-/* Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 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 MCview;\r
\r
import jalview.datamodel.*;\r
+\r
import jalview.schemes.ResidueProperties;\r
\r
import java.awt.*;\r
+\r
import java.util.*;\r
+import jalview.analysis.AlignSeq;\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 = true;\r
+ public int pdbstart = 0;\r
+ public int pdbend = 0;\r
+ public int seqstart = 0;\r
+ public int seqend = 0;\r
+\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
+ public String print() {\r
+ String tmp = "";\r
\r
- public Sequence sequence;\r
- public boolean isVisible = false;\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
- public int pdbstart=0, pdbend=0, seqstart=0, seqend=0;\r
+ return tmp;\r
+ }\r
\r
- //public DrawableSequence ds;\r
+ void makeExactMapping(AlignSeq as, Sequence s1)\r
+ {\r
+ int pdbpos = as.getSeq2Start()-2;\r
+ int alignpos = s1.getStart() + as.getSeq1Start()-3;\r
+\r
+ for(int i=0; i<as.astr1.length(); i++)\r
+ {\r
+ if (as.astr1.charAt(i) != '-')\r
+ {\r
+ alignpos++;\r
+ }\r
+\r
+ if (as.astr2.charAt(i) != '-')\r
+ {\r
+ pdbpos++;\r
+ }\r
+\r
+ if (as.astr1.charAt(i) == as.astr2.charAt(i))\r
+ {\r
+ Residue res = (Residue) residues.elementAt(pdbpos);\r
+ Enumeration en = res.atoms.elements();\r
+ while (en.hasMoreElements())\r
+ {\r
+ Atom atom = (Atom) en.nextElement();\r
+ atom.alignmentMapping = alignpos;\r
+ }\r
+ }\r
+ }\r
\r
- public PDBChain(String id) {\r
- this.id = id;\r
- }\r
+ }\r
\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
- }\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.out.println("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
- sequence = new Sequence("PDB_seq",seq,1,seq.length());\r
- System.out.println("Sequence = " + 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
+ public void makeCaBondList()\r
+ {\r
+ for (int i = 0; i < (residues.size() - 1); i++)\r
+ {\r
+ Residue tmpres = (Residue) residues.elementAt(i);\r
+ Residue tmpres2 = (Residue) residues.elementAt(i + 1);\r
+ Atom at1 = tmpres.findAtom("CA");\r
+ Atom at2 = tmpres2.findAtom("CA");\r
+\r
+ if ((at1 != null) && (at2 != null))\r
+ {\r
+ if (at1.chain.equals(at2.chain))\r
+ {\r
+ makeBond(at1, at2);\r
+ }\r
+ }\r
+ else\r
+ System.out.println("not found "+i);\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(Atom at1, Atom 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
+ StringBuffer seq = new StringBuffer();\r
+\r
+ int i, iSize = atoms.size()-1;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ Atom tmp = (Atom) atoms.elementAt(i);\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((Atom) atoms.elementAt(i));\r
+ i++;\r
+ resNumber = ((Atom) 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((Atom) atoms.elementAt(i));\r
+ i++;\r
+\r
+ if (i < atoms.size()) {\r
+ resNumber = ((Atom) 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
+ Atom tmpat = (Atom) tmpres.atoms.elementAt(0);\r
+\r
+ // Keep totting up the sequence\r
+ if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)\r
+ {\r
+ seq.append("X") ;\r
+ // System.err.println("PDBReader:Null aa3Hash for " +\r
+ // tmpat.resName);\r
+ } else {\r
+\r
+ seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()\r
+ .get(tmpat.resName)).intValue()]);\r
+ }\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
+ if(id.length()<1 || id.equals(" "))\r
+ id = "_";\r
\r
- red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);\r
+ sequence = new Sequence(id, seq.toString(), 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
+ public void setHydrophobicityColours() {\r
+ float hydmin = (float) ResidueProperties.getHydmin();\r
+ float hydmax = (float) ResidueProperties.getHydmax();\r
+ double[] hyd = ResidueProperties.getHyd();\r
\r
- public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {\r
-jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);\r
+ Hashtable AA3Hash = ResidueProperties.getAA3Hash();\r
\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ try {\r
+ Bond b = (Bond) bonds.elementAt(i);\r
\r
- for (int i = 0; i < bonds.size(); i++) {\r
- Bond tmp = (Bond)bonds.elementAt(i);\r
- try {\r
+ int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();\r
+ float red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);\r
\r
- if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {\r
+ if (red > (float) 1.0) {\r
+ red = (float) 1.0;\r
+ }\r
\r
- int pos = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;\r
- int index = seq.findIndex(pos);\r
+ if (red < (float) 0.0) {\r
+ red = (float) 0.0;\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
- tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);\r
+ red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);\r
\r
- } else {\r
- tmp.startCol = Color.gray;\r
- }\r
+ if (red > (float) 1.0) {\r
+ red = (float) 1.0;\r
+ }\r
\r
- if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {\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
- int pos = seqstart + (tmp.at2.resNumber - pdbstart-offset);\r
- int index = seq.findIndex(pos);\r
\r
- tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);\r
\r
- } else {\r
- tmp.endCol = Color.gray;\r
+ public void setChainColours(Color col)\r
+ {\r
+ for (int i = 0; i < bonds.size(); i++)\r
+ {\r
+ Bond tmp = (Bond) bonds.elementAt(i);\r
+ tmp.startCol = col;\r
+ tmp.endCol = col;\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
- }\r
}\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff