vector) codonHash.get(res);\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+ public static String codonTranslate(String codon) {\r
+ Enumeration e = codonHash.keys();\r
+\r
+ while (e.hasMoreElements()) {\r
+ String key = (String) e.nextElement();\r
+ Vector tmp = (Vector) codonHash.get(key);\r
+\r
+ if (tmp.contains(codon)) {\r
+ return key;\r
+ }\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+ public static Hashtable getChainColours() {\r
+ return chainColours;\r
}\r
- return null;\r
- }\r
- public static Hashtable codonHash2 = new Hashtable();\r
- static {\r
- codonHash2.put("AAA","K");\r
- codonHash2.put("AAG","K");\r
- codonHash2.put("AAC","N");\r
- codonHash2.put("AAT","N");\r
-\r
- codonHash2.put("CAA","E");\r
- codonHash2.put("CAG","E");\r
- codonHash2.put("CAC","H");\r
- codonHash2.put("CAT","H");\r
-\r
- codonHash2.put("GAA","Q");\r
- codonHash2.put("GAG","Q");\r
- codonHash2.put("GAC","D");\r
- codonHash2.put("GAT","D");\r
-\r
- codonHash2.put("TAC","Y");\r
- codonHash2.put("TAT","Y");\r
-\r
- codonHash2.put("ACA","T");\r
- codonHash2.put("AAG","T");\r
- codonHash2.put("ACC","T");\r
- codonHash2.put("ACT","T");\r
-\r
- codonHash2.put("CCA","P");\r
- codonHash2.put("CCG","P");\r
- codonHash2.put("CCC","P");\r
- codonHash2.put("CCT","P");\r
-\r
- codonHash2.put("GCA","A");\r
- codonHash2.put("GCG","A");\r
- codonHash2.put("GCC","A");\r
- codonHash2.put("GCT","A");\r
-\r
- codonHash2.put("TCA","S");\r
- codonHash2.put("TCG","S");\r
- codonHash2.put("TCC","S");\r
- codonHash2.put("TCT","S");\r
- codonHash2.put("AGC","S");\r
- codonHash2.put("AGT","S");\r
-\r
- codonHash2.put("AGA","R");\r
- codonHash2.put("AGG","R");\r
- codonHash2.put("CGA","R");\r
- codonHash2.put("CGG","R");\r
- codonHash2.put("CGC","R");\r
- codonHash2.put("CGT","R");\r
-\r
- codonHash2.put("GGA","G");\r
- codonHash2.put("GGG","G");\r
- codonHash2.put("GGC","G");\r
- codonHash2.put("GGT","G");\r
-\r
- codonHash2.put("TGA","*");\r
- codonHash2.put("TAA","*");\r
- codonHash2.put("TAG","*");\r
-\r
- codonHash2.put("TGG","W");\r
-\r
- codonHash2.put("TGC","C");\r
- codonHash2.put("TGT","C");\r
-\r
- codonHash2.put("ATA","I");\r
- codonHash2.put("ATC","I");\r
- codonHash2.put("ATT","I");\r
-\r
- codonHash2.put("ATG","M");\r
-\r
- codonHash2.put("CTA","L");\r
- codonHash2.put("CTG","L");\r
- codonHash2.put("CTC","L");\r
- codonHash2.put("CTT","L");\r
- codonHash2.put("TTA","L");\r
- codonHash2.put("TTG","L");\r
-\r
- codonHash2.put("GTA","V");\r
- codonHash2.put("GTG","V");\r
- codonHash2.put("GTC","V");\r
- codonHash2.put("GTT","V");\r
-\r
- codonHash2.put("TTC","F");\r
- codonHash2.put("TTT","F");\r
-\r
- }\r
-\r
- static {\r
- Lys.addElement("AAA");\r
- Lys.addElement("AAG");\r
- Asn.addElement("AAC");\r
- Asn.addElement("AAT");\r
-\r
- Gln.addElement("CAA");\r
- Gln.addElement("CAG");\r
- His.addElement("CAC");\r
- His.addElement("CAT");\r
-\r
- Glu.addElement("GAA");\r
- Glu.addElement("GAG");\r
- Asp.addElement("GAC");\r
- Asp.addElement("GAT");\r
-\r
- Tyr.addElement("TAC");\r
- Tyr.addElement("TAT");\r
-\r
- Thr.addElement("ACA");\r
- Thr.addElement("ACG");\r
- Thr.addElement("ACC");\r
- Thr.addElement("ACT");\r
-\r
- Pro.addElement("CCA");\r
- Pro.addElement("CCG");\r
- Pro.addElement("CCC");\r
- Pro.addElement("CCT");\r
-\r
- Ala.addElement("GCA");\r
- Ala.addElement("GCG");\r
- Ala.addElement("GCC");\r
- Ala.addElement("GCT");\r
-\r
- Ser.addElement("TCA");\r
- Ser.addElement("TCG");\r
- Ser.addElement("TCC");\r
- Ser.addElement("TCT");\r
- Ser.addElement("AGC");\r
- Ser.addElement("AGT");\r
-\r
- Arg.addElement("AGA");\r
- Arg.addElement("AGG");\r
- Arg.addElement("CGA");\r
- Arg.addElement("CGG");\r
- Arg.addElement("CGC");\r
- Arg.addElement("CGT");\r
-\r
- Gly.addElement("GGA");\r
- Gly.addElement("GGG");\r
- Gly.addElement("GGC");\r
- Gly.addElement("GGT");\r
-\r
- STOP.addElement("TGA");\r
- STOP.addElement("TAA");\r
- STOP.addElement("TAG");\r
-\r
- Trp.addElement("TGG");\r
-\r
- Cys.addElement("TGC");\r
- Cys.addElement("TGT");\r
-\r
- Ile.addElement("ATA");\r
- Ile.addElement("ATC");\r
- Ile.addElement("ATT");\r
-\r
- Met.addElement("ATG");\r
-\r
- Leu.addElement("CTA");\r
- Leu.addElement("CTG");\r
- Leu.addElement("CTC");\r
- Leu.addElement("CTT");\r
- Leu.addElement("TTA");\r
- Leu.addElement("TTG");\r
-\r
- Val.addElement("GTA");\r
- Val.addElement("GTG");\r
- Val.addElement("GTC");\r
- Val.addElement("GTT");\r
-\r
- Phe.addElement("TTC");\r
- Phe.addElement("TTT");\r
- }\r
-\r
- public static Color[][] groupColors = {\r
- {Color.red,Color.red.brighter(),Color.red.brighter().brighter()},\r
- {Color.orange,Color.orange.brighter(),Color.orange.brighter().brighter()},\r
- {Color.green,Color.green.brighter(),Color.green.brighter().brighter()},\r
- {Color.blue,Color.blue.brighter(),Color.blue.brighter().brighter()},\r
- {Color.magenta,Color.magenta.brighter(),Color.magenta.brighter().brighter()},\r
- {Color.cyan,Color.cyan.brighter(),Color.cyan.brighter().brighter()},\r
- {Color.pink,Color.pink.brighter(),Color.pink.brighter().brighter()},\r
-\r
- };\r
-\r
-\r
-\r
- //Stores residue codes/names and colours and other things\r
- public static Hashtable propHash = new Hashtable();\r
- public static Hashtable hydrophobic = new Hashtable();\r
- public static Hashtable polar = new Hashtable();\r
- public static Hashtable small = new Hashtable();\r
- public static Hashtable positive = new Hashtable();\r
- public static Hashtable negative = new Hashtable();\r
- public static Hashtable charged = new Hashtable();\r
- public static Hashtable aromatic = new Hashtable();\r
- public static Hashtable aliphatic = new Hashtable();\r
- public static Hashtable tiny = new Hashtable();\r
- public static Hashtable proline = new Hashtable();\r
-\r
- static {\r
- hydrophobic.put("I",new Integer(1));\r
- hydrophobic.put("L",new Integer(1));\r
- hydrophobic.put("V",new Integer(1));\r
- hydrophobic.put("C",new Integer(1));\r
- hydrophobic.put("A",new Integer(1));\r
- hydrophobic.put("G",new Integer(1));\r
- hydrophobic.put("M",new Integer(1));\r
- hydrophobic.put("F",new Integer(1));\r
- hydrophobic.put("Y",new Integer(1));\r
- hydrophobic.put("W",new Integer(1));\r
- hydrophobic.put("H",new Integer(1));\r
- hydrophobic.put("K",new Integer(1));\r
- hydrophobic.put("X",new Integer(1));\r
- hydrophobic.put("-",new Integer(1));\r
- hydrophobic.put("*",new Integer(1));\r
- hydrophobic.put("R",new Integer(0));\r
- hydrophobic.put("E",new Integer(0));\r
- hydrophobic.put("Q",new Integer(0));\r
- hydrophobic.put("D",new Integer(0));\r
- hydrophobic.put("N",new Integer(0));\r
- hydrophobic.put("S",new Integer(0));\r
- hydrophobic.put("T",new Integer(0));\r
- hydrophobic.put("P",new Integer(0));\r
- }\r
- static {\r
- polar.put("Y",new Integer(1));\r
- polar.put("W",new Integer(1));\r
- polar.put("H",new Integer(1));\r
- polar.put("K",new Integer(1));\r
- polar.put("R",new Integer(1));\r
- polar.put("E",new Integer(1));\r
- polar.put("Q",new Integer(1));\r
- polar.put("D",new Integer(1));\r
- polar.put("N",new Integer(1));\r
- polar.put("S",new Integer(1));\r
- polar.put("T",new Integer(1));\r
- polar.put("X",new Integer(1));\r
- polar.put("-",new Integer(1));\r
- polar.put("*",new Integer(1));\r
- polar.put("I",new Integer(0));\r
- polar.put("L",new Integer(0));\r
- polar.put("V",new Integer(0));\r
- polar.put("C",new Integer(0));\r
- polar.put("A",new Integer(0));\r
- polar.put("G",new Integer(0));\r
- polar.put("M",new Integer(0));\r
- polar.put("F",new Integer(0));\r
- polar.put("P",new Integer(0));\r
-\r
- }\r
- static {\r
- small.put("I",new Integer(0));\r
- small.put("L",new Integer(0));\r
- small.put("V",new Integer(1));\r
- small.put("C",new Integer(1));\r
- small.put("A",new Integer(1));\r
- small.put("G",new Integer(1));\r
- small.put("M",new Integer(0));\r
- small.put("F",new Integer(0));\r
- small.put("Y",new Integer(0));\r
- small.put("W",new Integer(0));\r
- small.put("H",new Integer(0));\r
- small.put("K",new Integer(0));\r
- small.put("R",new Integer(0));\r
- small.put("E",new Integer(0));\r
- small.put("Q",new Integer(0));\r
- small.put("D",new Integer(1));\r
- small.put("N",new Integer(1));\r
- small.put("S",new Integer(1));\r
- small.put("T",new Integer(1));\r
- small.put("P",new Integer(1));\r
- small.put("-",new Integer(1));\r
- small.put("*",new Integer(1));\r
- }\r
- static {\r
- positive.put("I",new Integer(0));\r
- positive.put("L",new Integer(0));\r
- positive.put("V",new Integer(0));\r
- positive.put("C",new Integer(0));\r
- positive.put("A",new Integer(0));\r
- positive.put("G",new Integer(0));\r
- positive.put("M",new Integer(0));\r
- positive.put("F",new Integer(0));\r
- positive.put("Y",new Integer(0));\r
- positive.put("W",new Integer(0));\r
- positive.put("H",new Integer(1));\r
- positive.put("K",new Integer(1));\r
- positive.put("R",new Integer(1));\r
- positive.put("E",new Integer(0));\r
- positive.put("Q",new Integer(0));\r
- positive.put("D",new Integer(0));\r
- positive.put("N",new Integer(0));\r
- positive.put("S",new Integer(0));\r
- positive.put("T",new Integer(0));\r
- positive.put("P",new Integer(0));\r
- positive.put("-",new Integer(1));\r
- positive.put("*",new Integer(1));\r
- }\r
- static {\r
- negative.put("I",new Integer(0));\r
- negative.put("L",new Integer(0));\r
- negative.put("V",new Integer(0));\r
- negative.put("C",new Integer(0));\r
- negative.put("A",new Integer(0));\r
- negative.put("G",new Integer(0));\r
- negative.put("M",new Integer(0));\r
- negative.put("F",new Integer(0));\r
- negative.put("Y",new Integer(0));\r
- negative.put("W",new Integer(0));\r
- negative.put("H",new Integer(0));\r
- negative.put("K",new Integer(0));\r
- negative.put("R",new Integer(0));\r
- negative.put("E",new Integer(1));\r
- negative.put("Q",new Integer(0));\r
- negative.put("D",new Integer(1));\r
- negative.put("N",new Integer(0));\r
- negative.put("S",new Integer(0));\r
- negative.put("T",new Integer(0));\r
- negative.put("P",new Integer(0));\r
- negative.put("-",new Integer(1));\r
- negative.put("*",new Integer(1));\r
- }\r
- static {\r
- charged.put("I",new Integer(0));\r
- charged.put("L",new Integer(0));\r
- charged.put("V",new Integer(0));\r
- charged.put("C",new Integer(0));\r
- charged.put("A",new Integer(0));\r
- charged.put("G",new Integer(0));\r
- charged.put("M",new Integer(0));\r
- charged.put("F",new Integer(0));\r
- charged.put("Y",new Integer(0));\r
- charged.put("W",new Integer(0));\r
- charged.put("H",new Integer(1));\r
- charged.put("K",new Integer(1));\r
- charged.put("R",new Integer(1));\r
- charged.put("E",new Integer(1));\r
- charged.put("Q",new Integer(0));\r
- charged.put("D",new Integer(1));\r
- charged.put("N",new Integer(1));\r
- charged.put("S",new Integer(0));\r
- charged.put("T",new Integer(0));\r
- charged.put("P",new Integer(0));\r
- charged.put("-",new Integer(1));\r
- charged.put("*",new Integer(1));\r
- }\r
- static {\r
- aromatic.put("I",new Integer(0));\r
- aromatic.put("L",new Integer(0));\r
- aromatic.put("V",new Integer(0));\r
- aromatic.put("C",new Integer(0));\r
- aromatic.put("A",new Integer(0));\r
- aromatic.put("G",new Integer(0));\r
- aromatic.put("M",new Integer(0));\r
- aromatic.put("F",new Integer(1));\r
- aromatic.put("Y",new Integer(1));\r
- aromatic.put("W",new Integer(1));\r
- aromatic.put("H",new Integer(1));\r
- aromatic.put("K",new Integer(0));\r
- aromatic.put("R",new Integer(0));\r
- aromatic.put("E",new Integer(0));\r
- aromatic.put("Q",new Integer(0));\r
- aromatic.put("D",new Integer(0));\r
- aromatic.put("N",new Integer(0));\r
- aromatic.put("S",new Integer(0));\r
- aromatic.put("T",new Integer(0));\r
- aromatic.put("P",new Integer(0));\r
- aromatic.put("-",new Integer(1));\r
- aromatic.put("*",new Integer(1));\r
- }\r
- static {\r
- aliphatic.put("I",new Integer(1));\r
- aliphatic.put("L",new Integer(1));\r
- aliphatic.put("V",new Integer(1));\r
- aliphatic.put("C",new Integer(0));\r
- aliphatic.put("A",new Integer(0));\r
- aliphatic.put("G",new Integer(0));\r
- aliphatic.put("M",new Integer(0));\r
- aliphatic.put("F",new Integer(0));\r
- aliphatic.put("Y",new Integer(0));\r
- aliphatic.put("W",new Integer(0));\r
- aliphatic.put("H",new Integer(0));\r
- aliphatic.put("K",new Integer(0));\r
- aliphatic.put("R",new Integer(0));\r
- aliphatic.put("E",new Integer(0));\r
- aliphatic.put("Q",new Integer(0));\r
- aliphatic.put("D",new Integer(0));\r
- aliphatic.put("N",new Integer(0));\r
- aliphatic.put("S",new Integer(0));\r
- aliphatic.put("T",new Integer(0));\r
- aliphatic.put("P",new Integer(0));\r
- aliphatic.put("-",new Integer(1));\r
- aliphatic.put("*",new Integer(1));\r
- }\r
-\r
- static {\r
- tiny.put("I",new Integer(0));\r
- tiny.put("L",new Integer(0));\r
- tiny.put("V",new Integer(0));\r
- tiny.put("C",new Integer(0));\r
- tiny.put("A",new Integer(1));\r
- tiny.put("G",new Integer(1));\r
- tiny.put("M",new Integer(0));\r
- tiny.put("F",new Integer(0));\r
- tiny.put("Y",new Integer(0));\r
- tiny.put("W",new Integer(0));\r
- tiny.put("H",new Integer(0));\r
- tiny.put("K",new Integer(0));\r
- tiny.put("R",new Integer(0));\r
- tiny.put("E",new Integer(0));\r
- tiny.put("Q",new Integer(0));\r
- tiny.put("D",new Integer(0));\r
- tiny.put("N",new Integer(0));\r
- tiny.put("S",new Integer(1));\r
- tiny.put("T",new Integer(0));\r
- tiny.put("P",new Integer(0));\r
- tiny.put("-",new Integer(1));\r
- tiny.put("*",new Integer(1));\r
- }\r
-\r
- static {\r
- proline.put("I",new Integer(0));\r
- proline.put("L",new Integer(0));\r
- proline.put("V",new Integer(0));\r
- proline.put("C",new Integer(0));\r
- proline.put("A",new Integer(0));\r
- proline.put("G",new Integer(0));\r
- proline.put("M",new Integer(0));\r
- proline.put("F",new Integer(0));\r
- proline.put("Y",new Integer(0));\r
- proline.put("W",new Integer(0));\r
- proline.put("H",new Integer(0));\r
- proline.put("K",new Integer(0));\r
- proline.put("R",new Integer(0));\r
- proline.put("E",new Integer(0));\r
- proline.put("Q",new Integer(0));\r
- proline.put("D",new Integer(0));\r
- proline.put("N",new Integer(0));\r
- proline.put("S",new Integer(0));\r
- proline.put("T",new Integer(0));\r
- proline.put("P",new Integer(1));\r
- proline.put("-",new Integer(1));\r
- proline.put("*",new Integer(1));\r
- }\r
-\r
-\r
- static {\r
- propHash.put("hydrophobic",hydrophobic);\r
- propHash.put("small",small);\r
- propHash.put("positive",positive);\r
- propHash.put("negative",negative);\r
- propHash.put("charged",charged);\r
- propHash.put("aromatic",aromatic);\r
- propHash.put("aliphatic",aliphatic);\r
- propHash.put("tiny",tiny);\r
- propHash.put("proline",proline);\r
- propHash.put("polar",polar);\r
- }\r
-\r
- public static Hashtable chainColours = new Hashtable();\r
- static {\r
- chainColours.put("A",Color.red);\r
- chainColours.put("B",Color.orange);\r
- chainColours.put("C",Color.yellow);\r
- chainColours.put("D",Color.green);\r
- chainColours.put("E",Color.cyan);\r
- chainColours.put("F",Color.blue);\r
- chainColours.put("G",Color.magenta);\r
- chainColours.put("H",Color.pink);\r
- }\r
- public static Hashtable getChainColours() {\r
- return chainColours;\r
- }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
\r
-public class ScoreColourScheme extends ResidueColourScheme {\r
- public double min;\r
- public double max;\r
- public double[] scores;\r
-\r
- public ScoreColourScheme( double[] scores,\r
- double min,\r
- double max) {\r
\r
- super();\r
+public class ScoreColourScheme extends ResidueColourScheme {\r
+ public double min;\r
+ public double max;\r
+ public double[] scores;\r
\r
- this.scores = scores;\r
- this.min = min;\r
- this.max = max;\r
- }\r
+ public ScoreColourScheme(double[] scores, double min, double max) {\r
+ super();\r
\r
+ this.scores = scores;\r
+ this.min = min;\r
+ this.max = max;\r
+ }\r
\r
- public Color findColour(String s,int j)\r
- {\r
+ public Color findColour(String s, int j) {\r
+ if (threshold > 0) {\r
+ if (!aboveThreshold(s, j)) {\r
+ return Color.white;\r
+ }\r
+ }\r
\r
- if (threshold > 0)\r
- {\r
- if (!aboveThreshold(s,j))\r
- return Color.white;\r
- }\r
+ float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -\r
+ (float) min) / (float) (max - min);\r
\r
- float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]\r
- - (float)min)/(float)(max - min);\r
- if (red > 1.0f)\r
- red = 1.0f;\r
+ if (red > 1.0f) {\r
+ red = 1.0f;\r
+ }\r
\r
- if (red < 0.0f)\r
- red = 0.0f;\r
+ if (red < 0.0f) {\r
+ red = 0.0f;\r
+ }\r
\r
- char c = s.charAt(0);\r
+ char c = s.charAt(0);\r
\r
- if(jalview.util.Comparison.isGap((c)))\r
- return Color.white;\r
+ if (jalview.util.Comparison.isGap((c))) {\r
+ return Color.white;\r
+ }\r
\r
- // This isn';t great - pool of colours in here?\r
- return makeColour(red);\r
+ // This isn';t great - pool of colours in here?\r
+ return makeColour(red);\r
}\r
+\r
public Color makeColour(float c) {\r
- return new Color(c,(float)0.0,(float)1.0-c);\r
+ return new Color(c, (float) 0.0, (float) 1.0 - c);\r
}\r
}\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
\r
-public class StrandColourScheme extends ScoreColourScheme {\r
-\r
\r
- public StrandColourScheme() {\r
- super(ResidueProperties.strand,ResidueProperties.strandmin,ResidueProperties.strandmax);\r
- }\r
+public class StrandColourScheme extends ScoreColourScheme {\r
+ public StrandColourScheme() {\r
+ super(ResidueProperties.strand, ResidueProperties.strandmin,\r
+ ResidueProperties.strandmax);\r
+ }\r
\r
- public Color makeColour(float c) {\r
- return new Color(c,c,(float)1.0-c);\r
- }\r
+ public Color makeColour(float c) {\r
+ return new Color(c, c, (float) 1.0 - c);\r
+ }\r
}\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
public class TaylorColourScheme extends ResidueColourScheme {\r
-\r
- public TaylorColourScheme() {\r
- super(ResidueProperties.taylor,0);\r
- }\r
-\r
+ public TaylorColourScheme() {\r
+ super(ResidueProperties.taylor, 0);\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
\r
-public class TurnColourScheme extends ScoreColourScheme {\r
\r
- public TurnColourScheme() {\r
- super(ResidueProperties.turn,ResidueProperties.turnmin,ResidueProperties.turnmax);\r
- }\r
+public class TurnColourScheme extends ScoreColourScheme {\r
+ public TurnColourScheme() {\r
+ super(ResidueProperties.turn, ResidueProperties.turnmin,\r
+ ResidueProperties.turnmax);\r
+ }\r
\r
- public Color makeColour(float c) {\r
- return new Color(c,1-c,1-c);\r
- }\r
+ public Color makeColour(float c) {\r
+ return new Color(c, 1 - c, 1 - c);\r
+ }\r
}\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
import java.awt.*;\r
\r
-public class UserColourScheme extends ResidueColourScheme\r
-{\r
- public UserColourScheme(Color [] newColors)\r
- {\r
- colors = newColors;\r
- }\r
\r
- public Color[] getColours()\r
- {\r
- return colors;\r
- }\r
+public class UserColourScheme extends ResidueColourScheme {\r
+ public UserColourScheme(Color[] newColors) {\r
+ colors = newColors;\r
+ }\r
+\r
+ public Color[] getColours() {\r
+ return colors;\r
+ }\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
public class ZappoColourScheme extends ResidueColourScheme {\r
-\r
- public ZappoColourScheme() {\r
- super(ResidueProperties.color,0);\r
- }\r
+ public ZappoColourScheme() {\r
+ super(ResidueProperties.color, 0);\r
+ }\r
}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.util;
-
-import java.io.File;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.lang.reflect.Field;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-
+*/\r
+package jalview.util;\r
+\r
+import java.io.File;\r
+import java.io.IOException;\r
+\r
+import java.lang.reflect.Constructor;\r
+import java.lang.reflect.Field;\r
+import java.lang.reflect.InvocationTargetException;\r
+import java.lang.reflect.Method;\r
+\r
+\r
/**
* BrowserLauncher is a class that provides one static method, openURL, which opens the default
* web browser for the current user of the system to the given URL. It may support other
*
* @author Eric Albert (<a href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
* @version 1.4b1 (Released June 20, 2001)
- */
-public class BrowserLauncher {
-
- /**
- * The Java virtual machine that we are running on. Actually, in most cases we only care
- * about the operating system, but some operating systems require us to switch on the VM. */
- private static int jvm;
-
- /** The browser for the system */
- private static Object browser;
-
- /**
- * Caches whether any classes, methods, and fields that are not part of the JDK and need to
- * be dynamically loaded at runtime loaded successfully.
- * <p>
- * Note that if this is <code>false</code>, <code>openURL()</code> will always return an
- * IOException.
- */
- private static boolean loadedWithoutErrors;
-
- /** The com.apple.mrj.MRJFileUtils class */
- private static Class mrjFileUtilsClass;
-
- /** The com.apple.mrj.MRJOSType class */
- private static Class mrjOSTypeClass;
-
- /** The com.apple.MacOS.AEDesc class */
- private static Class aeDescClass;
-
- /** The <init>(int) method of com.apple.MacOS.AETarget */
- private static Constructor aeTargetConstructor;
-
- /** The <init>(int, int, int) method of com.apple.MacOS.AppleEvent */
- private static Constructor appleEventConstructor;
-
- /** The <init>(String) method of com.apple.MacOS.AEDesc */
- private static Constructor aeDescConstructor;
-
- /** The findFolder method of com.apple.mrj.MRJFileUtils */
- private static Method findFolder;
-
- /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
- private static Method getFileCreator;
-
- /** The getFileType method of com.apple.mrj.MRJFileUtils */
- private static Method getFileType;
-
- /** The openURL method of com.apple.mrj.MRJFileUtils */
- private static Method openURL;
-
- /** The makeOSType method of com.apple.MacOS.OSUtils */
- private static Method makeOSType;
-
- /** The putParameter method of com.apple.MacOS.AppleEvent */
- private static Method putParameter;
-
- /** The sendNoReply method of com.apple.MacOS.AppleEvent */
- private static Method sendNoReply;
-
- /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
- private static Object kSystemFolderType;
-
- /** The keyDirectObject AppleEvent parameter type */
- private static Integer keyDirectObject;
-
- /** The kAutoGenerateReturnID AppleEvent code */
- private static Integer kAutoGenerateReturnID;
-
- /** The kAnyTransactionID AppleEvent code */
- private static Integer kAnyTransactionID;
-
- /** The linkage object required for JDirect 3 on Mac OS X. */
- private static Object linkage;
-
- /** The framework to reference on Mac OS X */
- private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";
-
- /** JVM constant for MRJ 2.0 */
- private static final int MRJ_2_0 = 0;
-
- /** JVM constant for MRJ 2.1 or later */
- private static final int MRJ_2_1 = 1;
-
- /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */
- private static final int MRJ_3_0 = 3;
-
- /** JVM constant for MRJ 3.1 */
- private static final int MRJ_3_1 = 4;
-
- /** JVM constant for any Windows NT JVM */
- private static final int WINDOWS_NT = 5;
-
- /** JVM constant for any Windows 9x JVM */
- private static final int WINDOWS_9x = 6;
-
- /** JVM constant for any other platform */
- private static final int OTHER = -1;
-
- /**
- * The file type of the Finder on a Macintosh. Hardcoding "Finder" would keep non-U.S. English
- * systems from working properly.
- */
- private static final String FINDER_TYPE = "FNDR";
-
- /**
- * The creator code of the Finder on a Macintosh, which is needed to send AppleEvents to the
- * application.
- */
- private static final String FINDER_CREATOR = "MACS";
-
- /** The name for the AppleEvent type corresponding to a GetURL event. */
- private static final String GURL_EVENT = "GURL";
-
- /**
- * The first parameter that needs to be passed into Runtime.exec() to open the default web
- * browser on Windows.
- */
- private static final String FIRST_WINDOWS_PARAMETER = "/c";
-
- /** The second parameter for Runtime.exec() on Windows. */
- private static final String SECOND_WINDOWS_PARAMETER = "start";
-
+ */\r
+public class BrowserLauncher {\r
/**
- * The third parameter for Runtime.exec() on Windows. This is a "title"
- * parameter that the command line expects. Setting this parameter allows
- * URLs containing spaces to work.
- */
- private static final String THIRD_WINDOWS_PARAMETER = "\"\"";
-
- /**
- * The shell parameters for Netscape that opens a given URL in an already-open copy of Netscape
- * on many command-line systems.
- */
- private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";
- private static final String NETSCAPE_OPEN_PARAMETER_START = "openURL(";
- private static final String NETSCAPE_OPEN_NEW_WINDOW = ", new-window";
- private static final String NETSCAPE_OPEN_PARAMETER_END = ")";
-
- /**
- * The message from any exception thrown throughout the initialization process.
- */
- private static String errorMessage;
-
- /**
- * An initialization block that determines the operating system and loads the necessary
- * runtime data.
- */
- static {
- loadedWithoutErrors = true;
- String osName = System.getProperty("os.name");
- if (osName.startsWith("Mac OS")) {
- String mrjVersion = System.getProperty("mrj.version");
- String majorMRJVersion = mrjVersion.substring(0, 3);
- try {
- double version = Double.valueOf(majorMRJVersion).doubleValue();
- if (version == 2) {
- jvm = MRJ_2_0;
- } else if (version >= 2.1 && version < 3) {
- // Assume that all 2.x versions of MRJ work the same. MRJ 2.1 actually
- // works via Runtime.exec() and 2.2 supports that but has an openURL() method
- // as well that we currently ignore.
- jvm = MRJ_2_1;
- } else if (version == 3.0) {
- jvm = MRJ_3_0;
- } else if (version >= 3.1) {
- // Assume that all 3.1 and later versions of MRJ work the same.
- jvm = MRJ_3_1;
- } else {
- loadedWithoutErrors = false;
- errorMessage = "Unsupported MRJ version: " + version;
- }
- } catch (NumberFormatException nfe) {
- loadedWithoutErrors = false;
- errorMessage = "Invalid MRJ version: " + mrjVersion;
- }
- } else if (osName.startsWith("Windows")) {
- if (osName.indexOf("9") != -1) {
- jvm = WINDOWS_9x;
- } else {
- jvm = WINDOWS_NT;
- }
- } else {
- jvm = OTHER;
- }
-
- if (loadedWithoutErrors) { // if we haven't hit any errors yet
- loadedWithoutErrors = loadClasses();
- }
- }
-
- /**
- * This class should be never be instantiated; this just ensures so.
- */
- private BrowserLauncher() { }
-
- /**
- * Called by a static initializer to load any classes, fields, and methods required at runtime
- * to locate the user's web browser.
- * @return <code>true</code> if all intialization succeeded
- * <code>false</code> if any portion of the initialization failed
- */
- private static boolean loadClasses() {
- switch (jvm) {
- case MRJ_2_0:
- try {
- Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");
- Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");
- Class appleEventClass = Class.forName("com.apple.MacOS.AppleEvent");
- Class aeClass = Class.forName("com.apple.MacOS.ae");
- aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
-
- aeTargetConstructor = aeTargetClass.getDeclaredConstructor(new Class [] { int.class });
- appleEventConstructor = appleEventClass.getDeclaredConstructor(new Class[] { int.class, int.class, aeTargetClass, int.class, int.class });
- aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[] { String.class });
-
- makeOSType = osUtilsClass.getDeclaredMethod("makeOSType", new Class [] { String.class });
- putParameter = appleEventClass.getDeclaredMethod("putParameter", new Class[] { int.class, aeDescClass });
- sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply", new Class[] { });
-
- Field keyDirectObjectField = aeClass.getDeclaredField("keyDirectObject");
- keyDirectObject = (Integer) keyDirectObjectField.get(null);
- Field autoGenerateReturnIDField = appleEventClass.getDeclaredField("kAutoGenerateReturnID");
- kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField.get(null);
- Field anyTransactionIDField = appleEventClass.getDeclaredField("kAnyTransactionID");
- kAnyTransactionID = (Integer) anyTransactionIDField.get(null);
- } catch (ClassNotFoundException cnfe) {
- errorMessage = cnfe.getMessage();
- return false;
- } catch (NoSuchMethodException nsme) {
- errorMessage = nsme.getMessage();
- return false;
- } catch (NoSuchFieldException nsfe) {
- errorMessage = nsfe.getMessage();
- return false;
- } catch (IllegalAccessException iae) {
- errorMessage = iae.getMessage();
- return false;
- }
- break;
- case MRJ_2_1:
- try {
- mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
- mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");
- Field systemFolderField = mrjFileUtilsClass.getDeclaredField("kSystemFolderType");
- kSystemFolderType = systemFolderField.get(null);
- findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder", new Class[] { mrjOSTypeClass });
- getFileCreator = mrjFileUtilsClass.getDeclaredMethod("getFileCreator", new Class[] { File.class });
- getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType", new Class[] { File.class });
- } catch (ClassNotFoundException cnfe) {
- errorMessage = cnfe.getMessage();
- return false;
- } catch (NoSuchFieldException nsfe) {
- errorMessage = nsfe.getMessage();
- return false;
- } catch (NoSuchMethodException nsme) {
- errorMessage = nsme.getMessage();
- return false;
- } catch (SecurityException se) {
- errorMessage = se.getMessage();
- return false;
- } catch (IllegalAccessException iae) {
- errorMessage = iae.getMessage();
- return false;
- }
- break;
- case MRJ_3_0:
- try {
- Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
- Constructor constructor = linker.getConstructor(new Class[]{ Class.class });
- linkage = constructor.newInstance(new Object[] { BrowserLauncher.class });
- } catch (ClassNotFoundException cnfe) {
- errorMessage = cnfe.getMessage();
- return false;
- } catch (NoSuchMethodException nsme) {
- errorMessage = nsme.getMessage();
- return false;
- } catch (InvocationTargetException ite) {
- errorMessage = ite.getMessage();
- return false;
- } catch (InstantiationException ie) {
- errorMessage = ie.getMessage();
- return false;
- } catch (IllegalAccessException iae) {
- errorMessage = iae.getMessage();
- return false;
- }
- break;
- case MRJ_3_1:
- try {
- mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
- openURL = mrjFileUtilsClass.getDeclaredMethod("openURL", new Class[] { String.class });
- } catch (ClassNotFoundException cnfe) {
- errorMessage = cnfe.getMessage();
- return false;
- } catch (NoSuchMethodException nsme) {
- errorMessage = nsme.getMessage();
- return false;
- }
- break;
- default:
- break;
- }
- return true;
- }
-
- /**
- * Attempts to locate the default web browser on the local system. Caches results so it
- * only locates the browser once for each use of this class per JVM instance.
- * @return The browser for the system. Note that this may not be what you would consider
- * to be a standard web browser; instead, it's the application that gets called to
- * open the default web browser. In some cases, this will be a non-String object
- * that provides the means of calling the default browser.
- */
- private static Object locateBrowser() {
- if (browser != null) {
- return browser;
- }
- switch (jvm) {
- case MRJ_2_0:
- try {
- Integer finderCreatorCode = (Integer) makeOSType.invoke(null, new Object[] { FINDER_CREATOR });
- Object aeTarget = aeTargetConstructor.newInstance(new Object[] { finderCreatorCode });
- Integer gurlType = (Integer) makeOSType.invoke(null, new Object[] { GURL_EVENT });
- Object appleEvent = appleEventConstructor.newInstance(new Object[] { gurlType, gurlType, aeTarget, kAutoGenerateReturnID, kAnyTransactionID });
- // Don't set browser = appleEvent because then the next time we call
- // locateBrowser(), we'll get the same AppleEvent, to which we'll already have
- // added the relevant parameter. Instead, regenerate the AppleEvent every time.
- // There's probably a way to do this better; if any has any ideas, please let
- // me know.
- return appleEvent;
- } catch (IllegalAccessException iae) {
- browser = null;
- errorMessage = iae.getMessage();
- return browser;
- } catch (InstantiationException ie) {
- browser = null;
- errorMessage = ie.getMessage();
- return browser;
- } catch (InvocationTargetException ite) {
- browser = null;
- errorMessage = ite.getMessage();
- return browser;
- }
- case MRJ_2_1:
- File systemFolder;
- try {
- systemFolder = (File) findFolder.invoke(null, new Object[] { kSystemFolderType });
- } catch (IllegalArgumentException iare) {
- browser = null;
- errorMessage = iare.getMessage();
- return browser;
- } catch (IllegalAccessException iae) {
- browser = null;
- errorMessage = iae.getMessage();
- return browser;
- } catch (InvocationTargetException ite) {
- browser = null;
- errorMessage = ite.getTargetException().getClass() + ": " + ite.getTargetException().getMessage();
- return browser;
- }
- String[] systemFolderFiles = systemFolder.list();
- // Avoid a FilenameFilter because that can't be stopped mid-list
- for(int i = 0; i < systemFolderFiles.length; i++) {
- try {
- File file = new File(systemFolder, systemFolderFiles[i]);
- if (!file.isFile()) {
- continue;
- }
- // We're looking for a file with a creator code of 'MACS' and
- // a type of 'FNDR'. Only requiring the type results in non-Finder
- // applications being picked up on certain Mac OS 9 systems,
- // especially German ones, and sending a GURL event to those
- // applications results in a logout under Multiple Users.
- Object fileType = getFileType.invoke(null, new Object[] { file });
- if (FINDER_TYPE.equals(fileType.toString())) {
- Object fileCreator = getFileCreator.invoke(null, new Object[] { file });
- if (FINDER_CREATOR.equals(fileCreator.toString())) {
- browser = file.toString(); // Actually the Finder, but that's OK
- return browser;
- }
- }
- } catch (IllegalArgumentException iare) {
- browser = browser;
- errorMessage = iare.getMessage();
- return null;
- } catch (IllegalAccessException iae) {
- browser = null;
- errorMessage = iae.getMessage();
- return browser;
- } catch (InvocationTargetException ite) {
- browser = null;
- errorMessage = ite.getTargetException().getClass() + ": " + ite.getTargetException().getMessage();
- return browser;
- }
- }
- browser = null;
- break;
- case MRJ_3_0:
- case MRJ_3_1:
- browser = ""; // Return something non-null
- break;
- case WINDOWS_NT:
- browser = "cmd.exe";
- break;
- case WINDOWS_9x:
- browser = "command.com";
- break;
- case OTHER:
- default:
- browser = jalview.bin.Cache.applicationProperties.getProperty("jalview.browser");
- if (browser==null) {
- // hope firefox exists :-/
- browser = "firefox";
- }
- break;
- }
- return browser;
- }
-
- /**
- * Attempts to open the default web browser to the given URL.
- * @param url The URL to open
- * @throws IOException If the web browser could not be located or does not run
- */
- public static void openURL(String url) throws IOException {
- if (!loadedWithoutErrors) {
- throw new IOException("Exception in finding browser: " + errorMessage);
- }
- Object browser = locateBrowser();
- if (browser == null) {
- throw new IOException("Unable to locate browser: " + errorMessage);
- }
-
- switch (jvm) {
- case MRJ_2_0:
- Object aeDesc = null;
- try {
- aeDesc = aeDescConstructor.newInstance(new Object[] { url });
- putParameter.invoke(browser, new Object[] { keyDirectObject, aeDesc });
- sendNoReply.invoke(browser, new Object[] { });
- } catch (InvocationTargetException ite) {
- throw new IOException("InvocationTargetException while creating AEDesc: " + ite.getMessage());
- } catch (IllegalAccessException iae) {
- throw new IOException("IllegalAccessException while building AppleEvent: " + iae.getMessage());
- } catch (InstantiationException ie) {
- throw new IOException("InstantiationException while creating AEDesc: " + ie.getMessage());
- } finally {
- aeDesc = null; // Encourage it to get disposed if it was created
- browser = null; // Ditto
- }
- break;
- case MRJ_2_1:
- Runtime.getRuntime().exec(new String[] { (String) browser, url } );
- break;
- case MRJ_3_0:
- int[] instance = new int[1];
- int result = ICStart(instance, 0);
- if (result == 0) {
- int[] selectionStart = new int[] { 0 };
- byte[] urlBytes = url.getBytes();
- int[] selectionEnd = new int[] { urlBytes.length };
- result = ICLaunchURL(instance[0], new byte[] { 0 }, urlBytes,
- urlBytes.length, selectionStart,
- selectionEnd);
- if (result == 0) {
- // Ignore the return value; the URL was launched successfully
- // regardless of what happens here.
- ICStop(instance);
- } else {
- throw new IOException("Unable to launch URL: " + result);
- }
- } else {
- throw new IOException("Unable to create an Internet Config instance: " + result);
- }
- break;
- case MRJ_3_1:
- try {
- openURL.invoke(null, new Object[] { url });
- } catch (InvocationTargetException ite) {
- throw new IOException("InvocationTargetException while calling openURL: " + ite.getMessage());
- } catch (IllegalAccessException iae) {
- throw new IOException("IllegalAccessException while calling openURL: " + iae.getMessage());
- }
- break;
- case WINDOWS_NT:
- case WINDOWS_9x:
- // Add quotes around the URL to allow ampersands and other special
- // characters to work.
- Process process = Runtime.getRuntime().exec(new String[] { (String) browser,
- FIRST_WINDOWS_PARAMETER,
- SECOND_WINDOWS_PARAMETER,
- THIRD_WINDOWS_PARAMETER,
- '"' + url + '"' });
- // This avoids a memory leak on some versions of Java on Windows.
- // That's hinted at in <http://developer.java.sun.com/developer/qow/archive/68/>.
- try {
- process.waitFor();
- process.exitValue();
- } catch (InterruptedException ie) {
- throw new IOException("InterruptedException while launching browser: " + ie.getMessage());
- }
- break;
- case OTHER:
- // Assume that we're on Unix and that Netscape (actually Firefox) is installed
-
- // First, attempt to open the URL in a currently running session of Netscape
-
- // JBPNote log debug
- /* System.out.println("Executing : "+browser+" "+
- NETSCAPE_REMOTE_PARAMETER+" "+
- NETSCAPE_OPEN_PARAMETER_START +
- url +
- NETSCAPE_OPEN_NEW_WINDOW +
- NETSCAPE_OPEN_PARAMETER_END);
- */
- process = Runtime.getRuntime().exec(new String[] { (String) browser,
- NETSCAPE_REMOTE_PARAMETER,
- NETSCAPE_OPEN_PARAMETER_START +
- url +
- NETSCAPE_OPEN_NEW_WINDOW +
- NETSCAPE_OPEN_PARAMETER_END });
- try {
- int exitCode = process.waitFor();
- if (exitCode != 0) { // if Netscape was not open
- // JBPNote log debug
- // System.out.println("Executing : "+browser+" "+url+"\n");
- Runtime.getRuntime().exec(new String[] { (String) browser, url });
- }
- } catch (InterruptedException ie) {
- throw new IOException("InterruptedException while launching browser: " + ie.getMessage());
- }
- break;
- default:
- // This should never occur, but if it does, we'll try the simplest thing possible
- Runtime.getRuntime().exec(new String[] { (String) browser, url });
- break;
- }
- }
-
- /**
- * Methods required for Mac OS X. The presence of native methods does not cause
- * any problems on other platforms.
- */
- private native static int ICStart(int[] instance, int signature);
- private native static int ICStop(int[] instance);
- private native static int ICLaunchURL(int instance, byte[] hint, byte[] data, int len,
- int[] selectionStart, int[] selectionEnd);
-}
+ * The Java virtual machine that we are running on. Actually, in most cases we only care
+ * about the operating system, but some operating systems require us to switch on the VM. */\r
+ private static int jvm;\r
+\r
+ /** The browser for the system */\r
+ private static Object browser;\r
+\r
+ /**
+ * Caches whether any classes, methods, and fields that are not part of the JDK and need to
+ * be dynamically loaded at runtime loaded successfully.
+ * <p>
+ * Note that if this is <code>false</code>, <code>openURL()</code> will always return an
+ * IOException.
+ */\r
+ private static boolean loadedWithoutErrors;\r
+\r
+ /** The com.apple.mrj.MRJFileUtils class */\r
+ private static Class mrjFileUtilsClass;\r
+\r
+ /** The com.apple.mrj.MRJOSType class */\r
+ private static Class mrjOSTypeClass;\r
+\r
+ /** The com.apple.MacOS.AEDesc class */\r
+ private static Class aeDescClass;\r
+\r
+ /** The <init>(int) method of com.apple.MacOS.AETarget */\r
+ private static Constructor aeTargetConstructor;\r
+\r
+ /** The <init>(int, int, int) method of com.apple.MacOS.AppleEvent */\r
+ private static Constructor appleEventConstructor;\r
+\r
+ /** The <init>(String) method of com.apple.MacOS.AEDesc */\r
+ private static Constructor aeDescConstructor;\r
+\r
+ /** The findFolder method of com.apple.mrj.MRJFileUtils */\r
+ private static Method findFolder;\r
+\r
+ /** The getFileCreator method of com.apple.mrj.MRJFileUtils */\r
+ private static Method getFileCreator;\r
+\r
+ /** The getFileType method of com.apple.mrj.MRJFileUtils */\r
+ private static Method getFileType;\r
+\r
+ /** The openURL method of com.apple.mrj.MRJFileUtils */\r
+ private static Method openURL;\r
+\r
+ /** The makeOSType method of com.apple.MacOS.OSUtils */\r
+ private static Method makeOSType;\r
+\r
+ /** The putParameter method of com.apple.MacOS.AppleEvent */\r
+ private static Method putParameter;\r
+\r
+ /** The sendNoReply method of com.apple.MacOS.AppleEvent */\r
+ private static Method sendNoReply;\r
+\r
+ /** Actually an MRJOSType pointing to the System Folder on a Macintosh */\r
+ private static Object kSystemFolderType;\r
+\r
+ /** The keyDirectObject AppleEvent parameter type */\r
+ private static Integer keyDirectObject;\r
+\r
+ /** The kAutoGenerateReturnID AppleEvent code */\r
+ private static Integer kAutoGenerateReturnID;\r
+\r
+ /** The kAnyTransactionID AppleEvent code */\r
+ private static Integer kAnyTransactionID;\r
+\r
+ /** The linkage object required for JDirect 3 on Mac OS X. */\r
+ private static Object linkage;\r
+\r
+ /** The framework to reference on Mac OS X */\r
+ private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";\r
+\r
+ /** JVM constant for MRJ 2.0 */\r
+ private static final int MRJ_2_0 = 0;\r
+\r
+ /** JVM constant for MRJ 2.1 or later */\r
+ private static final int MRJ_2_1 = 1;\r
+\r
+ /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */\r
+ private static final int MRJ_3_0 = 3;\r
+\r
+ /** JVM constant for MRJ 3.1 */\r
+ private static final int MRJ_3_1 = 4;\r
+\r
+ /** JVM constant for any Windows NT JVM */\r
+ private static final int WINDOWS_NT = 5;\r
+\r
+ /** JVM constant for any Windows 9x JVM */\r
+ private static final int WINDOWS_9x = 6;\r
+\r
+ /** JVM constant for any other platform */\r
+ private static final int OTHER = -1;\r
+\r
+ /**
+ * The file type of the Finder on a Macintosh. Hardcoding "Finder" would keep non-U.S. English
+ * systems from working properly.
+ */\r
+ private static final String FINDER_TYPE = "FNDR";\r
+\r
+ /**
+ * The creator code of the Finder on a Macintosh, which is needed to send AppleEvents to the
+ * application.
+ */\r
+ private static final String FINDER_CREATOR = "MACS";\r
+\r
+ /** The name for the AppleEvent type corresponding to a GetURL event. */\r
+ private static final String GURL_EVENT = "GURL";\r
+\r
+ /**
+ * The first parameter that needs to be passed into Runtime.exec() to open the default web
+ * browser on Windows.
+ */\r
+ private static final String FIRST_WINDOWS_PARAMETER = "/c";\r
+\r
+ /** The second parameter for Runtime.exec() on Windows. */\r
+ private static final String SECOND_WINDOWS_PARAMETER = "start";\r
+\r
+ /**
+ * The third parameter for Runtime.exec() on Windows. This is a "title"
+ * parameter that the command line expects. Setting this parameter allows
+ * URLs containing spaces to work.
+ */\r
+ private static final String THIRD_WINDOWS_PARAMETER = "\"\"";\r
+\r
+ /**
+ * The shell parameters for Netscape that opens a given URL in an already-open copy of Netscape
+ * on many command-line systems.
+ */\r
+ private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";\r
+ private static final String NETSCAPE_OPEN_PARAMETER_START = "openURL(";\r
+ private static final String NETSCAPE_OPEN_NEW_WINDOW = ", new-window";\r
+ private static final String NETSCAPE_OPEN_PARAMETER_END = ")";\r
+\r
+ /**
+ * The message from any exception thrown throughout the initialization process.
+ */\r
+ private static String errorMessage;\r
+\r
+ /**
+ * An initialization block that determines the operating system and loads the necessary
+ * runtime data.
+ */\r
+ static {\r
+ loadedWithoutErrors = true;\r
+\r
+ String osName = System.getProperty("os.name");\r
+\r
+ if (osName.startsWith("Mac OS")) {\r
+ String mrjVersion = System.getProperty("mrj.version");\r
+ String majorMRJVersion = mrjVersion.substring(0, 3);\r
+\r
+ try {\r
+ double version = Double.valueOf(majorMRJVersion).doubleValue();\r
+\r
+ if (version == 2) {\r
+ jvm = MRJ_2_0;\r
+ } else if ((version >= 2.1) && (version < 3)) {\r
+ // Assume that all 2.x versions of MRJ work the same. MRJ 2.1 actually\r
+ // works via Runtime.exec() and 2.2 supports that but has an openURL() method\r
+ // as well that we currently ignore.\r
+ jvm = MRJ_2_1;\r
+ } else if (version == 3.0) {\r
+ jvm = MRJ_3_0;\r
+ } else if (version >= 3.1) {\r
+ // Assume that all 3.1 and later versions of MRJ work the same.\r
+ jvm = MRJ_3_1;\r
+ } else {\r
+ loadedWithoutErrors = false;\r
+ errorMessage = "Unsupported MRJ version: " + version;\r
+ }\r
+ } catch (NumberFormatException nfe) {\r
+ loadedWithoutErrors = false;\r
+ errorMessage = "Invalid MRJ version: " + mrjVersion;\r
+ }\r
+ } else if (osName.startsWith("Windows")) {\r
+ if (osName.indexOf("9") != -1) {\r
+ jvm = WINDOWS_9x;\r
+ } else {\r
+ jvm = WINDOWS_NT;\r
+ }\r
+ } else {\r
+ jvm = OTHER;\r
+ }\r
+\r
+ if (loadedWithoutErrors) { // if we haven't hit any errors yet\r
+ loadedWithoutErrors = loadClasses();\r
+ }\r
+ }\r
+\r
+ /**
+ * This class should be never be instantiated; this just ensures so.
+ */\r
+ private BrowserLauncher() {\r
+ }\r
+\r
+ /**
+ * Called by a static initializer to load any classes, fields, and methods required at runtime
+ * to locate the user's web browser.
+ * @return <code>true</code> if all intialization succeeded
+ * <code>false</code> if any portion of the initialization failed
+ */\r
+ private static boolean loadClasses() {\r
+ switch (jvm) {\r
+ case MRJ_2_0:\r
+\r
+ try {\r
+ Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");\r
+ Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");\r
+ Class appleEventClass = Class.forName(\r
+ "com.apple.MacOS.AppleEvent");\r
+ Class aeClass = Class.forName("com.apple.MacOS.ae");\r
+ aeDescClass = Class.forName("com.apple.MacOS.AEDesc");\r
+\r
+ aeTargetConstructor = aeTargetClass.getDeclaredConstructor(new Class[] {\r
+ int.class\r
+ });\r
+ appleEventConstructor = appleEventClass.getDeclaredConstructor(new Class[] {\r
+ int.class, int.class, aeTargetClass, int.class,\r
+ int.class\r
+ });\r
+ aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[] {\r
+ String.class\r
+ });\r
+\r
+ makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",\r
+ new Class[] { String.class });\r
+ putParameter = appleEventClass.getDeclaredMethod("putParameter",\r
+ new Class[] { int.class, aeDescClass });\r
+ sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",\r
+ new Class[] { });\r
+\r
+ Field keyDirectObjectField = aeClass.getDeclaredField(\r
+ "keyDirectObject");\r
+ keyDirectObject = (Integer) keyDirectObjectField.get(null);\r
+\r
+ Field autoGenerateReturnIDField = appleEventClass.getDeclaredField(\r
+ "kAutoGenerateReturnID");\r
+ kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField.get(null);\r
+\r
+ Field anyTransactionIDField = appleEventClass.getDeclaredField(\r
+ "kAnyTransactionID");\r
+ kAnyTransactionID = (Integer) anyTransactionIDField.get(null);\r
+ } catch (ClassNotFoundException cnfe) {\r
+ errorMessage = cnfe.getMessage();\r
+\r
+ return false;\r
+ } catch (NoSuchMethodException nsme) {\r
+ errorMessage = nsme.getMessage();\r
+\r
+ return false;\r
+ } catch (NoSuchFieldException nsfe) {\r
+ errorMessage = nsfe.getMessage();\r
+\r
+ return false;\r
+ } catch (IllegalAccessException iae) {\r
+ errorMessage = iae.getMessage();\r
+\r
+ return false;\r
+ }\r
+\r
+ break;\r
+\r
+ case MRJ_2_1:\r
+\r
+ try {\r
+ mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");\r
+ mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");\r
+\r
+ Field systemFolderField = mrjFileUtilsClass.getDeclaredField(\r
+ "kSystemFolderType");\r
+ kSystemFolderType = systemFolderField.get(null);\r
+ findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",\r
+ new Class[] { mrjOSTypeClass });\r
+ getFileCreator = mrjFileUtilsClass.getDeclaredMethod("getFileCreator",\r
+ new Class[] { File.class });\r
+ getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",\r
+ new Class[] { File.class });\r
+ } catch (ClassNotFoundException cnfe) {\r
+ errorMessage = cnfe.getMessage();\r
+\r
+ return false;\r
+ } catch (NoSuchFieldException nsfe) {\r
+ errorMessage = nsfe.getMessage();\r
+\r
+ return false;\r
+ } catch (NoSuchMethodException nsme) {\r
+ errorMessage = nsme.getMessage();\r
+\r
+ return false;\r
+ } catch (SecurityException se) {\r
+ errorMessage = se.getMessage();\r
+\r
+ return false;\r
+ } catch (IllegalAccessException iae) {\r
+ errorMessage = iae.getMessage();\r
+\r
+ return false;\r
+ }\r
+\r
+ break;\r
+\r
+ case MRJ_3_0:\r
+\r
+ try {\r
+ Class linker = Class.forName("com.apple.mrj.jdirect.Linker");\r
+ Constructor constructor = linker.getConstructor(new Class[] {\r
+ Class.class\r
+ });\r
+ linkage = constructor.newInstance(new Object[] {\r
+ BrowserLauncher.class\r
+ });\r
+ } catch (ClassNotFoundException cnfe) {\r
+ errorMessage = cnfe.getMessage();\r
+\r
+ return false;\r
+ } catch (NoSuchMethodException nsme) {\r
+ errorMessage = nsme.getMessage();\r
+\r
+ return false;\r
+ } catch (InvocationTargetException ite) {\r
+ errorMessage = ite.getMessage();\r
+\r
+ return false;\r
+ } catch (InstantiationException ie) {\r
+ errorMessage = ie.getMessage();\r
+\r
+ return false;\r
+ } catch (IllegalAccessException iae) {\r
+ errorMessage = iae.getMessage();\r
+\r
+ return false;\r
+ }\r
+\r
+ break;\r
+\r
+ case MRJ_3_1:\r
+\r
+ try {\r
+ mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");\r
+ openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",\r
+ new Class[] { String.class });\r
+ } catch (ClassNotFoundException cnfe) {\r
+ errorMessage = cnfe.getMessage();\r
+\r
+ return false;\r
+ } catch (NoSuchMethodException nsme) {\r
+ errorMessage = nsme.getMessage();\r
+\r
+ return false;\r
+ }\r
+\r
+ break;\r
+\r
+ default:\r
+ break;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ /**
+ * Attempts to locate the default web browser on the local system. Caches results so it
+ * only locates the browser once for each use of this class per JVM instance.
+ * @return The browser for the system. Note that this may not be what you would consider
+ * to be a standard web browser; instead, it's the application that gets called to
+ * open the default web browser. In some cases, this will be a non-String object
+ * that provides the means of calling the default browser.
+ */\r
+ private static Object locateBrowser() {\r
+ if (browser != null) {\r
+ return browser;\r
+ }\r
+\r
+ switch (jvm) {\r
+ case MRJ_2_0:\r
+\r
+ try {\r
+ Integer finderCreatorCode = (Integer) makeOSType.invoke(null,\r
+ new Object[] { FINDER_CREATOR });\r
+ Object aeTarget = aeTargetConstructor.newInstance(new Object[] {\r
+ finderCreatorCode\r
+ });\r
+ Integer gurlType = (Integer) makeOSType.invoke(null,\r
+ new Object[] { GURL_EVENT });\r
+ Object appleEvent = appleEventConstructor.newInstance(new Object[] {\r
+ gurlType, gurlType, aeTarget, kAutoGenerateReturnID,\r
+ kAnyTransactionID\r
+ });\r
+\r
+ // Don't set browser = appleEvent because then the next time we call\r
+ // locateBrowser(), we'll get the same AppleEvent, to which we'll already have\r
+ // added the relevant parameter. Instead, regenerate the AppleEvent every time.\r
+ // There's probably a way to do this better; if any has any ideas, please let\r
+ // me know.\r
+ return appleEvent;\r
+ } catch (IllegalAccessException iae) {\r
+ browser = null;\r
+ errorMessage = iae.getMessage();\r
+\r
+ return browser;\r
+ } catch (InstantiationException ie) {\r
+ browser = null;\r
+ errorMessage = ie.getMessage();\r
+\r
+ return browser;\r
+ } catch (InvocationTargetException ite) {\r
+ browser = null;\r
+ errorMessage = ite.getMessage();\r
+\r
+ return browser;\r
+ }\r
+\r
+ case MRJ_2_1:\r
+\r
+ File systemFolder;\r
+\r
+ try {\r
+ systemFolder = (File) findFolder.invoke(null,\r
+ new Object[] { kSystemFolderType });\r
+ } catch (IllegalArgumentException iare) {\r
+ browser = null;\r
+ errorMessage = iare.getMessage();\r
+\r
+ return browser;\r
+ } catch (IllegalAccessException iae) {\r
+ browser = null;\r
+ errorMessage = iae.getMessage();\r
+\r
+ return browser;\r
+ } catch (InvocationTargetException ite) {\r
+ browser = null;\r
+ errorMessage = ite.getTargetException().getClass() + ": " +\r
+ ite.getTargetException().getMessage();\r
+\r
+ return browser;\r
+ }\r
+\r
+ String[] systemFolderFiles = systemFolder.list();\r
+\r
+ // Avoid a FilenameFilter because that can't be stopped mid-list\r
+ for (int i = 0; i < systemFolderFiles.length; i++) {\r
+ try {\r
+ File file = new File(systemFolder, systemFolderFiles[i]);\r
+\r
+ if (!file.isFile()) {\r
+ continue;\r
+ }\r
+\r
+ // We're looking for a file with a creator code of 'MACS' and\r
+ // a type of 'FNDR'. Only requiring the type results in non-Finder\r
+ // applications being picked up on certain Mac OS 9 systems,\r
+ // especially German ones, and sending a GURL event to those\r
+ // applications results in a logout under Multiple Users.\r
+ Object fileType = getFileType.invoke(null,\r
+ new Object[] { file });\r
+\r
+ if (FINDER_TYPE.equals(fileType.toString())) {\r
+ Object fileCreator = getFileCreator.invoke(null,\r
+ new Object[] { file });\r
+\r
+ if (FINDER_CREATOR.equals(fileCreator.toString())) {\r
+ browser = file.toString(); // Actually the Finder, but that's OK\r
+\r
+ return browser;\r
+ }\r
+ }\r
+ } catch (IllegalArgumentException iare) {\r
+ browser = browser;\r
+ errorMessage = iare.getMessage();\r
+\r
+ return null;\r
+ } catch (IllegalAccessException iae) {\r
+ browser = null;\r
+ errorMessage = iae.getMessage();\r
+\r
+ return browser;\r
+ } catch (InvocationTargetException ite) {\r
+ browser = null;\r
+ errorMessage = ite.getTargetException().getClass() + ": " +\r
+ ite.getTargetException().getMessage();\r
+\r
+ return browser;\r
+ }\r
+ }\r
+\r
+ browser = null;\r
+\r
+ break;\r
+\r
+ case MRJ_3_0:\r
+ case MRJ_3_1:\r
+ browser = ""; // Return something non-null\r
+\r
+ break;\r
+\r
+ case WINDOWS_NT:\r
+ browser = "cmd.exe";\r
+\r
+ break;\r
+\r
+ case WINDOWS_9x:\r
+ browser = "command.com";\r
+\r
+ break;\r
+\r
+ case OTHER:default:\r
+ browser = jalview.bin.Cache.applicationProperties.getProperty(\r
+ "jalview.browser");\r
+\r
+ if (browser == null) {\r
+ // hope firefox exists :-/\r
+ browser = "firefox";\r
+ }\r
+\r
+ break;\r
+ }\r
+\r
+ return browser;\r
+ }\r
+\r
+ /**
+ * Attempts to open the default web browser to the given URL.
+ * @param url The URL to open
+ * @throws IOException If the web browser could not be located or does not run
+ */\r
+ public static void openURL(String url) throws IOException {\r
+ if (!loadedWithoutErrors) {\r
+ throw new IOException("Exception in finding browser: " +\r
+ errorMessage);\r
+ }\r
+\r
+ Object browser = locateBrowser();\r
+\r
+ if (browser == null) {\r
+ throw new IOException("Unable to locate browser: " + errorMessage);\r
+ }\r
+\r
+ switch (jvm) {\r
+ case MRJ_2_0:\r
+\r
+ Object aeDesc = null;\r
+\r
+ try {\r
+ aeDesc = aeDescConstructor.newInstance(new Object[] { url });\r
+ putParameter.invoke(browser,\r
+ new Object[] { keyDirectObject, aeDesc });\r
+ sendNoReply.invoke(browser, new Object[] { });\r
+ } catch (InvocationTargetException ite) {\r
+ throw new IOException(\r
+ "InvocationTargetException while creating AEDesc: " +\r
+ ite.getMessage());\r
+ } catch (IllegalAccessException iae) {\r
+ throw new IOException(\r
+ "IllegalAccessException while building AppleEvent: " +\r
+ iae.getMessage());\r
+ } catch (InstantiationException ie) {\r
+ throw new IOException(\r
+ "InstantiationException while creating AEDesc: " +\r
+ ie.getMessage());\r
+ } finally {\r
+ aeDesc = null; // Encourage it to get disposed if it was created\r
+ browser = null; // Ditto\r
+ }\r
+\r
+ break;\r
+\r
+ case MRJ_2_1:\r
+ Runtime.getRuntime().exec(new String[] { (String) browser, url });\r
+\r
+ break;\r
+\r
+ case MRJ_3_0:\r
+\r
+ int[] instance = new int[1];\r
+ int result = ICStart(instance, 0);\r
+\r
+ if (result == 0) {\r
+ int[] selectionStart = new int[] { 0 };\r
+ byte[] urlBytes = url.getBytes();\r
+ int[] selectionEnd = new int[] { urlBytes.length };\r
+ result = ICLaunchURL(instance[0], new byte[] { 0 }, urlBytes,\r
+ urlBytes.length, selectionStart, selectionEnd);\r
+\r
+ if (result == 0) {\r
+ // Ignore the return value; the URL was launched successfully\r
+ // regardless of what happens here.\r
+ ICStop(instance);\r
+ } else {\r
+ throw new IOException("Unable to launch URL: " + result);\r
+ }\r
+ } else {\r
+ throw new IOException(\r
+ "Unable to create an Internet Config instance: " + result);\r
+ }\r
+\r
+ break;\r
+\r
+ case MRJ_3_1:\r
+\r
+ try {\r
+ openURL.invoke(null, new Object[] { url });\r
+ } catch (InvocationTargetException ite) {\r
+ throw new IOException(\r
+ "InvocationTargetException while calling openURL: " +\r
+ ite.getMessage());\r
+ } catch (IllegalAccessException iae) {\r
+ throw new IOException(\r
+ "IllegalAccessException while calling openURL: " +\r
+ iae.getMessage());\r
+ }\r
+\r
+ break;\r
+\r
+ case WINDOWS_NT:\r
+ case WINDOWS_9x:\r
+\r
+ // Add quotes around the URL to allow ampersands and other special\r
+ // characters to work.\r
+ Process process = Runtime.getRuntime().exec(new String[] {\r
+ (String) browser, FIRST_WINDOWS_PARAMETER,\r
+ SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,\r
+ '"' + url + '"'\r
+ });\r
+\r
+ // This avoids a memory leak on some versions of Java on Windows.\r
+ // That's hinted at in <http://developer.java.sun.com/developer/qow/archive/68/>.\r
+ try {\r
+ process.waitFor();\r
+ process.exitValue();\r
+ } catch (InterruptedException ie) {\r
+ throw new IOException(\r
+ "InterruptedException while launching browser: " +\r
+ ie.getMessage());\r
+ }\r
+\r
+ break;\r
+\r
+ case OTHER:\r
+\r
+ // Assume that we're on Unix and that Netscape (actually Firefox) is installed\r
+ // First, attempt to open the URL in a currently running session of Netscape\r
+ // JBPNote log debug\r
+\r
+ /* System.out.println("Executing : "+browser+" "+
+ NETSCAPE_REMOTE_PARAMETER+" "+
+ NETSCAPE_OPEN_PARAMETER_START +
+ url +
+ NETSCAPE_OPEN_NEW_WINDOW +
+ NETSCAPE_OPEN_PARAMETER_END);
+ */\r
+ process = Runtime.getRuntime().exec(new String[] {\r
+ (String) browser, NETSCAPE_REMOTE_PARAMETER,\r
+ \r
+ NETSCAPE_OPEN_PARAMETER_START + url +\r
+ NETSCAPE_OPEN_NEW_WINDOW + NETSCAPE_OPEN_PARAMETER_END\r
+ });\r
+\r
+ try {\r
+ int exitCode = process.waitFor();\r
+\r
+ if (exitCode != 0) { // if Netscape was not open\r
+ Runtime.getRuntime().exec(new String[] { (String) browser, url });\r
+ }\r
+ } catch (InterruptedException ie) {\r
+ throw new IOException(\r
+ "InterruptedException while launching browser: " +\r
+ ie.getMessage());\r
+ }\r
+\r
+ break;\r
+\r
+ default:\r
+\r
+ // This should never occur, but if it does, we'll try the simplest thing possible\r
+ Runtime.getRuntime().exec(new String[] { (String) browser, url });\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ /**
+ * Methods required for Mac OS X. The presence of native methods does not cause
+ * any problems on other platforms.
+ */\r
+ private native static int ICStart(int[] instance, int signature);\r
+\r
+ private native static int ICStop(int[] instance);\r
+\r
+ private native static int ICLaunchURL(int instance, byte[] hint,\r
+ byte[] data, int len, int[] selectionStart, int[] selectionEnd);\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.util;\r
\r
import jalview.datamodel.*;\r
\r
+\r
public class Comparison {\r
+ public static String GapChars = " .-";\r
\r
- public static float compare(SequenceI ii, SequenceI jj)\r
- {\r
- return Comparison.compare(ii,jj,0,ii.getLength()-1);\r
- }\r
- /**\r
- * this was supposed to be an ungapped pid calculation\r
- * @param ii SequenceI\r
- * @param jj SequenceI\r
- * @param start int\r
- * @param end int\r
- * @return float\r
- */\r
- public static float compare(SequenceI ii, SequenceI jj, int start, int end) {\r
-\r
- String si = ii.getSequence();\r
- String sj = jj.getSequence();\r
-\r
- int ilen = si.length()-1;\r
- int jlen = sj.length()-1;\r
-\r
- while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r
- {\r
- ilen--;\r
- }\r
-\r
- while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))\r
- {\r
- jlen--;\r
- }\r
-\r
- int count = 0;\r
- int match = 0;\r
- float pid = -1;\r
-\r
- if (ilen > jlen) {\r
-\r
- for (int j = 0; j < jlen; j++) {\r
- if (si.substring(start + j,start + j+1).equals(sj.substring(start + j,start + j+1))) {\r
- match++;\r
- }\r
- count++;\r
- }\r
- pid = (float)match/(float)ilen * 100;\r
- } else {\r
- for (int j = 0; j < jlen; j++) {\r
- if (si.substring(start + j,start + j+1).equals(sj.substring(start + j,start + j+1))) {\r
- match++;\r
- }\r
- count++;\r
- }\r
- pid = (float)match/(float)jlen * 100;\r
- }\r
-\r
- return pid;\r
- }\r
-\r
- /**\r
- * this is a gapped PID calculation\r
- *\r
- * @param s1 SequenceI\r
- * @param s2 SequenceI\r
- * @return float\r
- */\r
- public static float PID(SequenceI s1 , SequenceI s2)\r
- {\r
- int len;\r
-\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- len = s1.getSequence().length();\r
- else\r
- len = s2.getSequence().length();\r
-\r
-\r
- int bad = 0;\r
-\r
- for (int i = 0; i < len; i++)\r
- {\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- chr1 = s1.getSequence().charAt(i);\r
- else\r
- chr1 = '.';\r
-\r
-\r
- if (i < s2.getSequence().length())\r
- chr2 = s2.getSequence().charAt(i);\r
- else\r
- chr2 = '.';\r
-\r
-\r
- if (!(jalview.util.Comparison.isGap( chr1 )) && !(jalview.util.Comparison.isGap( chr2 )))\r
- {\r
- if (chr1!=chr2)\r
- bad++;\r
- }\r
+ public static float compare(SequenceI ii, SequenceI jj) {\r
+ return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
}\r
\r
- return (float)100*(len-bad)/len;\r
- }\r
-\r
- // Another pid with region specification\r
-\r
- public static float PID(SequenceI s1 , SequenceI s2, int start, int end)\r
- {\r
- int len;\r
-\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- len = s1.getSequence().length();\r
- else\r
- len = s2.getSequence().length();\r
-\r
- if (end<len)\r
- len=end;\r
-\r
- if (len<start) {\r
- start = len - 1; // we just use a single residue for the difference\r
+ /**\r
+ * this was supposed to be an ungapped pid calculation\r
+ * @param ii SequenceI\r
+ * @param jj SequenceI\r
+ * @param start int\r
+ * @param end int\r
+ * @return float\r
+ */\r
+ public static float compare(SequenceI ii, SequenceI jj, int start, int end) {\r
+ String si = ii.getSequence();\r
+ String sj = jj.getSequence();\r
+\r
+ int ilen = si.length() - 1;\r
+ int jlen = sj.length() - 1;\r
+\r
+ while (jalview.util.Comparison.isGap(si.charAt(start + ilen))) {\r
+ ilen--;\r
+ }\r
+\r
+ while (jalview.util.Comparison.isGap(sj.charAt(start + jlen))) {\r
+ jlen--;\r
+ }\r
+\r
+ int count = 0;\r
+ int match = 0;\r
+ float pid = -1;\r
+\r
+ if (ilen > jlen) {\r
+ for (int j = 0; j < jlen; j++) {\r
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
+ j, start + j + 1))) {\r
+ match++;\r
+ }\r
+\r
+ count++;\r
+ }\r
+\r
+ pid = (float) match / (float) ilen * 100;\r
+ } else {\r
+ for (int j = 0; j < jlen; j++) {\r
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
+ j, start + j + 1))) {\r
+ match++;\r
+ }\r
+\r
+ count++;\r
+ }\r
+\r
+ pid = (float) match / (float) jlen * 100;\r
+ }\r
+\r
+ return pid;\r
}\r
\r
- int bad = 0;\r
-\r
- for (int i = start; i < len; i++)\r
- {\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- chr1 = s1.getSequence().charAt(i);\r
- else\r
- chr1 = '.';\r
-\r
-\r
- if (i < s2.getSequence().length())\r
- chr2 = s2.getSequence().charAt(i);\r
- else\r
- chr2 = '.';\r
-\r
-\r
- if (!(jalview.util.Comparison.isGap( chr1 )) && !(jalview.util.Comparison.isGap( chr2 )))\r
- {\r
- if (chr1!=chr2)\r
- bad++;\r
- }\r
+ /**\r
+ * this is a gapped PID calculation\r
+ *\r
+ * @param s1 SequenceI\r
+ * @param s2 SequenceI\r
+ * @return float\r
+ */\r
+ public static float PID(SequenceI s1, SequenceI s2) {\r
+ int len;\r
+\r
+ if (s1.getSequence().length() > s2.getSequence().length()) {\r
+ len = s1.getSequence().length();\r
+ } else {\r
+ len = s2.getSequence().length();\r
+ }\r
+\r
+ int bad = 0;\r
+\r
+ for (int i = 0; i < len; i++) {\r
+ char chr1;\r
+ char chr2;\r
+\r
+ if (i < s1.getSequence().length()) {\r
+ chr1 = s1.getSequence().charAt(i);\r
+ } else {\r
+ chr1 = '.';\r
+ }\r
+\r
+ if (i < s2.getSequence().length()) {\r
+ chr2 = s2.getSequence().charAt(i);\r
+ } else {\r
+ chr2 = '.';\r
+ }\r
+\r
+ if (!(jalview.util.Comparison.isGap(chr1)) &&\r
+ !(jalview.util.Comparison.isGap(chr2))) {\r
+ if (chr1 != chr2) {\r
+ bad++;\r
+ }\r
+ }\r
+ }\r
+\r
+ return ((float) 100 * (len - bad)) / len;\r
}\r
\r
- return (float)100*(len-bad)/len;\r
- }\r
-\r
+ // Another pid with region specification\r
+ public static float PID(SequenceI s1, SequenceI s2, int start, int end) {\r
+ int len;\r
+\r
+ if (s1.getSequence().length() > s2.getSequence().length()) {\r
+ len = s1.getSequence().length();\r
+ } else {\r
+ len = s2.getSequence().length();\r
+ }\r
+\r
+ if (end < len) {\r
+ len = end;\r
+ }\r
+\r
+ if (len < start) {\r
+ start = len - 1; // we just use a single residue for the difference\r
+ }\r
+\r
+ int bad = 0;\r
+\r
+ for (int i = start; i < len; i++) {\r
+ char chr1;\r
+ char chr2;\r
+\r
+ if (i < s1.getSequence().length()) {\r
+ chr1 = s1.getSequence().charAt(i);\r
+ } else {\r
+ chr1 = '.';\r
+ }\r
+\r
+ if (i < s2.getSequence().length()) {\r
+ chr2 = s2.getSequence().charAt(i);\r
+ } else {\r
+ chr2 = '.';\r
+ }\r
+\r
+ if (!(jalview.util.Comparison.isGap(chr1)) &&\r
+ !(jalview.util.Comparison.isGap(chr2))) {\r
+ if (chr1 != chr2) {\r
+ bad++;\r
+ }\r
+ }\r
+ }\r
+\r
+ return ((float) 100 * (len - bad)) / len;\r
+ }\r
\r
- public static String GapChars = " .-";\r
- public static boolean isGap(char c)\r
- {\r
- return (c != '.' && c != '-' && c != ' ') ? false : true;\r
- }\r
+ public static boolean isGap(char c) {\r
+ return ((c != '.') && (c != '-') && (c != ' ')) ? false : true;\r
+ }\r
}\r
* @version 1.03 25 Oct 1997\r
* @author Cay Horstmann\r
*/\r
-\r
-\r
package jalview.util;\r
\r
import java.io.*;\r
\r
+\r
public class Format {\r
+ private int width;\r
+ private int precision;\r
+ private String pre;\r
+ private String post;\r
+ private boolean leading_zeroes;\r
+ private boolean show_plus;\r
+ private boolean alternate;\r
+ private boolean show_space;\r
+ private boolean left_align;\r
+ private char fmt; // one of cdeEfgGiosxXos\r
+\r
+ public Format(String s) {\r
+ width = 0;\r
+ precision = -1;\r
+ pre = "";\r
+ post = "";\r
+ leading_zeroes = false;\r
+ show_plus = false;\r
+ alternate = false;\r
+ show_space = false;\r
+ left_align = false;\r
+ fmt = ' ';\r
+\r
+ int state = 0;\r
+ int length = s.length();\r
+ int parse_state = 0;\r
+\r
+ // 0 = prefix, 1 = flags, 2 = width, 3 = precision,\r
+ // 4 = format, 5 = end\r
+ int i = 0;\r
+\r
+ while (parse_state == 0) {\r
+ if (i >= length) {\r
+ parse_state = 5;\r
+ } else if (s.charAt(i) == '%') {\r
+ if (i < (length - 1)) {\r
+ if (s.charAt(i + 1) == '%') {\r
+ pre = pre + '%';\r
+ i++;\r
+ } else {\r
+ parse_state = 1;\r
+ }\r
+ } else {\r
+ throw new java.lang.IllegalArgumentException();\r
+ }\r
+ } else {\r
+ pre = pre + s.charAt(i);\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ while (parse_state == 1) {\r
+ if (i >= length) {\r
+ parse_state = 5;\r
+ } else if (s.charAt(i) == ' ') {\r
+ show_space = true;\r
+ } else if (s.charAt(i) == '-') {\r
+ left_align = true;\r
+ } else if (s.charAt(i) == '+') {\r
+ show_plus = true;\r
+ } else if (s.charAt(i) == '0') {\r
+ leading_zeroes = true;\r
+ } else if (s.charAt(i) == '#') {\r
+ alternate = true;\r
+ } else {\r
+ parse_state = 2;\r
+ i--;\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ while (parse_state == 2) {\r
+ if (i >= length) {\r
+ parse_state = 5;\r
+ } else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9')) {\r
+ width = ((width * 10) + s.charAt(i)) - '0';\r
+ i++;\r
+ } else if (s.charAt(i) == '.') {\r
+ parse_state = 3;\r
+ precision = 0;\r
+ i++;\r
+ } else {\r
+ parse_state = 4;\r
+ }\r
+ }\r
+\r
+ while (parse_state == 3) {\r
+ if (i >= length) {\r
+ parse_state = 5;\r
+ } else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9')) {\r
+ precision = ((precision * 10) + s.charAt(i)) - '0';\r
+ i++;\r
+ } else {\r
+ parse_state = 4;\r
+ }\r
+ }\r
+\r
+ if (parse_state == 4) {\r
+ if (i >= length) {\r
+ parse_state = 5;\r
+ } else {\r
+ fmt = s.charAt(i);\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ if (i < length) {\r
+ post = s.substring(i, length);\r
+ }\r
+ }\r
+\r
/**\r
* Formats the number following printf conventions.\r
* Main limitation: Can only handle one format parameter at a time\r
* @exception IllegalArgumentException if bad format\r
*\r
*/\r
+ public static String getHexString(java.awt.Color color) {\r
+ String r;\r
+ String g;\r
+ String b;\r
+ r = Integer.toHexString(color.getRed());\r
+\r
+ if (r.length() < 2) {\r
+ r = "0" + r;\r
+ }\r
\r
- public static String getHexString(java.awt.Color color)\r
- {\r
- String r, g, b;\r
- r = Integer.toHexString(color.getRed());\r
- if (r.length() < 2)\r
- r = "0" + r;\r
- g = Integer.toHexString(color.getGreen());\r
- if (g.length() < 2)\r
- g = "0" + g;\r
- b = Integer.toHexString(color.getBlue());\r
- if (b.length() < 2)\r
- b = "0" + b;\r
-\r
- return r+g+b;\r
- }\r
-\r
-\r
- public Format(String s) {\r
- width = 0;\r
- precision = -1;\r
- pre = "";\r
- post = "";\r
- leading_zeroes = false;\r
- show_plus = false;\r
- alternate = false;\r
- show_space = false;\r
- left_align = false;\r
- fmt = ' ';\r
-\r
- int state = 0;\r
- int length = s.length();\r
- int parse_state = 0;\r
- // 0 = prefix, 1 = flags, 2 = width, 3 = precision,\r
- // 4 = format, 5 = end\r
- int i = 0;\r
-\r
- while (parse_state == 0) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if (s.charAt(i) == '%') {\r
- if (i < length - 1) {\r
- if (s.charAt(i + 1) == '%') {\r
- pre = pre + '%';\r
- i++;\r
- } else\r
- parse_state = 1;\r
- } else\r
- throw new java.lang.IllegalArgumentException();\r
- } else\r
- pre = pre + s.charAt(i);\r
- i++;\r
+ g = Integer.toHexString(color.getGreen());\r
+\r
+ if (g.length() < 2) {\r
+ g = "0" + g;\r
+ }\r
+\r
+ b = Integer.toHexString(color.getBlue());\r
+\r
+ if (b.length() < 2) {\r
+ b = "0" + b;\r
+ }\r
+\r
+ return r + g + b;\r
}\r
- while (parse_state == 1) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if (s.charAt(i) == ' ')\r
- show_space = true;\r
- else if (s.charAt(i) == '-')\r
- left_align = true;\r
- else if (s.charAt(i) == '+')\r
- show_plus = true;\r
- else if (s.charAt(i) == '0')\r
- leading_zeroes = true;\r
- else if (s.charAt(i) == '#')\r
- alternate = true;\r
- else {\r
- parse_state = 2;\r
- i--;\r
- }\r
- i++;\r
+\r
+ /**\r
+ * prints a formatted number following printf conventions\r
+ * @param s a PrintStream\r
+ * @param fmt the format string\r
+ * @param x the double to print\r
+ */\r
+ public static void print(java.io.PrintStream s, String fmt, double x) {\r
+ s.print(new Format(fmt).form(x));\r
}\r
- while (parse_state == 2) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') {\r
- width = width * 10 + s.charAt(i) - '0';\r
- i++;\r
- } else if (s.charAt(i) == '.') {\r
- parse_state = 3;\r
- precision = 0;\r
- i++;\r
- } else\r
- parse_state = 4;\r
+\r
+ /**\r
+ * prints a formatted number following printf conventions\r
+ * @param s a PrintStream\r
+ * @param fmt the format string\r
+ * @param x the long to print\r
+ */\r
+ public static void print(java.io.PrintStream s, String fmt, long x) {\r
+ s.print(new Format(fmt).form(x));\r
}\r
- while (parse_state == 3) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') {\r
- precision = precision * 10 + s.charAt(i) - '0';\r
- i++;\r
- } else\r
- parse_state = 4;\r
+\r
+ /**\r
+ * prints a formatted number following printf conventions\r
+ * @param s a PrintStream\r
+ * @param fmt the format string\r
+ * @param x the character to\r
+ */\r
+ public static void print(java.io.PrintStream s, String fmt, char x) {\r
+ s.print(new Format(fmt).form(x));\r
}\r
- if (parse_state == 4) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else\r
- fmt = s.charAt(i);\r
- i++;\r
+\r
+ /**\r
+ * prints a formatted number following printf conventions\r
+ * @param s a PrintStream, fmt the format string\r
+ * @param x a string that represents the digits to print\r
+ */\r
+ public static void print(java.io.PrintStream s, String fmt, String x) {\r
+ s.print(new Format(fmt).form(x));\r
}\r
- if (i < length)\r
- post = s.substring(i, length);\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the double to print\r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, double x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the long to print\r
- */\r
- public static void print(java.io.PrintStream s, String fmt, long x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the character to\r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, char x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream, fmt the format string\r
- * @param x a string that represents the digits to print\r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, String x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * Converts a string of digits (decimal, octal or hex) to an integer\r
- * @param s a string\r
- * @return the numeric value of the prefix of s representing a base 10 integer\r
- */\r
-\r
- public static int atoi(String s) {\r
- return (int)atol(s);\r
- }\r
-\r
- /**\r
- * Converts a string of digits (decimal, octal or hex) to a long integer\r
- * @param s a string\r
- * @return the numeric value of the prefix of s representing a base 10 integer\r
- */\r
-\r
- public static long atol(String s) {\r
- int i = 0;\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '0') {\r
- if (i + 1 < s.length() && (s.charAt(i + 1) == 'x' || s.charAt(i + 1) == 'X'))\r
- return parseLong(s.substring(i + 2), 16);\r
- else\r
- return parseLong(s, 8);\r
- } else\r
- return parseLong(s, 10);\r
- }\r
-\r
- private static long parseLong(String s, int base) {\r
- int i = 0;\r
- int sign = 1;\r
- long r = 0;\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '-') {\r
- sign = -1;\r
- i++;\r
- } else if (i < s.length() && s.charAt(i) == '+') {\r
- i++;\r
+\r
+ /**\r
+ * Converts a string of digits (decimal, octal or hex) to an integer\r
+ * @param s a string\r
+ * @return the numeric value of the prefix of s representing a base 10 integer\r
+ */\r
+ public static int atoi(String s) {\r
+ return (int) atol(s);\r
}\r
- while (i < s.length()) {\r
- char ch = s.charAt(i);\r
- if ('0' <= ch && ch < '0' + base)\r
- r = r * base + ch - '0';\r
- else if ('A' <= ch && ch < 'A' + base - 10)\r
- r = r * base + ch - 'A' + 10 ;\r
- else if ('a' <= ch && ch < 'a' + base - 10)\r
- r = r * base + ch - 'a' + 10 ;\r
- else\r
- return r * sign;\r
- i++;\r
+\r
+ /**\r
+ * Converts a string of digits (decimal, octal or hex) to a long integer\r
+ * @param s a string\r
+ * @return the numeric value of the prefix of s representing a base 10 integer\r
+ */\r
+ public static long atol(String s) {\r
+ int i = 0;\r
+\r
+ while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))\r
+ i++;\r
+\r
+ if ((i < s.length()) && (s.charAt(i) == '0')) {\r
+ if (((i + 1) < s.length()) &&\r
+ ((s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X'))) {\r
+ return parseLong(s.substring(i + 2), 16);\r
+ } else {\r
+ return parseLong(s, 8);\r
+ }\r
+ } else {\r
+ return parseLong(s, 10);\r
+ }\r
}\r
- return r * sign;\r
- }\r
-\r
- /**\r
- * Converts a string of digits to an double\r
- * @param s a string\r
- */\r
-\r
- public static double atof(String s) {\r
- int i = 0;\r
- int sign = 1;\r
- double r = 0; // integer part\r
- double f = 0; // fractional part\r
- double p = 1; // exponent of fractional part\r
- int state = 0; // 0 = int part, 1 = frac part\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '-') {\r
- sign = -1;\r
- i++;\r
- } else if (i < s.length() && s.charAt(i) == '+') {\r
- i++;\r
+\r
+ private static long parseLong(String s, int base) {\r
+ int i = 0;\r
+ int sign = 1;\r
+ long r = 0;\r
+\r
+ while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))\r
+ i++;\r
+\r
+ if ((i < s.length()) && (s.charAt(i) == '-')) {\r
+ sign = -1;\r
+ i++;\r
+ } else if ((i < s.length()) && (s.charAt(i) == '+')) {\r
+ i++;\r
+ }\r
+\r
+ while (i < s.length()) {\r
+ char ch = s.charAt(i);\r
+\r
+ if (('0' <= ch) && (ch < ('0' + base))) {\r
+ r = ((r * base) + ch) - '0';\r
+ } else if (('A' <= ch) && (ch < (('A' + base) - 10))) {\r
+ r = ((r * base) + ch) - 'A' + 10;\r
+ } else if (('a' <= ch) && (ch < (('a' + base) - 10))) {\r
+ r = ((r * base) + ch) - 'a' + 10;\r
+ } else {\r
+ return r * sign;\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ return r * sign;\r
}\r
- while (i < s.length()) {\r
- char ch = s.charAt(i);\r
- if ('0' <= ch && ch <= '9') {\r
- if (state == 0)\r
- r = r * 10 + ch - '0';\r
- else if (state == 1) {\r
- p = p / 10;\r
- r = r + p * (ch - '0');\r
- }\r
- } else if (ch == '.') {\r
- if (state == 0)\r
- state = 1;\r
- else\r
- return sign * r;\r
- } else if (ch == 'e' || ch == 'E') {\r
- long e = (int)parseLong(s.substring(i + 1), 10);\r
- return sign * r * Math.pow(10, e);\r
- } else\r
+\r
+ /**\r
+ * Converts a string of digits to an double\r
+ * @param s a string\r
+ */\r
+ public static double atof(String s) {\r
+ int i = 0;\r
+ int sign = 1;\r
+ double r = 0; // integer part\r
+ double f = 0; // fractional part\r
+ double p = 1; // exponent of fractional part\r
+ int state = 0; // 0 = int part, 1 = frac part\r
+\r
+ while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))\r
+ i++;\r
+\r
+ if ((i < s.length()) && (s.charAt(i) == '-')) {\r
+ sign = -1;\r
+ i++;\r
+ } else if ((i < s.length()) && (s.charAt(i) == '+')) {\r
+ i++;\r
+ }\r
+\r
+ while (i < s.length()) {\r
+ char ch = s.charAt(i);\r
+\r
+ if (('0' <= ch) && (ch <= '9')) {\r
+ if (state == 0) {\r
+ r = ((r * 10) + ch) - '0';\r
+ } else if (state == 1) {\r
+ p = p / 10;\r
+ r = r + (p * (ch - '0'));\r
+ }\r
+ } else if (ch == '.') {\r
+ if (state == 0) {\r
+ state = 1;\r
+ } else {\r
+ return sign * r;\r
+ }\r
+ } else if ((ch == 'e') || (ch == 'E')) {\r
+ long e = (int) parseLong(s.substring(i + 1), 10);\r
+\r
+ return sign * r * Math.pow(10, e);\r
+ } else {\r
+ return sign * r;\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
return sign * r;\r
- i++;\r
}\r
- return sign * r;\r
- }\r
-\r
- /**\r
- * Formats a double into a string (like sprintf in C)\r
- * @param x the number to format\r
- * @return the formatted string\r
- * @exception IllegalArgumentException if bad argument\r
- */\r
-\r
- public String form(double x) {\r
- String r;\r
- if (precision < 0)\r
- precision = 6;\r
- int s = 1;\r
- if (x < 0) {\r
- x = -x;\r
- s = -1;\r
+\r
+ /**\r
+ * Formats a double into a string (like sprintf in C)\r
+ * @param x the number to format\r
+ * @return the formatted string\r
+ * @exception IllegalArgumentException if bad argument\r
+ */\r
+ public String form(double x) {\r
+ String r;\r
+\r
+ if (precision < 0) {\r
+ precision = 6;\r
+ }\r
+\r
+ int s = 1;\r
+\r
+ if (x < 0) {\r
+ x = -x;\r
+ s = -1;\r
+ }\r
+\r
+ if (fmt == 'f') {\r
+ r = fixed_format(x);\r
+ } else if ((fmt == 'e') || (fmt == 'E') || (fmt == 'g') ||\r
+ (fmt == 'G')) {\r
+ r = exp_format(x);\r
+ } else {\r
+ throw new java.lang.IllegalArgumentException();\r
+ }\r
+\r
+ return pad(sign(s, r));\r
}\r
- if (fmt == 'f')\r
- r = fixed_format(x);\r
- else if (fmt == 'e' || fmt == 'E' || fmt == 'g' || fmt == 'G')\r
- r = exp_format(x);\r
- else\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- return pad(sign(s, r));\r
- }\r
-\r
- /**\r
- * Formats a long integer into a string (like sprintf in C)\r
- * @param x the number to format\r
- * @return the formatted string\r
- */\r
-\r
- public String form(long x) {\r
- String r;\r
- int s = 0;\r
- if (fmt == 'd' || fmt == 'i') {\r
- if (x < 0) {\r
- r = ("" + x).substring(1);\r
- s = -1;\r
- } else {\r
- r = "" + x;\r
- s = 1;\r
- }\r
- } else if (fmt == 'o')\r
- r = convert(x, 3, 7, "01234567");\r
- else if (fmt == 'x')\r
- r = convert(x, 4, 15, "0123456789abcdef");\r
- else if (fmt == 'X')\r
- r = convert(x, 4, 15, "0123456789ABCDEF");\r
- else\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- return pad(sign(s, r));\r
- }\r
-\r
- /**\r
- * Formats a character into a string (like sprintf in C)\r
- * @param x the value to format\r
- * @return the formatted string\r
- */\r
-\r
- public String form(char c) {\r
- if (fmt != 'c')\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- String r = "" + c;\r
- return pad(r);\r
- }\r
-\r
- /**\r
- * Formats a string into a larger string (like sprintf in C)\r
- * @param x the value to format\r
- * @return the formatted string\r
- */\r
-\r
- public String form(String s) {\r
- if (fmt != 's')\r
- throw new java.lang.IllegalArgumentException();\r
- if (precision >= 0)\r
- s = s.substring(0, precision);\r
- return pad(s);\r
- }\r
-\r
-\r
- /**\r
- * a test stub for the format class\r
- */\r
-\r
- public static void main(String[] a) {\r
- double x = 1.23456789012;\r
- double y = 123;\r
- double z = 1.2345e30;\r
- double w = 1.02;\r
- double u = 1.234e-5;\r
- int d = 0xCAFE;\r
- Format.print(System.out, "x = |%f|\n", x);\r
- Format.print(System.out, "u = |%20f|\n", u);\r
- Format.print(System.out, "x = |% .5f|\n", x);\r
- Format.print(System.out, "w = |%20.5f|\n", w);\r
- Format.print(System.out, "x = |%020.5f|\n", x);\r
- Format.print(System.out, "x = |%+20.5f|\n", x);\r
- Format.print(System.out, "x = |%+020.5f|\n", x);\r
- Format.print(System.out, "x = |% 020.5f|\n", x);\r
- Format.print(System.out, "y = |%#+20.5f|\n", y);\r
- Format.print(System.out, "y = |%-+20.5f|\n", y);\r
- Format.print(System.out, "z = |%20.5f|\n", z);\r
-\r
- Format.print(System.out, "x = |%e|\n", x);\r
- Format.print(System.out, "u = |%20e|\n", u);\r
- Format.print(System.out, "x = |% .5e|\n", x);\r
- Format.print(System.out, "w = |%20.5e|\n", w);\r
- Format.print(System.out, "x = |%020.5e|\n", x);\r
- Format.print(System.out, "x = |%+20.5e|\n", x);\r
- Format.print(System.out, "x = |%+020.5e|\n", x);\r
- Format.print(System.out, "x = |% 020.5e|\n", x);\r
- Format.print(System.out, "y = |%#+20.5e|\n", y);\r
- Format.print(System.out, "y = |%-+20.5e|\n", y);\r
-\r
- Format.print(System.out, "x = |%g|\n", x);\r
- Format.print(System.out, "z = |%g|\n", z);\r
- Format.print(System.out, "w = |%g|\n", w);\r
- Format.print(System.out, "u = |%g|\n", u);\r
- Format.print(System.out, "y = |%.2g|\n", y);\r
- Format.print(System.out, "y = |%#.2g|\n", y);\r
-\r
- Format.print(System.out, "d = |%d|\n", d);\r
- Format.print(System.out, "d = |%20d|\n", d);\r
- Format.print(System.out, "d = |%020d|\n", d);\r
- Format.print(System.out, "d = |%+20d|\n", d);\r
- Format.print(System.out, "d = |% 020d|\n", d);\r
- Format.print(System.out, "d = |%-20d|\n", d);\r
- Format.print(System.out, "d = |%20.8d|\n", d);\r
- Format.print(System.out, "d = |%x|\n", d);\r
- Format.print(System.out, "d = |%20X|\n", d);\r
- Format.print(System.out, "d = |%#20x|\n", d);\r
- Format.print(System.out, "d = |%020X|\n", d);\r
- Format.print(System.out, "d = |%20.8x|\n", d);\r
- Format.print(System.out, "d = |%o|\n", d);\r
- Format.print(System.out, "d = |%020o|\n", d);\r
- Format.print(System.out, "d = |%#20o|\n", d);\r
- Format.print(System.out, "d = |%#020o|\n", d);\r
- Format.print(System.out, "d = |%20.12o|\n", d);\r
-\r
- Format.print(System.out, "s = |%-20s|\n", "Hello");\r
- Format.print(System.out, "s = |%-20c|\n", '!');\r
-\r
- // regression test to confirm fix of reported bugs\r
-\r
- Format.print(System.out, "|%i|\n", Long.MIN_VALUE);\r
-\r
- Format.print(System.out, "|%6.2e|\n", 0.0);\r
- Format.print(System.out, "|%6.2g|\n", 0.0);\r
-\r
- Format.print(System.out, "|%6.2f|\n", 9.99);\r
- Format.print(System.out, "|%6.2f|\n", 9.999);\r
-\r
- Format.print(System.out, "|%6.0f|\n", 9.999);\r
- }\r
-\r
- private static String repeat(char c, int n) {\r
- if (n <= 0)\r
- return "";\r
- StringBuffer s = new StringBuffer(n);\r
- for (int i = 0; i < n; i++)\r
- s.append(c);\r
- return s.toString();\r
- }\r
-\r
- private static String convert(long x, int n, int m, String d) {\r
- if (x == 0)\r
- return "0";\r
- String r = "";\r
- while (x != 0) {\r
- r = d.charAt((int)(x & m)) + r;\r
- x = x >>> n;\r
+\r
+ /**\r
+ * Formats a long integer into a string (like sprintf in C)\r
+ * @param x the number to format\r
+ * @return the formatted string\r
+ */\r
+ public String form(long x) {\r
+ String r;\r
+ int s = 0;\r
+\r
+ if ((fmt == 'd') || (fmt == 'i')) {\r
+ if (x < 0) {\r
+ r = ("" + x).substring(1);\r
+ s = -1;\r
+ } else {\r
+ r = "" + x;\r
+ s = 1;\r
+ }\r
+ } else if (fmt == 'o') {\r
+ r = convert(x, 3, 7, "01234567");\r
+ } else if (fmt == 'x') {\r
+ r = convert(x, 4, 15, "0123456789abcdef");\r
+ } else if (fmt == 'X') {\r
+ r = convert(x, 4, 15, "0123456789ABCDEF");\r
+ } else {\r
+ throw new java.lang.IllegalArgumentException();\r
+ }\r
+\r
+ return pad(sign(s, r));\r
}\r
- return r;\r
- }\r
-\r
- private String pad(String r) {\r
- String p = repeat(' ', width - r.length());\r
- if (left_align)\r
- return pre + r + p + post;\r
- else\r
- return pre + p + r + post;\r
- }\r
-\r
- private String sign(int s, String r) {\r
- String p = "";\r
- if (s < 0)\r
- p = "-";\r
- else if (s > 0) {\r
- if (show_plus)\r
- p = "+";\r
- else if (show_space)\r
- p = " ";\r
- } else {\r
- if (fmt == 'o' && alternate && r.length() > 0 && r.charAt(0) != '0')\r
- p = "0";\r
- else if (fmt == 'x' && alternate)\r
- p = "0x";\r
- else if (fmt == 'X' && alternate)\r
- p = "0X";\r
+\r
+ /**\r
+ * Formats a character into a string (like sprintf in C)\r
+ * @param x the value to format\r
+ * @return the formatted string\r
+ */\r
+ public String form(char c) {\r
+ if (fmt != 'c') {\r
+ throw new java.lang.IllegalArgumentException();\r
+ }\r
+\r
+ String r = "" + c;\r
+\r
+ return pad(r);\r
}\r
- int w = 0;\r
- if (leading_zeroes)\r
- w = width;\r
- else if ((fmt == 'd' || fmt == 'i' || fmt == 'x' || fmt == 'X' || fmt == 'o')\r
- && precision > 0)\r
- w = precision;\r
-\r
- return p + repeat('0', w - p.length() - r.length()) + r;\r
- }\r
-\r
- private String fixed_format(double d) {\r
- boolean removeTrailing\r
- = (fmt == 'G' || fmt == 'g') && !alternate;\r
- // remove trailing zeroes and decimal point\r
-\r
- if (d > 0x7FFFFFFFFFFFFFFFL)\r
- return exp_format(d);\r
- if (precision == 0)\r
- return (long)(d + 0.5) + (removeTrailing ? "" : ".");\r
-\r
- long whole = (long)d;\r
- double fr = d - whole; // fractional part\r
- if (fr >= 1 || fr < 0)\r
- return exp_format(d);\r
-\r
- double factor = 1;\r
- String leading_zeroes = "";\r
- for (int i = 1; i <= precision && factor <= 0x7FFFFFFFFFFFFFFFL; i++) {\r
- factor *= 10;\r
- leading_zeroes = leading_zeroes + "0";\r
+\r
+ /**\r
+ * Formats a string into a larger string (like sprintf in C)\r
+ * @param x the value to format\r
+ * @return the formatted string\r
+ */\r
+ public String form(String s) {\r
+ if (fmt != 's') {\r
+ throw new java.lang.IllegalArgumentException();\r
+ }\r
+\r
+ if (precision >= 0) {\r
+ s = s.substring(0, precision);\r
+ }\r
+\r
+ return pad(s);\r
}\r
- long l = (long) (factor * fr + 0.5);\r
- if (l >= factor) {\r
- l = 0;\r
- whole++;\r
- } // CSH 10-25-97\r
-\r
- String z = leading_zeroes + l;\r
- z = "." + z.substring(z.length() - precision, z.length());\r
-\r
- if (removeTrailing) {\r
- int t = z.length() - 1;\r
- while (t >= 0 && z.charAt(t) == '0')\r
- t--;\r
- if (t >= 0 && z.charAt(t) == '.')\r
- t--;\r
- z = z.substring(0, t + 1);\r
+\r
+ /**\r
+ * a test stub for the format class\r
+ */\r
+ public static void main(String[] a) {\r
+ double x = 1.23456789012;\r
+ double y = 123;\r
+ double z = 1.2345e30;\r
+ double w = 1.02;\r
+ double u = 1.234e-5;\r
+ int d = 0xCAFE;\r
+ Format.print(System.out, "x = |%f|\n", x);\r
+ Format.print(System.out, "u = |%20f|\n", u);\r
+ Format.print(System.out, "x = |% .5f|\n", x);\r
+ Format.print(System.out, "w = |%20.5f|\n", w);\r
+ Format.print(System.out, "x = |%020.5f|\n", x);\r
+ Format.print(System.out, "x = |%+20.5f|\n", x);\r
+ Format.print(System.out, "x = |%+020.5f|\n", x);\r
+ Format.print(System.out, "x = |% 020.5f|\n", x);\r
+ Format.print(System.out, "y = |%#+20.5f|\n", y);\r
+ Format.print(System.out, "y = |%-+20.5f|\n", y);\r
+ Format.print(System.out, "z = |%20.5f|\n", z);\r
+\r
+ Format.print(System.out, "x = |%e|\n", x);\r
+ Format.print(System.out, "u = |%20e|\n", u);\r
+ Format.print(System.out, "x = |% .5e|\n", x);\r
+ Format.print(System.out, "w = |%20.5e|\n", w);\r
+ Format.print(System.out, "x = |%020.5e|\n", x);\r
+ Format.print(System.out, "x = |%+20.5e|\n", x);\r
+ Format.print(System.out, "x = |%+020.5e|\n", x);\r
+ Format.print(System.out, "x = |% 020.5e|\n", x);\r
+ Format.print(System.out, "y = |%#+20.5e|\n", y);\r
+ Format.print(System.out, "y = |%-+20.5e|\n", y);\r
+\r
+ Format.print(System.out, "x = |%g|\n", x);\r
+ Format.print(System.out, "z = |%g|\n", z);\r
+ Format.print(System.out, "w = |%g|\n", w);\r
+ Format.print(System.out, "u = |%g|\n", u);\r
+ Format.print(System.out, "y = |%.2g|\n", y);\r
+ Format.print(System.out, "y = |%#.2g|\n", y);\r
+\r
+ Format.print(System.out, "d = |%d|\n", d);\r
+ Format.print(System.out, "d = |%20d|\n", d);\r
+ Format.print(System.out, "d = |%020d|\n", d);\r
+ Format.print(System.out, "d = |%+20d|\n", d);\r
+ Format.print(System.out, "d = |% 020d|\n", d);\r
+ Format.print(System.out, "d = |%-20d|\n", d);\r
+ Format.print(System.out, "d = |%20.8d|\n", d);\r
+ Format.print(System.out, "d = |%x|\n", d);\r
+ Format.print(System.out, "d = |%20X|\n", d);\r
+ Format.print(System.out, "d = |%#20x|\n", d);\r
+ Format.print(System.out, "d = |%020X|\n", d);\r
+ Format.print(System.out, "d = |%20.8x|\n", d);\r
+ Format.print(System.out, "d = |%o|\n", d);\r
+ Format.print(System.out, "d = |%020o|\n", d);\r
+ Format.print(System.out, "d = |%#20o|\n", d);\r
+ Format.print(System.out, "d = |%#020o|\n", d);\r
+ Format.print(System.out, "d = |%20.12o|\n", d);\r
+\r
+ Format.print(System.out, "s = |%-20s|\n", "Hello");\r
+ Format.print(System.out, "s = |%-20c|\n", '!');\r
+\r
+ // regression test to confirm fix of reported bugs\r
+ Format.print(System.out, "|%i|\n", Long.MIN_VALUE);\r
+\r
+ Format.print(System.out, "|%6.2e|\n", 0.0);\r
+ Format.print(System.out, "|%6.2g|\n", 0.0);\r
+\r
+ Format.print(System.out, "|%6.2f|\n", 9.99);\r
+ Format.print(System.out, "|%6.2f|\n", 9.999);\r
+\r
+ Format.print(System.out, "|%6.0f|\n", 9.999);\r
}\r
\r
- return whole + z;\r
- }\r
-\r
- private String exp_format(double d) {\r
- String f = "";\r
- int e = 0;\r
- double dd = d;\r
- double factor = 1;\r
- if (d != 0) {\r
- while (dd > 10) {\r
- e++;\r
- factor /= 10;\r
- dd = dd / 10;\r
- }\r
- while (dd < 1) {\r
- e--;\r
- factor *= 10;\r
- dd = dd * 10;\r
- }\r
+ private static String repeat(char c, int n) {\r
+ if (n <= 0) {\r
+ return "";\r
+ }\r
+\r
+ StringBuffer s = new StringBuffer(n);\r
+\r
+ for (int i = 0; i < n; i++)\r
+ s.append(c);\r
+\r
+ return s.toString();\r
}\r
- if ((fmt == 'g' || fmt == 'G') && e >= -4 && e < precision)\r
- return fixed_format(d);\r
-\r
- d = d * factor;\r
- f = f + fixed_format(d);\r
-\r
- if (fmt == 'e' || fmt == 'g')\r
- f = f + "e";\r
- else\r
- f = f + "E";\r
-\r
- String p = "000";\r
- if (e >= 0) {\r
- f = f + "+";\r
- p = p + e;\r
- } else {\r
- f = f + "-";\r
- p = p + (-e);\r
+\r
+ private static String convert(long x, int n, int m, String d) {\r
+ if (x == 0) {\r
+ return "0";\r
+ }\r
+\r
+ String r = "";\r
+\r
+ while (x != 0) {\r
+ r = d.charAt((int) (x & m)) + r;\r
+ x = x >>> n;\r
+ }\r
+\r
+ return r;\r
}\r
\r
- return f + p.substring(p.length() - 3, p.length());\r
- }\r
-\r
- private int width;\r
- private int precision;\r
- private String pre;\r
- private String post;\r
- private boolean leading_zeroes;\r
- private boolean show_plus;\r
- private boolean alternate;\r
- private boolean show_space;\r
- private boolean left_align;\r
- private char fmt; // one of cdeEfgGiosxXos\r
-}\r
+ private String pad(String r) {\r
+ String p = repeat(' ', width - r.length());\r
+\r
+ if (left_align) {\r
+ return pre + r + p + post;\r
+ } else {\r
+ return pre + p + r + post;\r
+ }\r
+ }\r
\r
+ private String sign(int s, String r) {\r
+ String p = "";\r
+\r
+ if (s < 0) {\r
+ p = "-";\r
+ } else if (s > 0) {\r
+ if (show_plus) {\r
+ p = "+";\r
+ } else if (show_space) {\r
+ p = " ";\r
+ }\r
+ } else {\r
+ if ((fmt == 'o') && alternate && (r.length() > 0) &&\r
+ (r.charAt(0) != '0')) {\r
+ p = "0";\r
+ } else if ((fmt == 'x') && alternate) {\r
+ p = "0x";\r
+ } else if ((fmt == 'X') && alternate) {\r
+ p = "0X";\r
+ }\r
+ }\r
+\r
+ int w = 0;\r
+\r
+ if (leading_zeroes) {\r
+ w = width;\r
+ } else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') ||\r
+ (fmt == 'X') || (fmt == 'o')) && (precision > 0)) {\r
+ w = precision;\r
+ }\r
+\r
+ return p + repeat('0', w - p.length() - r.length()) + r;\r
+ }\r
+\r
+ private String fixed_format(double d) {\r
+ boolean removeTrailing = ((fmt == 'G') || (fmt == 'g')) && !alternate;\r
\r
+ // remove trailing zeroes and decimal point\r
+ if (d > 0x7FFFFFFFFFFFFFFFL) {\r
+ return exp_format(d);\r
+ }\r
+\r
+ if (precision == 0) {\r
+ return (long) (d + 0.5) + (removeTrailing ? "" : ".");\r
+ }\r
+\r
+ long whole = (long) d;\r
+ double fr = d - whole; // fractional part\r
+\r
+ if ((fr >= 1) || (fr < 0)) {\r
+ return exp_format(d);\r
+ }\r
+\r
+ double factor = 1;\r
+ String leading_zeroes = "";\r
+\r
+ for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL);\r
+ i++) {\r
+ factor *= 10;\r
+ leading_zeroes = leading_zeroes + "0";\r
+ }\r
+\r
+ long l = (long) ((factor * fr) + 0.5);\r
+\r
+ if (l >= factor) {\r
+ l = 0;\r
+ whole++;\r
+ }\r
+ // CSH 10-25-97\r
\r
+ String z = leading_zeroes + l;\r
+ z = "." + z.substring(z.length() - precision, z.length());\r
\r
+ if (removeTrailing) {\r
+ int t = z.length() - 1;\r
\r
+ while ((t >= 0) && (z.charAt(t) == '0'))\r
+ t--;\r
+\r
+ if ((t >= 0) && (z.charAt(t) == '.')) {\r
+ t--;\r
+ }\r
+\r
+ z = z.substring(0, t + 1);\r
+ }\r
+\r
+ return whole + z;\r
+ }\r
+\r
+ private String exp_format(double d) {\r
+ String f = "";\r
+ int e = 0;\r
+ double dd = d;\r
+ double factor = 1;\r
+\r
+ if (d != 0) {\r
+ while (dd > 10) {\r
+ e++;\r
+ factor /= 10;\r
+ dd = dd / 10;\r
+ }\r
+\r
+ while (dd < 1) {\r
+ e--;\r
+ factor *= 10;\r
+ dd = dd * 10;\r
+ }\r
+ }\r
+\r
+ if (((fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision)) {\r
+ return fixed_format(d);\r
+ }\r
+\r
+ d = d * factor;\r
+ f = f + fixed_format(d);\r
+\r
+ if ((fmt == 'e') || (fmt == 'g')) {\r
+ f = f + "e";\r
+ } else {\r
+ f = f + "E";\r
+ }\r
+\r
+ String p = "000";\r
+\r
+ if (e >= 0) {\r
+ f = f + "+";\r
+ p = p + e;\r
+ } else {\r
+ f = f + "-";\r
+ p = p + (-e);\r
+ }\r
+\r
+ return f + p.substring(p.length() - 3, p.length());\r
+ }\r
+}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.util;\r
\r
-\r
public class QuickSort {\r
+ public static void sort(float[] arr, Object[] s) {\r
+ sort(arr, 0, arr.length - 1, s);\r
+ }\r
\r
- public static void sort(float[] arr,Object[] s) {\r
- sort(arr,0,arr.length-1,s);\r
- }\r
-\r
- public static void sort(String[] arr,Object[] s) {\r
- stringSort(arr,0,arr.length-1,s);\r
- }\r
+ public static void sort(String[] arr, Object[] s) {\r
+ stringSort(arr, 0, arr.length - 1, s);\r
+ }\r
\r
- public static void stringSort(String[] arr,int p, int r,Object[] s) {\r
- int q;\r
+ public static void stringSort(String[] arr, int p, int r, Object[] s) {\r
+ int q;\r
\r
- if (p < r) {\r
- q = stringPartition(arr,p,r,s);\r
- stringSort(arr,p,q,s);\r
- stringSort(arr,q+1,r,s);\r
+ if (p < r) {\r
+ q = stringPartition(arr, p, r, s);\r
+ stringSort(arr, p, q, s);\r
+ stringSort(arr, q + 1, r, s);\r
+ }\r
}\r
- }\r
\r
- public static void sort(float[] arr,int p, int r,Object[] s) {\r
- int q;\r
+ public static void sort(float[] arr, int p, int r, Object[] s) {\r
+ int q;\r
\r
- if (p < r) {\r
- q = partition(arr,p,r,s);\r
- sort(arr,p,q,s);\r
- sort(arr,q+1,r,s);\r
+ if (p < r) {\r
+ q = partition(arr, p, r, s);\r
+ sort(arr, p, q, s);\r
+ sort(arr, q + 1, r, s);\r
+ }\r
}\r
- }\r
-\r
- private static int partition(float[] arr, int p, int r,Object[] s) {\r
- float x = arr[p];\r
- int i = p-1;\r
- int j = r+1;\r
-\r
- while(true) {\r
- do {\r
- j = j-1;\r
- } while (arr[j] > x);\r
-\r
- do {\r
- i = i+1;\r
- } while (arr[i] < x);\r
-\r
- if ( i < j) {\r
- float tmp = arr[i];\r
- arr[i] = arr[j];\r
- arr[j] = tmp;\r
-\r
- Object tmp2 = s[i];\r
- s[i] = s[j];\r
- s[j] = tmp2;\r
- } else {\r
- return j;\r
- }\r
+\r
+ private static int partition(float[] arr, int p, int r, Object[] s) {\r
+ float x = arr[p];\r
+ int i = p - 1;\r
+ int j = r + 1;\r
+\r
+ while (true) {\r
+ do {\r
+ j = j - 1;\r
+ } while (arr[j] > x);\r
+\r
+ do {\r
+ i = i + 1;\r
+ } while (arr[i] < x);\r
+\r
+ if (i < j) {\r
+ float tmp = arr[i];\r
+ arr[i] = arr[j];\r
+ arr[j] = tmp;\r
+\r
+ Object tmp2 = s[i];\r
+ s[i] = s[j];\r
+ s[j] = tmp2;\r
+ } else {\r
+ return j;\r
+ }\r
+ }\r
}\r
- }\r
- private static int stringPartition(String[] arr, int p, int r,Object[] s) {\r
- String x = arr[p];\r
- int i = p-1;\r
- int j = r+1;\r
-\r
- while(true) {\r
- do {\r
- j = j-1;\r
- } while (arr[j].compareTo(x) < 0);\r
-\r
- do {\r
- i = i+1;\r
- } while (arr[i].compareTo(x) > 0);\r
-\r
- if ( i < j) {\r
- String tmp = arr[i];\r
- arr[i] = arr[j];\r
- arr[j] = tmp;\r
-\r
- Object tmp2 = s[i];\r
- s[i] = s[j];\r
- s[j] = tmp2;\r
- } else {\r
- return j;\r
- }\r
+\r
+ private static int stringPartition(String[] arr, int p, int r, Object[] s) {\r
+ String x = arr[p];\r
+ int i = p - 1;\r
+ int j = r + 1;\r
+\r
+ while (true) {\r
+ do {\r
+ j = j - 1;\r
+ } while (arr[j].compareTo(x) < 0);\r
+\r
+ do {\r
+ i = i + 1;\r
+ } while (arr[i].compareTo(x) > 0);\r
+\r
+ if (i < j) {\r
+ String tmp = arr[i];\r
+ arr[i] = arr[j];\r
+ arr[j] = tmp;\r
+\r
+ Object tmp2 = s[i];\r
+ s[i] = s[j];\r
+ s[j] = tmp2;\r
+ } else {\r
+ return j;\r
+ }\r
+ }\r
}\r
- }\r
}\r
-\r
-\r
-\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.ws;\r
\r
-import org.apache.axis.client.*;\r
-import javax.xml.namespace.QName;\r
-import java.util.*;\r
+import ext.vamsas.*;\r
+\r
+import jalview.analysis.AlignSeq;\r
+\r
import jalview.datamodel.*;\r
+\r
import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
+\r
+import org.apache.axis.client.*;\r
+\r
import java.awt.*;\r
-import jalview.analysis.AlignSeq;\r
-import ext.vamsas.*;\r
\r
-public class JPredClient\r
- extends WSClient\r
-{\r
- ext.vamsas.JPredWS server;\r
- String altitle = "";\r
- java.util.Hashtable SequenceInfo = null;\r
- private WebserviceInfo setWebService()\r
- {\r
- WebServiceName = "JNetWS";\r
- WebServiceJobTitle = "JNet secondary structure prediction";\r
- WebServiceReference =\r
- "\"Cuff J. A and Barton G.J (1999) Application of enhanced "\r
- + "multiple sequence alignment profiles to improve protein secondary structure prediction, "\r
- + "Proteins 40:502-511\".";\r
- WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
- WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
- WebServiceReference);\r
-\r
- return wsInfo;\r
- }\r
-\r
- private boolean locateWebService()\r
- {\r
-\r
- JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
- try\r
- {\r
- this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
- ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The Secondary Structure Prediction Service named "\r
- + WebServiceName + " at " + WsURL +\r
- " couldn't be located.",\r
- "Internal Jalview Error",\r
- JOptionPane.WARNING_MESSAGE);\r
- wsInfo.setProgressText("Serious! " + WebServiceName +\r
- " Service location failed\nfor URL :"\r
- + WsURL + "\n" + ex.getMessage());\r
- wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
- return false;\r
- }\r
- return true;\r
+import java.util.*;\r
+\r
+import javax.swing.*;\r
+\r
+import javax.xml.namespace.QName;\r
+\r
+\r
+public class JPredClient extends WSClient {\r
+ ext.vamsas.JPredWS server;\r
+ String altitle = "";\r
+ java.util.Hashtable SequenceInfo = null;\r
+\r
+ public JPredClient(String title, SequenceI[] msf) {\r
+ wsInfo = setWebService();\r
+\r
+ SequenceI seq = msf[0];\r
+ altitle = "JNet prediction on " + seq.getName() +\r
+ " using alignment from " + title;\r
+\r
+ wsInfo.setProgressText("Job details for MSA based prediction (" +\r
+ title + ") on sequence :\n>" + seq.getName() + "\n" +\r
+ AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");\r
+\r
+ SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+\r
+ if (!locateWebService()) {\r
+ return;\r
+ }\r
+\r
+ JPredThread jthread = new JPredThread(msf);\r
+ jthread.start();\r
}\r
\r
- public JPredClient(String title, SequenceI[] msf)\r
- {\r
- wsInfo = setWebService();\r
- SequenceI seq = msf[0];\r
- altitle = "JNet prediction on " + seq.getName() +\r
- " using alignment from " + title;\r
-\r
- wsInfo.setProgressText("Job details for MSA based prediction (" + title +\r
- ") on sequence :\n>"\r
- + seq.getName() + "\n"\r
- + AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
- "\n");\r
-\r
- SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
- if (!locateWebService())\r
- return;\r
-\r
- JPredThread jthread = new JPredThread(msf);\r
- jthread.start();\r
+ public JPredClient(String title, SequenceI seq) {\r
+ wsInfo = setWebService();\r
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
+ seq.getName() + "\n" +\r
+ AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");\r
+ altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
+ title;\r
+\r
+ SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+\r
+ if (!locateWebService()) {\r
+ return;\r
+ }\r
+\r
+ JPredThread jthread = new JPredThread(seq);\r
+ jthread.start();\r
}\r
\r
- public JPredClient(String title, SequenceI seq)\r
- {\r
- wsInfo = setWebService();\r
- wsInfo.setProgressText("Job details for prediction on sequence :\n>"\r
- + seq.getName() + "\n" +\r
- AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
- "\n");\r
- altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
- title;\r
+ private WebserviceInfo setWebService() {\r
+ WebServiceName = "JNetWS";\r
+ WebServiceJobTitle = "JNet secondary structure prediction";\r
+ WebServiceReference = "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +\r
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, " +\r
+ "Proteins 40:502-511\".";\r
+ WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
\r
- SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+ WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
+ WebServiceReference);\r
\r
- if (!locateWebService())\r
- return;\r
+ return wsInfo;\r
+ }\r
+\r
+ private boolean locateWebService() {\r
+ JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
+\r
+ try {\r
+ this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
+ ((JpredSoapBindingStub) this.server).setTimeout(60000); // one minute stub\r
+ } catch (Exception ex) {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The Secondary Structure Prediction Service named " +\r
+ WebServiceName + " at " + WsURL + " couldn't be located.",\r
+ "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
+ wsInfo.setProgressText("Serious! " + WebServiceName +\r
+ " Service location failed\nfor URL :" + WsURL + "\n" +\r
+ ex.getMessage());\r
+ wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+\r
+ return false;\r
+ }\r
\r
- JPredThread jthread = new JPredThread(seq);\r
- jthread.start();\r
+ return true;\r
}\r
\r
- class JPredThread\r
- extends Thread\r
- {\r
- String OutputHeader;\r
- ext.vamsas.JpredResult result;\r
- ext.vamsas.Sequence sequence;\r
- ext.vamsas.Msfalignment msa;\r
- String jobId;\r
- boolean jobComplete = false;\r
- int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
- JPredThread(SequenceI seq)\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new ext.vamsas.Sequence();\r
- this.sequence.setId(seq.getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
- }\r
-\r
- JPredThread(SequenceI[] msf)\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new ext.vamsas.Sequence();\r
- this.sequence.setId(msf[0].getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ", msf[0].getSequence()));\r
- jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
- this.msa = new ext.vamsas.Msfalignment();\r
- msa.setMsf(mwrite.print(msf));\r
- }\r
-\r
- public void run()\r
- {\r
-\r
- StartJob();\r
-\r
- while (!jobComplete && (allowedServerExceptions > 0))\r
- {\r
- try\r
- {\r
- if ( (result = server.getresult(jobId)) == null)\r
- {\r
- throw (new Exception(\r
- "Timed out when communicating with server\nTry again later.\n"));\r
- }\r
+ class JPredThread extends Thread {\r
+ String OutputHeader;\r
+ ext.vamsas.JpredResult result;\r
+ ext.vamsas.Sequence sequence;\r
+ ext.vamsas.Msfalignment msa;\r
+ String jobId;\r
+ boolean jobComplete = false;\r
+ int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
+\r
+ JPredThread(SequenceI seq) {\r
+ OutputHeader = wsInfo.getProgressText();\r
+ this.sequence = new ext.vamsas.Sequence();\r
+ this.sequence.setId(seq.getName());\r
+ this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
+ }\r
\r
- if (result.isRunning())\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
- }\r
- else if (result.isQueued())\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ JPredThread(SequenceI[] msf) {\r
+ OutputHeader = wsInfo.getProgressText();\r
+ this.sequence = new ext.vamsas.Sequence();\r
+ this.sequence.setId(msf[0].getName());\r
+ this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
+ msf[0].getSequence()));\r
+\r
+ jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
+ this.msa = new ext.vamsas.Msfalignment();\r
+ msa.setMsf(mwrite.print(msf));\r
+ }\r
+\r
+ public void run() {\r
+ StartJob();\r
+\r
+ while (!jobComplete && (allowedServerExceptions > 0)) {\r
+ try {\r
+ if ((result = server.getresult(jobId)) == null) {\r
+ throw (new Exception(\r
+ "Timed out when communicating with server\nTry again later.\n"));\r
+ }\r
+\r
+ if (result.isRunning()) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+ } else if (result.isQueued()) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ }\r
+\r
+ if (result.isFinished()) {\r
+ parseResult();\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ } else {\r
+ wsInfo.setProgressText(OutputHeader + "\n" +\r
+ result.getStatus());\r
+\r
+ if (!(result.isJobFailed() || result.isServerError())) {\r
+ try {\r
+ Thread.sleep(5000);\r
+ } catch (InterruptedException ex1) {\r
+ }\r
+\r
+ // System.out.println("I'm alive "+seqid+" "+jobid);\r
+ } else {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
+ }\r
+ } catch (Exception ex) {\r
+ allowedServerExceptions--;\r
+ wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
+ ex.getMessage());\r
+\r
+ try {\r
+ if (allowedServerExceptions > 0) {\r
+ Thread.sleep(5000);\r
+ }\r
+ } catch (InterruptedException ex1) {\r
+ }\r
+ }\r
}\r
\r
- if (result.isFinished())\r
- {\r
- parseResult();\r
- jobComplete = true;\r
- jobsRunning--;\r
+ if (!(result.isJobFailed() || result.isServerError())) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ } else {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
}\r
- else\r
- {\r
- wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- {\r
- try\r
- {\r
- Thread.sleep(5000);\r
+ }\r
+\r
+ void StartJob() {\r
+ try {\r
+ if (msa != null) {\r
+ jobId = server.predictOnMsa(msa);\r
+ } else {\r
+ jobId = server.predict(sequence);\r
}\r
- catch (InterruptedException ex1)\r
- {\r
+\r
+ if (jobId != null) {\r
+ if (jobId.startsWith("Broken")) {\r
+ throw new Exception("Submission " + jobId);\r
+ } else {\r
+ System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+ }\r
+ } else {\r
+ throw new Exception("Server timed out - try again later\n");\r
}\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\r
- }\r
- else\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- allowedServerExceptions--;\r
- wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
- ex.getMessage());\r
- try\r
- {\r
- if (allowedServerExceptions > 0)\r
- {\r
- Thread.sleep(5000);\r
- }\r
- }\r
- catch (InterruptedException ex1)\r
- {\r
+ } catch (Exception e) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ allowedServerExceptions = 0;\r
+ jobComplete = false;\r
+ wsInfo.appendProgressText("Failed to submit the prediction: " +\r
+ e.toString() + "\nJust close the window\n");\r
+ System.err.println(\r
+ "JPredWS Client: Failed to submit the prediction\n" +\r
+ e.toString() + "\n");\r
+\r
+ // e.printStackTrace(); TODO: JBPNote DEBUG\r
}\r
- }\r
}\r
\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- }\r
- else\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ private void addFloatAnnotations(Alignment al, int[] gapmap,\r
+ Vector values, String Symname, String Visname, float min,\r
+ float max, int winLength) {\r
+ Annotation[] annotations = new Annotation[al.getWidth()];\r
+\r
+ for (int j = 0; j < values.size(); j++) {\r
+ float value = Float.parseFloat(values.get(j).toString());\r
+ annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
+ value);\r
+ }\r
+\r
+ al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
+ annotations, min, max, winLength));\r
}\r
- }\r
-\r
- void StartJob()\r
- {\r
- try\r
- {\r
- if (msa != null)\r
- {\r
- jobId = server.predictOnMsa(msa);\r
- }\r
- else\r
- {\r
- jobId = server.predict(sequence);\r
- }\r
- if (jobId != null)\r
- {\r
- if (jobId.startsWith("Broken"))\r
- {\r
- throw new Exception("Submission " + jobId);\r
+\r
+ void parseResult() {\r
+ // OutputHeader = output.getText();\r
+ if (result.isFailed()) {\r
+ OutputHeader += "Job failed.\n";\r
}\r
- else\r
- {\r
- System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+\r
+ if (result.getStatus() != null) {\r
+ OutputHeader += ("\n" + result.getStatus());\r
}\r
- }\r
- else\r
- {\r
- throw new Exception("Server timed out - try again later\n");\r
\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- allowedServerExceptions = 0;\r
- jobComplete = false;\r
- wsInfo.appendProgressText("Failed to submit the prediction: " +\r
- e.toString() + "\nJust close the window\n");\r
- System.err.println(\r
- "JPredWS Client: Failed to submit the prediction\n" +\r
- e.toString() + "\n");\r
- // e.printStackTrace(); TODO: JBPNote DEBUG\r
- }\r
- }\r
-\r
- private void addFloatAnnotations(Alignment al, int[] gapmap,\r
- Vector values, String Symname,\r
- String Visname, float min, float max,\r
- int winLength)\r
- {\r
-\r
- Annotation[] annotations = new Annotation[al.getWidth()];\r
- for (int j = 0; j < values.size(); j++)\r
- {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[gapmap[j]] = new Annotation("", value + "", ' ', value);\r
- }\r
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations,\r
- min, max, winLength));\r
- }\r
-\r
- void parseResult()\r
- {\r
- // OutputHeader = output.getText();\r
- if (result.isFailed())\r
- {\r
- OutputHeader += "Job failed.\n";\r
- }\r
- if (result.getStatus() != null)\r
- {\r
- OutputHeader += "\n" + result.getStatus();\r
- }\r
- if (result.getPredfile() != null)\r
- {\r
- OutputHeader += "\n" + result.getPredfile();\r
- // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
- }\r
- if (result.getAligfile() != null)\r
- {\r
- OutputHeader += "\n" + result.getAligfile();\r
- }\r
- wsInfo.setProgressText(OutputHeader);\r
- try\r
- {\r
- // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
- getPredfile(), "Paste");\r
- SequenceI[] preds = prediction.getSeqsAsArray();\r
- Alignment al;\r
- int FirstSeq; // the position of the query sequence in Alignment al\r
- boolean noMsa = true; // set if no MSA has been returned by JPred\r
-\r
- if (this.msa != null && result.getAligfile() != null)\r
- {\r
- // we ignore the returned alignment if we only predicted on a single sequence\r
- String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
- "Paste");\r
- if (jalview.io.FormatAdapter.formats.contains(format))\r
- {\r
- al = new Alignment(jalview.io.FormatAdapter.readFile(result.\r
- getAligfile(), "Paste", format));\r
- noMsa = false;\r
- FirstSeq = 0;\r
+ if (result.getPredfile() != null) {\r
+ OutputHeader += ("\n" + result.getPredfile());\r
+\r
+ // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
}\r
- else\r
- {\r
- throw (new Exception("Unknown format 'format' for file : \n" +\r
- result.getAligfile()));\r
+\r
+ if (result.getAligfile() != null) {\r
+ OutputHeader += ("\n" + result.getAligfile());\r
}\r
\r
- }\r
- else\r
- {\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.getQuerySeqPosition();\r
- }\r
-\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al.getSequenceAt(\r
- FirstSeq), SequenceInfo))\r
- {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for JNet Query sequence!"));\r
- }\r
-\r
- AlignmentAnnotation annot;\r
- Annotation[] annotations = null;\r
- int i = 0;\r
- int width = preds[0].getSequence().length();\r
-\r
- int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
-\r
- if (gapmap.length != width)\r
- {\r
- throw (new Exception(\r
- "Jnet Client Error\nNumber of residues in supposed query sequence :\n"\r
- + al.getSequenceAt(FirstSeq).getName() + "\n"\r
- + al.getSequenceAt(FirstSeq).getSequence()\r
- + "\nDiffer from number of prediction sites in \n" +\r
- result.getPredfile() + "\n"));\r
- }\r
- // JBPNote Should also rename the query sequence sometime...\r
- i = 0;\r
- while (i < preds.length)\r
- {\r
- String id = preds[i].getName().toUpperCase();\r
- if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
- id.startsWith("JPRED"))\r
- {\r
- annotations = new Annotation[al.getWidth()];\r
-\r
- if (id.equals("JNETPRED")\r
- || id.equals("JNETPSSM")\r
- || id.equals("JNETFREQ")\r
- || id.equals("JNETHMM")\r
- || id.equals("JNETALIGN")\r
- || id.equals("JPRED"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- annotations[gapmap[j]] = new Annotation("", "",\r
- preds[i].getCharAt(j), 0);\r
+ wsInfo.setProgressText(OutputHeader);\r
+\r
+ try {\r
+ // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(),\r
+ "Paste");\r
+ SequenceI[] preds = prediction.getSeqsAsArray();\r
+ Alignment al;\r
+ int FirstSeq; // the position of the query sequence in Alignment al\r
+ boolean noMsa = true; // set if no MSA has been returned by JPred\r
+\r
+ if ((this.msa != null) && (result.getAligfile() != null)) {\r
+ // we ignore the returned alignment if we only predicted on a single sequence\r
+ String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
+ "Paste");\r
+\r
+ if (jalview.io.FormatAdapter.formats.contains(format)) {\r
+ al = new Alignment(jalview.io.FormatAdapter.readFile(\r
+ result.getAligfile(), "Paste", format));\r
+ noMsa = false;\r
+ FirstSeq = 0;\r
+ } else {\r
+ throw (new Exception(\r
+ "Unknown format 'format' for file : \n" +\r
+ result.getAligfile()));\r
+ }\r
+ } else {\r
+ al = new Alignment(preds);\r
+ FirstSeq = prediction.getQuerySeqPosition();\r
}\r
- }\r
- else if (id.equals("JNETCONF"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- float value = Float.parseFloat(preds[i].getCharAt(j) + "");\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j) +\r
- "", "", preds[i].getCharAt(j), value);\r
+\r
+ if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
+ al.getSequenceAt(FirstSeq), SequenceInfo)) {\r
+ throw (new Exception(\r
+ "Couldn't recover sequence properties for JNet Query sequence!"));\r
}\r
- }\r
- else\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j) +\r
- "", "", ' ', 0);\r
+\r
+ AlignmentAnnotation annot;\r
+ Annotation[] annotations = null;\r
+ int i = 0;\r
+ int width = preds[0].getSequence().length();\r
+\r
+ int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
+\r
+ if (gapmap.length != width) {\r
+ throw (new Exception(\r
+ "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +\r
+ al.getSequenceAt(FirstSeq).getName() + "\n" +\r
+ al.getSequenceAt(FirstSeq).getSequence() +\r
+ "\nDiffer from number of prediction sites in \n" +\r
+ result.getPredfile() + "\n"));\r
}\r
- }\r
-\r
- if (id.equals("JNETCONF"))\r
- {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output",\r
- annotations, 0f, 10f, 1);\r
- }\r
-\r
- else\r
- {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output",\r
- annotations);\r
- }\r
- al.addAnnotation(annot);\r
- if (noMsa)\r
- {\r
- al.deleteSequence(preds[i]);\r
- }\r
- }\r
- i++;\r
- }\r
\r
- Hashtable scores = prediction.getScores();\r
- /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),\r
- "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
+ // JBPNote Should also rename the query sequence sometime...\r
+ i = 0;\r
+\r
+ while (i < preds.length) {\r
+ String id = preds[i].getName().toUpperCase();\r
+\r
+ if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
+ id.startsWith("JPRED")) {\r
+ annotations = new Annotation[al.getWidth()];\r
+\r
+ if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||\r
+ id.equals("JNETFREQ") || id.equals("JNETHMM") ||\r
+ id.equals("JNETALIGN") || id.equals("JPRED")) {\r
+ for (int j = 0; j < width; j++) {\r
+ annotations[gapmap[j]] = new Annotation("", "",\r
+ preds[i].getCharAt(j), 0);\r
+ }\r
+ } else if (id.equals("JNETCONF")) {\r
+ for (int j = 0; j < width; j++) {\r
+ float value = Float.parseFloat(preds[i].getCharAt(\r
+ j) + "");\r
+ annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
+ j) + "", "", preds[i].getCharAt(j),\r
+ value);\r
+ }\r
+ } else {\r
+ for (int j = 0; j < width; j++) {\r
+ annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
+ j) + "", "", ' ', 0);\r
+ }\r
+ }\r
+\r
+ if (id.equals("JNETCONF")) {\r
+ annot = new AlignmentAnnotation(preds[i].getName(),\r
+ "JNet Output", annotations, 0f, 10f, 1);\r
+ }\r
+ else {\r
+ annot = new AlignmentAnnotation(preds[i].getName(),\r
+ "JNet Output", annotations);\r
+ }\r
+\r
+ al.addAnnotation(annot);\r
+\r
+ if (noMsa) {\r
+ al.deleteSequence(preds[i]);\r
+ }\r
+ }\r
+\r
+ i++;\r
+ }\r
\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),\r
- "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
+ Hashtable scores = prediction.getScores();\r
\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),\r
- "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
- */\r
- AlignFrame af = new AlignFrame(al);\r
+ /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),\r
+ "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
\r
- Desktop.addInternalFrame(af,\r
- altitle,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),\r
+ "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
\r
- }\r
+ addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),\r
+ "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
+ */\r
+ AlignFrame af = new AlignFrame(al);\r
\r
+ Desktop.addInternalFrame(af, altitle,\r
+ AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
- }\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.ws;
-
-import org.apache.axis.client.*;
-import javax.xml.namespace.QName;
-import java.util.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import javax.swing.*;
-import java.util.*;
-import java.awt.*;
-import jalview.analysis.AlignSeq;
-import ext.vamsas.*;
-import vamsas.objects.*;
-
-
-
-
-public class MsaWSClient
- extends WSClient
-{
+*/\r
+package jalview.ws;\r
+\r
+import ext.vamsas.*;\r
+\r
+import jalview.analysis.AlignSeq;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import jalview.gui.*;\r
+\r
+import org.apache.axis.client.*;\r
+\r
+import vamsas.objects.*;\r
+\r
+import java.awt.*;\r
+\r
+import java.util.*;\r
+\r
+import javax.swing.*;\r
+\r
+import javax.xml.namespace.QName;\r
+\r
+\r
+public class MsaWSClient extends WSClient {\r
/**
- * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
- */
- ext.vamsas.MuscleWS server;
- // JBPNote Nasty object-global state setting methods shouldn't be allowed
- private boolean setWebService(String MsaWSName) {
- if (MsaWServices.info.containsKey(MsaWSName)) {
- WebServiceName = MsaWSName;
- String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
- WsURL = wsinfo[0];
- WebServiceJobTitle = wsinfo[1];
- WebServiceReference = wsinfo[2];
- return true;
- } else {
- return false;
- }
- }
-
- private boolean locateWebService() {
- // TODO: MuscleWS transmuted to generic MsaWS client
- MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
- try {
- this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
- ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout
- }
- catch (Exception ex) {
- wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
- +WsURL+"\n"+ex.getMessage());
- wsInfo.setStatus(wsInfo.ERROR);
- ex.printStackTrace();
- return false;
- }
- loc.getEngine().setOption("axis","1");
- return true;
- }
-
- public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa, boolean submitGaps, boolean preserveOrder)
- {
- if (setWebService(MsaWSName)==false) {
- JOptionPane.showMessageDialog(Desktop.desktop, "The Multiple Sequence Alignment Service named "+MsaWSName+" is unknown",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, WebServiceReference);
-
- if (!locateWebService())
- return;
-
- wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")+" of "+altitle+"\nJob details\n");
-
- MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
- wsInfo.setthisService(musclethread);
- musclethread.start();
- }
-
-
- protected class MsaWSThread extends Thread implements WSClientI
- {
- String ServiceName = WebServiceName;
-
- public boolean isCancellable()
- {
- return true;
- }
-
- String OutputHeader;
- vamsas.objects.simple.MsaResult result = null;
-
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
- SequenceSet();
-
- Hashtable SeqNames = null;
- boolean submitGaps = false,// default is to strip gaps from sequences
- preserveOrder = true; // and always store and recover sequence order
-
- String jobId;
- String alTitle; // name which will be used to form new alignment window.
- int allowedServerExceptions = 3; // thread dies if too many exceptions.
- MsaWSThread(String title, SequenceI[] msa, boolean subgaps, boolean presorder)
- {
- alTitle = title;
- submitGaps = subgaps;
- preserveOrder = presorder;
-
- OutputHeader = wsInfo.getProgressText();
- SeqNames = new Hashtable();
- vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
- Sequence[msa.length];
-
- for (int i = 0; i < msa.length; i++)
- {
- String newname = jalview.analysis.SeqsetUtils.unique_name(i);
- // uniquify as we go
- // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
- SeqNames.put(newname, jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
- seqarray[i] = new vamsas.objects.simple.Sequence();
- seqarray[i].setId(newname);
- seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()
- : AlignSeq.extractGaps(jalview.util.Comparison.GapChars, msa[i].getSequence()));
- }
-
- this.seqs = new vamsas.objects.simple.SequenceSet();
- this.seqs.setSeqs(seqarray);
- }
-
- boolean jobComplete = false;
-
- public void cancelJob() {
- if (jobId!=null && !jobId.equals("") && !jobComplete) {
- String cancelledMessage="";
- try {
- vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
- if (cancelledJob.getStatus() == 2)
- {
- // CANCELLED_JOB
- cancelledMessage = "Job cancelled.";
- wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
- jobComplete = true;
- jobsRunning--;
- result = null;
- }
- else
- if (cancelledJob.getStatus() == 3)
- {
- // VALID UNSTOPPABLE JOB
- cancelledMessage +=
- "Server cannot cancel this job. just close the window.\n";
- }
- if (cancelledJob.getJobId() != null)
- cancelledMessage += "[" + cancelledJob.getJobId() + "]";
- cancelledMessage +="\n";
- } catch (Exception exc) {
- cancelledMessage +="\nProblems cancelling the job : Exception received...\n"+exc+"\n";
- exc.printStackTrace();
- }
- wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");
- } else {
- if (!jobComplete)
- {
- wsInfo.setProgressText(OutputHeader + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
- }
- }
- }
-
- public void run()
- {
-
- StartJob();
-
- while (!jobComplete && (allowedServerExceptions > 0))
- {
- try
- {
- if ((result = server.getResult(jobId))==null)
- throw(new Exception("Timed out when communicating with server\nTry again later.\n"));
-
- if (result.isRunning())
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- else if (result.isQueued())
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-
- if (result.isFinished())
- {
- parseResult();
- jobComplete = true;
- jobsRunning--;
- }
- else
- {
- if (result.getStatus() != null)
- wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
- if (! (result.isJobFailed() || result.isServerError()))
- {
- Thread.sleep(5000);
- // System.out.println("I'm alive "+seqid+" "+jobid);
- }
- else
- {
- break;
- }
- }
- }
- catch (Exception ex)
- {
- allowedServerExceptions--;
- wsInfo.appendProgressText("\n" + ServiceName + " Server exception!\n" +
- ex.getMessage());
- System.err.println(ServiceName + " Server exception: " +
- ex.getMessage());
- // ex.printStackTrace(); JBPNote Debug
- try
- {
- if (allowedServerExceptions>0)
- Thread.sleep(5000);
- }
- catch (InterruptedException ex1)
- {
- }
-
- }
- }
- if (allowedServerExceptions == 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- else
- {
- if (! (result != null && (result.isJobFailed() || result.isServerError())))
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- else
- {
- if (result.isFailed())
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- if (result.isServerError())
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
- }
- void StartJob()
- {
- try
- {
- vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
- if (jobsubmit!=null && jobsubmit.getStatus()==1) {
- jobId=jobsubmit.getJobId();
- System.out.println(WsURL+" Job Id '"+jobId+"'");
- } else {
- if (jobsubmit == null) {
- throw new Exception("Server at "+WsURL+" returned null object, it probably cannot be contacted. Try again later ?");
- }
- throw new Exception(jobsubmit.getJobId());
- }
- }
- catch (Exception e)
- {
- // TODO: JBPNote catch timeout or other fault types explicitly
- // For unexpected errors
- System.err.println(WebServiceName + " Client: Failed to submit the sequences for alignment.\n"+WsURL+" : " +
- e.toString() + "\n");
- this.allowedServerExceptions=0;
- wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.appendProgressText("Server problems! "+e.toString()+"\nFailed to submit sequences for alignment. Just close the window\n");
- // e.printStackTrace(); // TODO: JBPNote DEBUG
- }
- }
-
- private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) {
-
- Annotation[] annotations = new Annotation[al.getWidth()];
- for (int j = 0; j < values.size(); j++)
- {
- float value = Float.parseFloat(values.get(j).toString());
- annotations[gapmap[j]] = new Annotation("", value+"",' ',value);
- }
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength));
- }
- private jalview.datamodel.Sequence[] getVamsasAlignment(vamsas.objects.simple.Alignment valign) {
- vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
- for (int i=0, j=seqs.length; i<j;i++)
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i].getSeq());
- return msa;
- }
- void parseResult()
- {
- SequenceI[] seqs=null;
- try {
- // OutputHeader = output.getText();
- if (result.isFailed()) {
- OutputHeader +="Job failed.\n";
- }
- if (result.getStatus()!=null) {
- OutputHeader += "\n"+result.getStatus();
- }
- if (result.getMsa()!=null) {
- OutputHeader += "\nAlignment Object Method Notes\n";
- String lines[] = result.getMsa().getMethod();
- for (int line=0;line<lines.length; line++)
- OutputHeader+=lines[line]+"\n";
-
- // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
- seqs = getVamsasAlignment(result.getMsa());
- }
-
- wsInfo.setProgressText(OutputHeader);
- if (seqs!=null) {
- AlignmentOrder msaorder = new AlignmentOrder(seqs);
-
- if (preserveOrder) {
- jalview.analysis.AlignmentSorter.recoverOrder(seqs);
- }
-
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
-
- Alignment al = new Alignment(seqs);
-
- // TODO: JBPNote Should also rename the query sequence sometime...
- AlignFrame af = new AlignFrame(al);
- af.addSortByOrderMenuItem(ServiceName+" Ordering", msaorder);
-
- Desktop.addInternalFrame(af,
- alTitle,
- AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
- }
- }catch(Exception ex){ex.printStackTrace();}
-
- }
-
- }
-}
-
-
+ * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+ */\r
+ ext.vamsas.MuscleWS server;\r
+\r
+ public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,\r
+ boolean submitGaps, boolean preserveOrder) {\r
+ if (setWebService(MsaWSName) == false) {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The Multiple Sequence Alignment Service named " + MsaWSName +\r
+ " is unknown", "Internal Jalview Error",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,\r
+ WebServiceReference);\r
+\r
+ if (!locateWebService()) {\r
+ return;\r
+ }\r
+\r
+ wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") +\r
+ " of " + altitle + "\nJob details\n");\r
+\r
+ MsaWSThread musclethread = new MsaWSThread(WebServiceName +\r
+ " alignment of " + altitle, msa, submitGaps, preserveOrder);\r
+ wsInfo.setthisService(musclethread);\r
+ musclethread.start();\r
+ }\r
+\r
+ // JBPNote Nasty object-global state setting methods shouldn't be allowed\r
+ private boolean setWebService(String MsaWSName) {\r
+ if (MsaWServices.info.containsKey(MsaWSName)) {\r
+ WebServiceName = MsaWSName;\r
+\r
+ String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);\r
+ WsURL = wsinfo[0];\r
+ WebServiceJobTitle = wsinfo[1];\r
+ WebServiceReference = wsinfo[2];\r
+\r
+ return true;\r
+ } else {\r
+ return false;\r
+ }\r
+ }\r
+\r
+ private boolean locateWebService() {\r
+ // TODO: MuscleWS transmuted to generic MsaWS client\r
+ MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
+\r
+ try {\r
+ this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));\r
+ ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout\r
+ } catch (Exception ex) {\r
+ wsInfo.setProgressText("Serious! " + WebServiceName +\r
+ " Service location failed\nfor URL :" + WsURL + "\n" +\r
+ ex.getMessage());\r
+ wsInfo.setStatus(wsInfo.ERROR);\r
+ ex.printStackTrace();\r
+\r
+ return false;\r
+ }\r
+\r
+ loc.getEngine().setOption("axis", "1");\r
+\r
+ return true;\r
+ }\r
+\r
+ protected class MsaWSThread extends Thread implements WSClientI {\r
+ String ServiceName = WebServiceName;\r
+ String OutputHeader;\r
+ vamsas.objects.simple.MsaResult result = null;\r
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
+ Hashtable SeqNames = null;\r
+ boolean submitGaps = false; // and always store and recover sequence order\r
+ boolean preserveOrder = true; // and always store and recover sequence order\r
+ String jobId;\r
+ String alTitle; // name which will be used to form new alignment window.\r
+ int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
+ boolean jobComplete = false;\r
+\r
+ MsaWSThread(String title, SequenceI[] msa, boolean subgaps,\r
+ boolean presorder) {\r
+ alTitle = title;\r
+ submitGaps = subgaps;\r
+ preserveOrder = presorder;\r
+\r
+ OutputHeader = wsInfo.getProgressText();\r
+ SeqNames = new Hashtable();\r
+\r
+ vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.Sequence[msa.length];\r
+\r
+ for (int i = 0; i < msa.length; i++) {\r
+ String newname = jalview.analysis.SeqsetUtils.unique_name(i);\r
+\r
+ // uniquify as we go\r
+ // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation\r
+ SeqNames.put(newname,\r
+ jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));\r
+ seqarray[i] = new vamsas.objects.simple.Sequence();\r
+ seqarray[i].setId(newname);\r
+ seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()\r
+ : AlignSeq.extractGaps(\r
+ jalview.util.Comparison.GapChars, msa[i].getSequence()));\r
+ }\r
+\r
+ this.seqs = new vamsas.objects.simple.SequenceSet();\r
+ this.seqs.setSeqs(seqarray);\r
+ }\r
+\r
+ public boolean isCancellable() {\r
+ return true;\r
+ }\r
+\r
+ public void cancelJob() {\r
+ if ((jobId != null) && !jobId.equals("") && !jobComplete) {\r
+ String cancelledMessage = "";\r
+\r
+ try {\r
+ vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);\r
+\r
+ if (cancelledJob.getStatus() == 2) {\r
+ // CANCELLED_JOB\r
+ cancelledMessage = "Job cancelled.";\r
+ wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ result = null;\r
+ } else if (cancelledJob.getStatus() == 3) {\r
+ // VALID UNSTOPPABLE JOB\r
+ cancelledMessage += "Server cannot cancel this job. just close the window.\n";\r
+ }\r
+\r
+ if (cancelledJob.getJobId() != null) {\r
+ cancelledMessage += ("[" + cancelledJob.getJobId() +\r
+ "]");\r
+ }\r
+\r
+ cancelledMessage += "\n";\r
+ } catch (Exception exc) {\r
+ cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" +\r
+ exc + "\n");\r
+ exc.printStackTrace();\r
+ }\r
+\r
+ wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");\r
+ } else {\r
+ if (!jobComplete) {\r
+ wsInfo.setProgressText(OutputHeader +\r
+ "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
+ }\r
+ }\r
+ }\r
+\r
+ public void run() {\r
+ StartJob();\r
+\r
+ while (!jobComplete && (allowedServerExceptions > 0)) {\r
+ try {\r
+ if ((result = server.getResult(jobId)) == null) {\r
+ throw (new Exception(\r
+ "Timed out when communicating with server\nTry again later.\n"));\r
+ }\r
+\r
+ if (result.isRunning()) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+ } else if (result.isQueued()) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ }\r
+\r
+ if (result.isFinished()) {\r
+ parseResult();\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ } else {\r
+ if (result.getStatus() != null) {\r
+ wsInfo.setProgressText(OutputHeader + "\n" +\r
+ result.getStatus());\r
+ }\r
+\r
+ if (!(result.isJobFailed() || result.isServerError())) {\r
+ Thread.sleep(5000);\r
+\r
+ // System.out.println("I'm alive "+seqid+" "+jobid);\r
+ } else {\r
+ break;\r
+ }\r
+ }\r
+ } catch (Exception ex) {\r
+ allowedServerExceptions--;\r
+ wsInfo.appendProgressText("\n" + ServiceName +\r
+ " Server exception!\n" + ex.getMessage());\r
+ System.err.println(ServiceName + " Server exception: " +\r
+ ex.getMessage());\r
+\r
+ // ex.printStackTrace(); JBPNote Debug\r
+ try {\r
+ if (allowedServerExceptions > 0) {\r
+ Thread.sleep(5000);\r
+ }\r
+ } catch (InterruptedException ex1) {\r
+ }\r
+ }\r
+ }\r
+\r
+ if (allowedServerExceptions == 0) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ } else {\r
+ if (!((result != null) &&\r
+ (result.isJobFailed() || result.isServerError()))) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ } else {\r
+ if (result.isFailed()) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
+\r
+ if (result.isServerError()) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ void StartJob() {\r
+ try {\r
+ vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);\r
+\r
+ if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {\r
+ jobId = jobsubmit.getJobId();\r
+ System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+ } else {\r
+ if (jobsubmit == null) {\r
+ throw new Exception("Server at " + WsURL +\r
+ " returned null object, it probably cannot be contacted. Try again later ?");\r
+ }\r
+\r
+ throw new Exception(jobsubmit.getJobId());\r
+ }\r
+ } catch (Exception e) {\r
+ // TODO: JBPNote catch timeout or other fault types explicitly\r
+ // For unexpected errors\r
+ System.err.println(WebServiceName +\r
+ " Client: Failed to submit the sequences for alignment.\n" +\r
+ WsURL + " : " + e.toString() + "\n");\r
+ this.allowedServerExceptions = 0;\r
+ wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo.appendProgressText("Server problems! " + e.toString() +\r
+ "\nFailed to submit sequences for alignment. Just close the window\n");\r
+\r
+ // e.printStackTrace(); // TODO: JBPNote DEBUG\r
+ }\r
+ }\r
+\r
+ private void addFloatAnnotations(Alignment al, int[] gapmap,\r
+ Vector values, String Symname, String Visname, float min,\r
+ float max, int winLength) {\r
+ Annotation[] annotations = new Annotation[al.getWidth()];\r
+\r
+ for (int j = 0; j < values.size(); j++) {\r
+ float value = Float.parseFloat(values.get(j).toString());\r
+ annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
+ value);\r
+ }\r
+\r
+ al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
+ annotations, min, max, winLength));\r
+ }\r
+\r
+ private jalview.datamodel.Sequence[] getVamsasAlignment(\r
+ vamsas.objects.simple.Alignment valign) {\r
+ vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
+ jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
+\r
+ for (int i = 0, j = seqs.length; i < j; i++)\r
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),\r
+ seqs[i].getSeq());\r
+\r
+ return msa;\r
+ }\r
+\r
+ void parseResult() {\r
+ SequenceI[] seqs = null;\r
+\r
+ try {\r
+ // OutputHeader = output.getText();\r
+ if (result.isFailed()) {\r
+ OutputHeader += "Job failed.\n";\r
+ }\r
+\r
+ if (result.getStatus() != null) {\r
+ OutputHeader += ("\n" + result.getStatus());\r
+ }\r
+\r
+ if (result.getMsa() != null) {\r
+ OutputHeader += "\nAlignment Object Method Notes\n";\r
+\r
+ String[] lines = result.getMsa().getMethod();\r
+\r
+ for (int line = 0; line < lines.length; line++)\r
+ OutputHeader += (lines[line] + "\n");\r
+\r
+ // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
+ seqs = getVamsasAlignment(result.getMsa());\r
+ }\r
+\r
+ wsInfo.setProgressText(OutputHeader);\r
+\r
+ if (seqs != null) {\r
+ AlignmentOrder msaorder = new AlignmentOrder(seqs);\r
+\r
+ if (preserveOrder) {\r
+ jalview.analysis.AlignmentSorter.recoverOrder(seqs);\r
+ }\r
+\r
+ jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);\r
+\r
+ Alignment al = new Alignment(seqs);\r
+\r
+ // TODO: JBPNote Should also rename the query sequence sometime...\r
+ AlignFrame af = new AlignFrame(al);\r
+ af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
+ msaorder);\r
+\r
+ Desktop.addInternalFrame(af, alTitle,\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ }\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.ws;
-import java.util.Hashtable;
+*/\r
+package jalview.ws;\r
+\r
+import java.util.Hashtable;\r
+\r
+\r
/**
* <p>Title: MsaWServices </p>
*
*
* @author not attributable
* @version 1.0
- */
+ */\r
/**
* TODO: MsaWServices will be set from properties and be dynamically discovered.
- */
-public class MsaWServices {
- public static Hashtable info;
- static
- {
- info = new Hashtable();
- info.put("ClustalWS",
- new String[]
- {
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
- "ClustalW Alignment job",
- "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +
- " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
- + " Nucleic Acids Research, submitted, June 1994."
- });
- info.put("MuscleWS",
- new String[]
- {
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
- "Muscle Alignment job",
- "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
- +
- "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97."
- });
- };
-}
+ */\r
+public class MsaWServices {\r
+ public static Hashtable info;\r
+\r
+ static {\r
+ info = new Hashtable();\r
+ info.put("ClustalWS",\r
+ new String[] {\r
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",\r
+ "ClustalW Alignment job",\r
+ \r
+ "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +\r
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." +\r
+ " Nucleic Acids Research, submitted, June 1994."\r
+ });\r
+ info.put("MuscleWS",\r
+ new String[] {\r
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",\r
+ "Muscle Alignment job",\r
+ \r
+ "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " +\r
+ "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97."\r
+ });\r
+ }\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+*/\r
+package jalview.ws;\r
+\r
+import jalview.gui.WebserviceInfo;\r
+\r
+\r
+public class WSClient {\r
+ /**
-package jalview.ws;
-
-import jalview.gui.WebserviceInfo;
-
-public class WSClient
-{
- public WSClient()
- {
- }
- /**
-
- * MsaWSClient
- *
- * @param msa SequenceI[]
- */
-
- protected String WebServiceName;
- protected String WebServiceJobTitle;
- protected String WebServiceReference;
- protected String WsURL;
- protected WebserviceInfo wsInfo;
- int jobsRunning = 0;
-}
+* MsaWSClient
+*
+* @param msa SequenceI[]
+*/\r
+ protected String WebServiceName;\r
+ protected String WebServiceJobTitle;\r
+ protected String WebServiceReference;\r
+ protected String WsURL;\r
+ protected WebserviceInfo wsInfo;\r
+ int jobsRunning = 0;\r
+\r
+ public WSClient() {\r
+ }\r
+}\r
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.ws;
-
-public interface WSClientI
-{
- boolean isCancellable();
- void cancelJob();
-}
+*/\r
+package jalview.ws;\r
+\r
+public interface WSClientI {\r
+ boolean isCancellable();\r
+\r
+ void cancelJob();\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class Alignment extends vamsas.objects.simple.Object implements java.io.Serializable {
- private java.lang.String gapchar;
- private java.lang.String[] method;
- private vamsas.objects.simple.SequenceSet seqs;
-
- public Alignment() {
- }
-
- public Alignment(
- java.lang.String gapchar,
- java.lang.String[] method,
- vamsas.objects.simple.SequenceSet seqs) {
- this.gapchar = gapchar;
- this.method = method;
- this.seqs = seqs;
- }
-
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class Alignment extends vamsas.objects.simple.Object\r
+ implements java.io.Serializable {\r
+ private java.lang.String gapchar;\r
+ private java.lang.String[] method;\r
+ private vamsas.objects.simple.SequenceSet seqs;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Alignment() {\r
+ }\r
+\r
+ public Alignment(java.lang.String gapchar, java.lang.String[] method,\r
+ vamsas.objects.simple.SequenceSet seqs) {\r
+ this.gapchar = gapchar;\r
+ this.method = method;\r
+ this.seqs = seqs;\r
+ }\r
+\r
/**
- * Gets the gapchar value for this Alignment.
- *
- * @return gapchar
- */
- public java.lang.String getGapchar() {
- return gapchar;
- }
-
-
+ * Gets the gapchar value for this Alignment.
+ *
+ * @return gapchar
+ */\r
+ public java.lang.String getGapchar() {\r
+ return gapchar;\r
+ }\r
+\r
/**
- * Sets the gapchar value for this Alignment.
- *
- * @param gapchar
- */
- public void setGapchar(java.lang.String gapchar) {
- this.gapchar = gapchar;
- }
-
-
+ * Sets the gapchar value for this Alignment.
+ *
+ * @param gapchar
+ */\r
+ public void setGapchar(java.lang.String gapchar) {\r
+ this.gapchar = gapchar;\r
+ }\r
+\r
/**
- * Gets the method value for this Alignment.
- *
- * @return method
- */
- public java.lang.String[] getMethod() {
- return method;
- }
-
-
+ * Gets the method value for this Alignment.
+ *
+ * @return method
+ */\r
+ public java.lang.String[] getMethod() {\r
+ return method;\r
+ }\r
+\r
/**
- * Sets the method value for this Alignment.
- *
- * @param method
- */
- public void setMethod(java.lang.String[] method) {
- this.method = method;
- }
-
-
+ * Sets the method value for this Alignment.
+ *
+ * @param method
+ */\r
+ public void setMethod(java.lang.String[] method) {\r
+ this.method = method;\r
+ }\r
+\r
/**
- * Gets the seqs value for this Alignment.
- *
- * @return seqs
- */
- public vamsas.objects.simple.SequenceSet getSeqs() {
- return seqs;
- }
-
-
+ * Gets the seqs value for this Alignment.
+ *
+ * @return seqs
+ */\r
+ public vamsas.objects.simple.SequenceSet getSeqs() {\r
+ return seqs;\r
+ }\r
+\r
/**
- * Sets the seqs value for this Alignment.
- *
- * @param seqs
- */
- public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
- this.seqs = seqs;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof Alignment)) return false;
- Alignment other = (Alignment) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = super.equals(obj) &&
- ((this.gapchar==null && other.getGapchar()==null) ||
- (this.gapchar!=null &&
- this.gapchar.equals(other.getGapchar()))) &&
- ((this.method==null && other.getMethod()==null) ||
- (this.method!=null &&
- java.util.Arrays.equals(this.method, other.getMethod()))) &&
- ((this.seqs==null && other.getSeqs()==null) ||
- (this.seqs!=null &&
- this.seqs.equals(other.getSeqs())));
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = super.hashCode();
- if (getGapchar() != null) {
- _hashCode += getGapchar().hashCode();
- }
- if (getMethod() != null) {
- for (int i=0;
- i<java.lang.reflect.Array.getLength(getMethod());
- i++) {
- java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i);
- if (obj != null &&
- !obj.getClass().isArray()) {
- _hashCode += obj.hashCode();
- }
- }
- }
- if (getSeqs() != null) {
- _hashCode += getSeqs().hashCode();
- }
- __hashCodeCalc = false;
- return _hashCode;
- }
-
-}
+ * Sets the seqs value for this Alignment.
+ *
+ * @param seqs
+ */\r
+ public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {\r
+ this.seqs = seqs;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof Alignment)) {\r
+ return false;\r
+ }\r
+\r
+ Alignment other = (Alignment) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = super.equals(obj) &&\r
+ (((this.gapchar == null) && (other.getGapchar() == null)) ||\r
+ ((this.gapchar != null) && this.gapchar.equals(other.getGapchar()))) &&\r
+ (((this.method == null) && (other.getMethod() == null)) ||\r
+ ((this.method != null) &&\r
+ java.util.Arrays.equals(this.method, other.getMethod()))) &&\r
+ (((this.seqs == null) && (other.getSeqs() == null)) ||\r
+ ((this.seqs != null) && this.seqs.equals(other.getSeqs())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = super.hashCode();\r
+\r
+ if (getGapchar() != null) {\r
+ _hashCode += getGapchar().hashCode();\r
+ }\r
+\r
+ if (getMethod() != null) {\r
+ for (int i = 0; i < java.lang.reflect.Array.getLength(getMethod());\r
+ i++) {\r
+ java.lang.Object obj = java.lang.reflect.Array.get(getMethod(),\r
+ i);\r
+\r
+ if ((obj != null) && !obj.getClass().isArray()) {\r
+ _hashCode += obj.hashCode();\r
+ }\r
+ }\r
+ }\r
+\r
+ if (getSeqs() != null) {\r
+ _hashCode += getSeqs().hashCode();\r
+ }\r
+\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class Alignment_Helper {
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(Alignment.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("gapchar");
- elemField.setXmlName(new javax.xml.namespace.QName("", "gapchar"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("method");
- elemField.setXmlName(new javax.xml.namespace.QName("", "method"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("seqs");
- elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
- elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"));
- typeDesc.addFieldDesc(elemField);
- }
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class Alignment_Helper {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Alignment.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "Alignment"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("gapchar");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "gapchar"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://schemas.xmlsoap.org/soap/encoding/", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("method");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "method"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://schemas.xmlsoap.org/soap/encoding/", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("seqs");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "SequenceSet"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class MsaResult extends vamsas.objects.simple.Result implements java.io.Serializable {
- private vamsas.objects.simple.Alignment msa;
-
- public MsaResult() {
- }
-
- public MsaResult(
- vamsas.objects.simple.Alignment msa) {
- this.msa = msa;
- }
-
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class MsaResult extends vamsas.objects.simple.Result\r
+ implements java.io.Serializable {\r
+ private vamsas.objects.simple.Alignment msa;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public MsaResult() {\r
+ }\r
+\r
+ public MsaResult(vamsas.objects.simple.Alignment msa) {\r
+ this.msa = msa;\r
+ }\r
+\r
/**
- * Gets the msa value for this MsaResult.
- *
- * @return msa
- */
- public vamsas.objects.simple.Alignment getMsa() {
- return msa;
- }
-
-
+ * Gets the msa value for this MsaResult.
+ *
+ * @return msa
+ */\r
+ public vamsas.objects.simple.Alignment getMsa() {\r
+ return msa;\r
+ }\r
+\r
/**
- * Sets the msa value for this MsaResult.
- *
- * @param msa
- */
- public void setMsa(vamsas.objects.simple.Alignment msa) {
- this.msa = msa;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof MsaResult)) return false;
- MsaResult other = (MsaResult) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = super.equals(obj) &&
- ((this.msa==null && other.getMsa()==null) ||
- (this.msa!=null &&
- this.msa.equals(other.getMsa())));
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = super.hashCode();
- if (getMsa() != null) {
- _hashCode += getMsa().hashCode();
- }
- __hashCodeCalc = false;
- return _hashCode;
- }
-
-}
+ * Sets the msa value for this MsaResult.
+ *
+ * @param msa
+ */\r
+ public void setMsa(vamsas.objects.simple.Alignment msa) {\r
+ this.msa = msa;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof MsaResult)) {\r
+ return false;\r
+ }\r
+\r
+ MsaResult other = (MsaResult) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = super.equals(obj) &&\r
+ (((this.msa == null) && (other.getMsa() == null)) ||\r
+ ((this.msa != null) && this.msa.equals(other.getMsa())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = super.hashCode();\r
+\r
+ if (getMsa() != null) {\r
+ _hashCode += getMsa().hashCode();\r
+ }\r
+\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class MsaResult_Helper {
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(MsaResult.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "MsaResult"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("msa");
- elemField.setXmlName(new javax.xml.namespace.QName("", "msa"));
- elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
- typeDesc.addFieldDesc(elemField);
- }
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class MsaResult_Helper {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(MsaResult.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "MsaResult"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("msa");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "msa"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "Alignment"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public abstract class Object implements java.io.Serializable {
-
- public Object() {
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof Object)) return false;
- Object other = (Object) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true;
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- __hashCodeCalc = false;
- return _hashCode;
- }
-
-}
+*/\r
+package vamsas.objects.simple;\r
+\r
+public abstract class Object implements java.io.Serializable {\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Object() {\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof Object)) {\r
+ return false;\r
+ }\r
+\r
+ Object other = (Object) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true;\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class Object_Helper {
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(Object.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("http://simple.objects.vamsas", "Object"));
- }
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class Object_Helper {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Object.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "http://simple.objects.vamsas", "Object"));\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class Result implements java.io.Serializable {
- private boolean broken;
- private boolean failed;
- private boolean finished;
- private boolean invalid;
- private boolean jobFailed;
- private boolean queued;
- private boolean running;
- private boolean serverError;
- private int state;
- private java.lang.String status;
- private boolean suspended;
-
- public Result() {
- }
-
- public Result(
- boolean broken,
- boolean failed,
- boolean finished,
- boolean invalid,
- boolean jobFailed,
- boolean queued,
- boolean running,
- boolean serverError,
- int state,
- java.lang.String status,
- boolean suspended) {
- this.broken = broken;
- this.failed = failed;
- this.finished = finished;
- this.invalid = invalid;
- this.jobFailed = jobFailed;
- this.queued = queued;
- this.running = running;
- this.serverError = serverError;
- this.state = state;
- this.status = status;
- this.suspended = suspended;
- }
-
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class Result implements java.io.Serializable {\r
+ private boolean broken;\r
+ private boolean failed;\r
+ private boolean finished;\r
+ private boolean invalid;\r
+ private boolean jobFailed;\r
+ private boolean queued;\r
+ private boolean running;\r
+ private boolean serverError;\r
+ private int state;\r
+ private java.lang.String status;\r
+ private boolean suspended;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Result() {\r
+ }\r
+\r
+ public Result(boolean broken, boolean failed, boolean finished,\r
+ boolean invalid, boolean jobFailed, boolean queued, boolean running,\r
+ boolean serverError, int state, java.lang.String status,\r
+ boolean suspended) {\r
+ this.broken = broken;\r
+ this.failed = failed;\r
+ this.finished = finished;\r
+ this.invalid = invalid;\r
+ this.jobFailed = jobFailed;\r
+ this.queued = queued;\r
+ this.running = running;\r
+ this.serverError = serverError;\r
+ this.state = state;\r
+ this.status = status;\r
+ this.suspended = suspended;\r
+ }\r
+\r
/**
- * Gets the broken value for this Result.
- *
- * @return broken
- */
- public boolean isBroken() {
- return broken;
- }
-
-
+ * Gets the broken value for this Result.
+ *
+ * @return broken
+ */\r
+ public boolean isBroken() {\r
+ return broken;\r
+ }\r
+\r
/**
- * Sets the broken value for this Result.
- *
- * @param broken
- */
- public void setBroken(boolean broken) {
- this.broken = broken;
- }
-
-
+ * Sets the broken value for this Result.
+ *
+ * @param broken
+ */\r
+ public void setBroken(boolean broken) {\r
+ this.broken = broken;\r
+ }\r
+\r
/**
- * Gets the failed value for this Result.
- *
- * @return failed
- */
- public boolean isFailed() {
- return failed;
- }
-
-
+ * Gets the failed value for this Result.
+ *
+ * @return failed
+ */\r
+ public boolean isFailed() {\r
+ return failed;\r
+ }\r
+\r
/**
- * Sets the failed value for this Result.
- *
- * @param failed
- */
- public void setFailed(boolean failed) {
- this.failed = failed;
- }
-
-
+ * Sets the failed value for this Result.
+ *
+ * @param failed
+ */\r
+ public void setFailed(boolean failed) {\r
+ this.failed = failed;\r
+ }\r
+\r
/**
- * Gets the finished value for this Result.
- *
- * @return finished
- */
- public boolean isFinished() {
- return finished;
- }
-
-
+ * Gets the finished value for this Result.
+ *
+ * @return finished
+ */\r
+ public boolean isFinished() {\r
+ return finished;\r
+ }\r
+\r
/**
- * Sets the finished value for this Result.
- *
- * @param finished
- */
- public void setFinished(boolean finished) {
- this.finished = finished;
- }
-
-
+ * Sets the finished value for this Result.
+ *
+ * @param finished
+ */\r
+ public void setFinished(boolean finished) {\r
+ this.finished = finished;\r
+ }\r
+\r
/**
- * Gets the invalid value for this Result.
- *
- * @return invalid
- */
- public boolean isInvalid() {
- return invalid;
- }
-
-
+ * Gets the invalid value for this Result.
+ *
+ * @return invalid
+ */\r
+ public boolean isInvalid() {\r
+ return invalid;\r
+ }\r
+\r
/**
- * Sets the invalid value for this Result.
- *
- * @param invalid
- */
- public void setInvalid(boolean invalid) {
- this.invalid = invalid;
- }
-
-
+ * Sets the invalid value for this Result.
+ *
+ * @param invalid
+ */\r
+ public void setInvalid(boolean invalid) {\r
+ this.invalid = invalid;\r
+ }\r
+\r
/**
- * Gets the jobFailed value for this Result.
- *
- * @return jobFailed
- */
- public boolean isJobFailed() {
- return jobFailed;
- }
-
-
+ * Gets the jobFailed value for this Result.
+ *
+ * @return jobFailed
+ */\r
+ public boolean isJobFailed() {\r
+ return jobFailed;\r
+ }\r
+\r
/**
- * Sets the jobFailed value for this Result.
- *
- * @param jobFailed
- */
- public void setJobFailed(boolean jobFailed) {
- this.jobFailed = jobFailed;
- }
-
-
+ * Sets the jobFailed value for this Result.
+ *
+ * @param jobFailed
+ */\r
+ public void setJobFailed(boolean jobFailed) {\r
+ this.jobFailed = jobFailed;\r
+ }\r
+\r
/**
- * Gets the queued value for this Result.
- *
- * @return queued
- */
- public boolean isQueued() {
- return queued;
- }
-
-
+ * Gets the queued value for this Result.
+ *
+ * @return queued
+ */\r
+ public boolean isQueued() {\r
+ return queued;\r
+ }\r
+\r
/**
- * Sets the queued value for this Result.
- *
- * @param queued
- */
- public void setQueued(boolean queued) {
- this.queued = queued;
- }
-
-
+ * Sets the queued value for this Result.
+ *
+ * @param queued
+ */\r
+ public void setQueued(boolean queued) {\r
+ this.queued = queued;\r
+ }\r
+\r
/**
- * Gets the running value for this Result.
- *
- * @return running
- */
- public boolean isRunning() {
- return running;
- }
-
-
+ * Gets the running value for this Result.
+ *
+ * @return running
+ */\r
+ public boolean isRunning() {\r
+ return running;\r
+ }\r
+\r
/**
- * Sets the running value for this Result.
- *
- * @param running
- */
- public void setRunning(boolean running) {
- this.running = running;
- }
-
-
+ * Sets the running value for this Result.
+ *
+ * @param running
+ */\r
+ public void setRunning(boolean running) {\r
+ this.running = running;\r
+ }\r
+\r
/**
- * Gets the serverError value for this Result.
- *
- * @return serverError
- */
- public boolean isServerError() {
- return serverError;
- }
-
-
+ * Gets the serverError value for this Result.
+ *
+ * @return serverError
+ */\r
+ public boolean isServerError() {\r
+ return serverError;\r
+ }\r
+\r
/**
- * Sets the serverError value for this Result.
- *
- * @param serverError
- */
- public void setServerError(boolean serverError) {
- this.serverError = serverError;
- }
-
-
+ * Sets the serverError value for this Result.
+ *
+ * @param serverError
+ */\r
+ public void setServerError(boolean serverError) {\r
+ this.serverError = serverError;\r
+ }\r
+\r
/**
- * Gets the state value for this Result.
- *
- * @return state
- */
- public int getState() {
- return state;
- }
-
-
+ * Gets the state value for this Result.
+ *
+ * @return state
+ */\r
+ public int getState() {\r
+ return state;\r
+ }\r
+\r
/**
- * Sets the state value for this Result.
- *
- * @param state
- */
- public void setState(int state) {
- this.state = state;
- }
-
-
+ * Sets the state value for this Result.
+ *
+ * @param state
+ */\r
+ public void setState(int state) {\r
+ this.state = state;\r
+ }\r
+\r
/**
- * Gets the status value for this Result.
- *
- * @return status
- */
- public java.lang.String getStatus() {
- return status;
- }
-
-
+ * Gets the status value for this Result.
+ *
+ * @return status
+ */\r
+ public java.lang.String getStatus() {\r
+ return status;\r
+ }\r
+\r
/**
- * Sets the status value for this Result.
- *
- * @param status
- */
- public void setStatus(java.lang.String status) {
- this.status = status;
- }
-
-
+ * Sets the status value for this Result.
+ *
+ * @param status
+ */\r
+ public void setStatus(java.lang.String status) {\r
+ this.status = status;\r
+ }\r
+\r
/**
- * Gets the suspended value for this Result.
- *
- * @return suspended
- */
- public boolean isSuspended() {
- return suspended;
- }
-
-
+ * Gets the suspended value for this Result.
+ *
+ * @return suspended
+ */\r
+ public boolean isSuspended() {\r
+ return suspended;\r
+ }\r
+\r
/**
- * Sets the suspended value for this Result.
- *
- * @param suspended
- */
- public void setSuspended(boolean suspended) {
- this.suspended = suspended;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof Result)) return false;
- Result other = (Result) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true &&
- this.broken == other.isBroken() &&
- this.failed == other.isFailed() &&
- this.finished == other.isFinished() &&
- this.invalid == other.isInvalid() &&
- this.jobFailed == other.isJobFailed() &&
- this.queued == other.isQueued() &&
- this.running == other.isRunning() &&
- this.serverError == other.isServerError() &&
- this.state == other.getState() &&
- ((this.status==null && other.getStatus()==null) ||
- (this.status!=null &&
- this.status.equals(other.getStatus()))) &&
- this.suspended == other.isSuspended();
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- _hashCode += getState();
- if (getStatus() != null) {
- _hashCode += getStatus().hashCode();
- }
- _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
- __hashCodeCalc = false;
- return _hashCode;
- }
-
-}
+ * Sets the suspended value for this Result.
+ *
+ * @param suspended
+ */\r
+ public void setSuspended(boolean suspended) {\r
+ this.suspended = suspended;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof Result)) {\r
+ return false;\r
+ }\r
+\r
+ Result other = (Result) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true && (this.broken == other.isBroken()) &&\r
+ (this.failed == other.isFailed()) &&\r
+ (this.finished == other.isFinished()) &&\r
+ (this.invalid == other.isInvalid()) &&\r
+ (this.jobFailed == other.isJobFailed()) &&\r
+ (this.queued == other.isQueued()) &&\r
+ (this.running == other.isRunning()) &&\r
+ (this.serverError == other.isServerError()) &&\r
+ (this.state == other.getState()) &&\r
+ (((this.status == null) && (other.getStatus() == null)) ||\r
+ ((this.status != null) && this.status.equals(other.getStatus()))) &&\r
+ (this.suspended == other.isSuspended());\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+ _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ _hashCode += getState();\r
+\r
+ if (getStatus() != null) {\r
+ _hashCode += getStatus().hashCode();\r
+ }\r
+\r
+ _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class Result_Helper {
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(Result.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Result"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("broken");
- elemField.setXmlName(new javax.xml.namespace.QName("", "broken"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("failed");
- elemField.setXmlName(new javax.xml.namespace.QName("", "failed"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("finished");
- elemField.setXmlName(new javax.xml.namespace.QName("", "finished"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("invalid");
- elemField.setXmlName(new javax.xml.namespace.QName("", "invalid"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("jobFailed");
- elemField.setXmlName(new javax.xml.namespace.QName("", "jobFailed"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("queued");
- elemField.setXmlName(new javax.xml.namespace.QName("", "queued"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("running");
- elemField.setXmlName(new javax.xml.namespace.QName("", "running"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("serverError");
- elemField.setXmlName(new javax.xml.namespace.QName("", "serverError"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("state");
- elemField.setXmlName(new javax.xml.namespace.QName("", "state"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("status");
- elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("suspended");
- elemField.setXmlName(new javax.xml.namespace.QName("", "suspended"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
- typeDesc.addFieldDesc(elemField);
- }
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class Result_Helper {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Result.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "Result"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("broken");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "broken"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("failed");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "failed"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("finished");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "finished"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("invalid");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "invalid"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("jobFailed");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "jobFailed"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("queued");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "queued"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("running");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "running"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("serverError");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "serverError"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("state");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "state"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "int"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("status");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "status"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://schemas.xmlsoap.org/soap/encoding/", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("suspended");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "suspended"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "boolean"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class Sequence implements java.io.Serializable {
- private java.lang.String id;
- private java.lang.String seq;
-
- public Sequence() {
- }
-
- public Sequence(
- java.lang.String id,
- java.lang.String seq) {
- this.id = id;
- this.seq = seq;
- }
-
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class Sequence implements java.io.Serializable {\r
+ private java.lang.String id;\r
+ private java.lang.String seq;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Sequence() {\r
+ }\r
+\r
+ public Sequence(java.lang.String id, java.lang.String seq) {\r
+ this.id = id;\r
+ this.seq = seq;\r
+ }\r
+\r
/**
- * Gets the id value for this Sequence.
- *
- * @return id
- */
- public java.lang.String getId() {
- return id;
- }
-
-
+ * Gets the id value for this Sequence.
+ *
+ * @return id
+ */\r
+ public java.lang.String getId() {\r
+ return id;\r
+ }\r
+\r
/**
- * Sets the id value for this Sequence.
- *
- * @param id
- */
- public void setId(java.lang.String id) {
- this.id = id;
- }
-
-
+ * Sets the id value for this Sequence.
+ *
+ * @param id
+ */\r
+ public void setId(java.lang.String id) {\r
+ this.id = id;\r
+ }\r
+\r
/**
- * Gets the seq value for this Sequence.
- *
- * @return seq
- */
- public java.lang.String getSeq() {
- return seq;
- }
-
-
+ * Gets the seq value for this Sequence.
+ *
+ * @return seq
+ */\r
+ public java.lang.String getSeq() {\r
+ return seq;\r
+ }\r
+\r
/**
- * Sets the seq value for this Sequence.
- *
- * @param seq
- */
- public void setSeq(java.lang.String seq) {
- this.seq = seq;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof Sequence)) return false;
- Sequence other = (Sequence) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true &&
- ((this.id==null && other.getId()==null) ||
- (this.id!=null &&
- this.id.equals(other.getId()))) &&
- ((this.seq==null && other.getSeq()==null) ||
- (this.seq!=null &&
- this.seq.equals(other.getSeq())));
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- if (getId() != null) {
- _hashCode += getId().hashCode();
- }
- if (getSeq() != null) {
- _hashCode += getSeq().hashCode();
- }
- __hashCodeCalc = false;
- return _hashCode;
- }
-
-}
+ * Sets the seq value for this Sequence.
+ *
+ * @param seq
+ */\r
+ public void setSeq(java.lang.String seq) {\r
+ this.seq = seq;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof Sequence)) {\r
+ return false;\r
+ }\r
+\r
+ Sequence other = (Sequence) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true &&\r
+ (((this.id == null) && (other.getId() == null)) ||\r
+ ((this.id != null) && this.id.equals(other.getId()))) &&\r
+ (((this.seq == null) && (other.getSeq() == null)) ||\r
+ ((this.seq != null) && this.seq.equals(other.getSeq())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+\r
+ if (getId() != null) {\r
+ _hashCode += getId().hashCode();\r
+ }\r
+\r
+ if (getSeq() != null) {\r
+ _hashCode += getSeq().hashCode();\r
+ }\r
+\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class SequenceSet implements java.io.Serializable {
- private vamsas.objects.simple.Sequence[] seqs;
-
- public SequenceSet() {
- }
-
- public SequenceSet(
- vamsas.objects.simple.Sequence[] seqs) {
- this.seqs = seqs;
- }
-
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class SequenceSet implements java.io.Serializable {\r
+ private vamsas.objects.simple.Sequence[] seqs;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public SequenceSet() {\r
+ }\r
+\r
+ public SequenceSet(vamsas.objects.simple.Sequence[] seqs) {\r
+ this.seqs = seqs;\r
+ }\r
+\r
/**
- * Gets the seqs value for this SequenceSet.
- *
- * @return seqs
- */
- public vamsas.objects.simple.Sequence[] getSeqs() {
- return seqs;
- }
-
-
+ * Gets the seqs value for this SequenceSet.
+ *
+ * @return seqs
+ */\r
+ public vamsas.objects.simple.Sequence[] getSeqs() {\r
+ return seqs;\r
+ }\r
+\r
/**
- * Sets the seqs value for this SequenceSet.
- *
- * @param seqs
- */
- public void setSeqs(vamsas.objects.simple.Sequence[] seqs) {
- this.seqs = seqs;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof SequenceSet)) return false;
- SequenceSet other = (SequenceSet) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true &&
- ((this.seqs==null && other.getSeqs()==null) ||
- (this.seqs!=null &&
- java.util.Arrays.equals(this.seqs, other.getSeqs())));
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- if (getSeqs() != null) {
- for (int i=0;
- i<java.lang.reflect.Array.getLength(getSeqs());
- i++) {
- java.lang.Object obj = java.lang.reflect.Array.get(getSeqs(), i);
- if (obj != null &&
- !obj.getClass().isArray()) {
- _hashCode += obj.hashCode();
- }
- }
- }
- __hashCodeCalc = false;
- return _hashCode;
- }
-
-}
+ * Sets the seqs value for this SequenceSet.
+ *
+ * @param seqs
+ */\r
+ public void setSeqs(vamsas.objects.simple.Sequence[] seqs) {\r
+ this.seqs = seqs;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof SequenceSet)) {\r
+ return false;\r
+ }\r
+\r
+ SequenceSet other = (SequenceSet) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true &&\r
+ (((this.seqs == null) && (other.getSeqs() == null)) ||\r
+ ((this.seqs != null) &&\r
+ java.util.Arrays.equals(this.seqs, other.getSeqs())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+\r
+ if (getSeqs() != null) {\r
+ for (int i = 0; i < java.lang.reflect.Array.getLength(getSeqs());\r
+ i++) {\r
+ java.lang.Object obj = java.lang.reflect.Array.get(getSeqs(), i);\r
+\r
+ if ((obj != null) && !obj.getClass().isArray()) {\r
+ _hashCode += obj.hashCode();\r
+ }\r
+ }\r
+ }\r
+\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class SequenceSet_Helper {
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(SequenceSet.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("seqs");
- elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
- elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
- typeDesc.addFieldDesc(elemField);
- }
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class SequenceSet_Helper {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(SequenceSet.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "SequenceSet"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("seqs");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "Sequence"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class Sequence_Helper {
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(Sequence.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("id");
- elemField.setXmlName(new javax.xml.namespace.QName("", "id"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("seq");
- elemField.setXmlName(new javax.xml.namespace.QName("", "seq"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
- typeDesc.addFieldDesc(elemField);
- }
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class Sequence_Helper {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Sequence.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "Sequence"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("id");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "id"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://schemas.xmlsoap.org/soap/encoding/", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("seq");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "seq"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://schemas.xmlsoap.org/soap/encoding/", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class WsJobId implements java.io.Serializable {
- private java.lang.String jobId;
- private int status;
-
- public WsJobId() {
- }
-
- public WsJobId(
- java.lang.String jobId,
- int status) {
- this.jobId = jobId;
- this.status = status;
- }
-
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class WsJobId implements java.io.Serializable {\r
+ private java.lang.String jobId;\r
+ private int status;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public WsJobId() {\r
+ }\r
+\r
+ public WsJobId(java.lang.String jobId, int status) {\r
+ this.jobId = jobId;\r
+ this.status = status;\r
+ }\r
+\r
/**
- * Gets the jobId value for this WsJobId.
- *
- * @return jobId
- */
- public java.lang.String getJobId() {
- return jobId;
- }
-
-
+ * Gets the jobId value for this WsJobId.
+ *
+ * @return jobId
+ */\r
+ public java.lang.String getJobId() {\r
+ return jobId;\r
+ }\r
+\r
/**
- * Sets the jobId value for this WsJobId.
- *
- * @param jobId
- */
- public void setJobId(java.lang.String jobId) {
- this.jobId = jobId;
- }
-
-
+ * Sets the jobId value for this WsJobId.
+ *
+ * @param jobId
+ */\r
+ public void setJobId(java.lang.String jobId) {\r
+ this.jobId = jobId;\r
+ }\r
+\r
/**
- * Gets the status value for this WsJobId.
- *
- * @return status
- */
- public int getStatus() {
- return status;
- }
-
-
+ * Gets the status value for this WsJobId.
+ *
+ * @return status
+ */\r
+ public int getStatus() {\r
+ return status;\r
+ }\r
+\r
/**
- * Sets the status value for this WsJobId.
- *
- * @param status
- */
- public void setStatus(int status) {
- this.status = status;
- }
-
- private java.lang.Object __equalsCalc = null;
- public synchronized boolean equals(java.lang.Object obj) {
- if (!(obj instanceof WsJobId)) return false;
- WsJobId other = (WsJobId) obj;
- if (obj == null) return false;
- if (this == obj) return true;
- if (__equalsCalc != null) {
- return (__equalsCalc == obj);
- }
- __equalsCalc = obj;
- boolean _equals;
- _equals = true &&
- ((this.jobId==null && other.getJobId()==null) ||
- (this.jobId!=null &&
- this.jobId.equals(other.getJobId()))) &&
- this.status == other.getStatus();
- __equalsCalc = null;
- return _equals;
- }
-
- private boolean __hashCodeCalc = false;
- public synchronized int hashCode() {
- if (__hashCodeCalc) {
- return 0;
- }
- __hashCodeCalc = true;
- int _hashCode = 1;
- if (getJobId() != null) {
- _hashCode += getJobId().hashCode();
- }
- _hashCode += getStatus();
- __hashCodeCalc = false;
- return _hashCode;
- }
-
-}
+ * Sets the status value for this WsJobId.
+ *
+ * @param status
+ */\r
+ public void setStatus(int status) {\r
+ this.status = status;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj) {\r
+ if (!(obj instanceof WsJobId)) {\r
+ return false;\r
+ }\r
+\r
+ WsJobId other = (WsJobId) obj;\r
+\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+\r
+ if (__equalsCalc != null) {\r
+ return (__equalsCalc == obj);\r
+ }\r
+\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = true &&\r
+ (((this.jobId == null) && (other.getJobId() == null)) ||\r
+ ((this.jobId != null) && this.jobId.equals(other.getJobId()))) &&\r
+ (this.status == other.getStatus());\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode() {\r
+ if (__hashCodeCalc) {\r
+ return 0;\r
+ }\r
+\r
+ __hashCodeCalc = true;\r
+\r
+ int _hashCode = 1;\r
+\r
+ if (getJobId() != null) {\r
+ _hashCode += getJobId().hashCode();\r
+ }\r
+\r
+ _hashCode += getStatus();\r
+ __hashCodeCalc = false;\r
+\r
+ return _hashCode;\r
+ }\r
+}\r
*
* This file was auto-generated from WSDL
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */\r
+\r
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package vamsas.objects.simple;
-
-public class WsJobId_Helper {
- // Type metadata
- private static org.apache.axis.description.TypeDesc typeDesc =
- new org.apache.axis.description.TypeDesc(WsJobId.class, true);
-
- static {
- typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
- org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("jobId");
- elemField.setXmlName(new javax.xml.namespace.QName("", "jobId"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
- typeDesc.addFieldDesc(elemField);
- elemField = new org.apache.axis.description.ElementDesc();
- elemField.setFieldName("status");
- elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
- elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
- typeDesc.addFieldDesc(elemField);
- }
-
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class WsJobId_Helper {\r
+ // Type metadata\r
+ private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(WsJobId.class,\r
+ true);\r
+\r
+ static {\r
+ typeDesc.setXmlType(new javax.xml.namespace.QName(\r
+ "simple.objects.vamsas", "WsJobId"));\r
+\r
+ org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("jobId");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "jobId"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://schemas.xmlsoap.org/soap/encoding/", "string"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ elemField = new org.apache.axis.description.ElementDesc();\r
+ elemField.setFieldName("status");\r
+ elemField.setXmlName(new javax.xml.namespace.QName("", "status"));\r
+ elemField.setXmlType(new javax.xml.namespace.QName(\r
+ "http://www.w3.org/2001/XMLSchema", "int"));\r
+ typeDesc.addFieldDesc(elemField);\r
+ }\r
+\r
/**
- * Return type metadata object
- */
- public static org.apache.axis.description.TypeDesc getTypeDesc() {
- return typeDesc;
- }
-
+ * Return type metadata object
+ */\r
+ public static org.apache.axis.description.TypeDesc getTypeDesc() {\r
+ return typeDesc;\r
+ }\r
+\r
/**
- * Get Custom Serializer
- */
- public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanSerializer(
- _javaType, _xmlType, typeDesc);
- }
-
+ * Get Custom Serializer
+ */\r
+ public static org.apache.axis.encoding.Serializer getSerializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+\r
/**
- * Get Custom Deserializer
- */
- public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
- javax.xml.namespace.QName _xmlType) {
- return
- new org.apache.axis.encoding.ser.BeanDeserializer(
- _javaType, _xmlType, typeDesc);
- }
-
-}
+ * Get Custom Deserializer
+ */\r
+ public static org.apache.axis.encoding.Deserializer getDeserializer(\r
+ java.lang.String mechType, java.lang.Class _javaType,\r
+ javax.xml.namespace.QName _xmlType) {\r
+ return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,\r
+ _xmlType, typeDesc);\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / commitdiff