/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 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
import java.awt.*;\r
\r
import java.util.*;\r
+import jalview.analysis.AlignSeq;\r
\r
\r
public class PDBChain {\r
public Vector residues = new Vector();\r
public int offset;\r
public Sequence sequence;\r
- public boolean isVisible = false;\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 DrawableSequence ds;\r
public PDBChain(String id) {\r
this.id = id;\r
}\r
return tmp;\r
}\r
\r
- public void makeCaBondList() {\r
- for (int i = 0; i < (residues.size() - 1); i++) {\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
+ }\r
+\r
+\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
- myAtom at1 = tmpres.findAtom("CA");\r
- myAtom at2 = tmpres2.findAtom("CA");\r
+ Atom at1 = tmpres.findAtom("CA");\r
+ Atom at2 = tmpres2.findAtom("CA");\r
\r
- if ((at1 != null) && (at2 != null)) {\r
- if (at1.chain.equals(at2.chain)) {\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
}\r
\r
- public void makeBond(myAtom at1, myAtom at2) {\r
+ public void makeBond(Atom at1, Atom at2) {\r
float[] start = new float[3];\r
float[] end = new float[3];\r
\r
\r
public void makeResidueList() {\r
int count = 0;\r
- String seq = "";\r
+ StringBuffer seq = new StringBuffer();\r
\r
- for (int i = 0; i < atoms.size(); i++) {\r
- myAtom tmp = (myAtom) atoms.elementAt(i);\r
- String resName = tmp.resName;\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
\r
Vector resAtoms = new Vector();\r
\r
- resAtoms.addElement((myAtom) atoms.elementAt(i));\r
+ resAtoms.addElement((Atom) atoms.elementAt(i));\r
i++;\r
- resNumber = ((myAtom) atoms.elementAt(i)).resNumber;\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((myAtom) atoms.elementAt(i));\r
+ resAtoms.addElement((Atom) atoms.elementAt(i));\r
i++;\r
\r
if (i < atoms.size()) {\r
- resNumber = ((myAtom) atoms.elementAt(i)).resNumber;\r
+ resNumber = ((Atom) atoms.elementAt(i)).resNumber;\r
} else {\r
resNumber++;\r
}\r
count++;\r
\r
Residue tmpres = (Residue) residues.lastElement();\r
- myAtom tmpat = (myAtom) tmpres.atoms.elementAt(0);\r
+ Atom tmpat = (Atom) 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
+ 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
- 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
+ seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()\r
+ .get(tmpat.resName)).intValue()]);\r
+ }\r
}\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
+ if(id.length()<1 || id.equals(" "))\r
+ id = "_";\r
+\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
public void setChargeColours() {\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
+ if (b.at1.resName.equalsIgnoreCase("ASP") ||\r
+ b.at1.resName.equalsIgnoreCase("GLU")) {\r
b.startCol = Color.red;\r
- } else if (b.at1.resName.toUpperCase().equals("LYS") ||\r
- b.at1.resName.toUpperCase().equals("ARG")) {\r
+ } else if (b.at1.resName.equalsIgnoreCase("LYS") ||\r
+ b.at1.resName.equalsIgnoreCase("ARG")) {\r
b.startCol = Color.blue;\r
- } else if (b.at1.resName.toUpperCase().equals("CYS")) {\r
+ } else if (b.at1.resName.equalsIgnoreCase("CYS")) {\r
b.startCol = Color.yellow;\r
} else {\r
- int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();\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
+ if (b.at2.resName.equalsIgnoreCase("ASP") ||\r
+ b.at2.resName.equalsIgnoreCase("GLU")) {\r
b.endCol = Color.red;\r
- } else if (b.at2.resName.toUpperCase().equals("LYS") ||\r
- b.at2.resName.toUpperCase().equals("ARG")) {\r
+ } else if (b.at2.resName.equalsIgnoreCase("LYS") ||\r
+ b.at2.resName.equalsIgnoreCase("ARG")) {\r
b.endCol = Color.blue;\r
- } else if (b.at2.resName.toUpperCase().equals("CYS")) {\r
+ } else if (b.at2.resName.equalsIgnoreCase("CYS")) {\r
b.endCol = Color.yellow;\r
} else {\r
- int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();\r
+ //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();\r
b.endCol = Color.lightGray;\r
}\r
} catch (Exception e) {\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
- Hashtable AA3Hash = ResidueProperties.getAA3Hash();\r
\r
+ public void setChainColours(jalview.schemes.ColourSchemeI cs)\r
+ {\r
+ Bond b;\r
for (int i = 0; i < bonds.size(); i++) {\r
try {\r
- Bond b = (Bond) bonds.elementAt(i);\r
-\r
- int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();\r
- float red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);\r
+ b = (Bond) bonds.elementAt(i);\r
\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
+ /* ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(\r
+ ResidueProperties.codonTranslate(\r
+ ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(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
- red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);\r
-\r
- if (red > (float) 1.0) {\r
- red = (float) 1.0;\r
- }\r
+ b.endCol = cs.findColour(\r
+ ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.\r
+ get(b.at2.resName)).intValue()]\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
+ } catch (Exception e)\r
+ {\r
+ b = (Bond) bonds.elementAt(i);\r
b.startCol = Color.gray;\r
b.endCol = Color.gray;\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
-\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
- }\r
-\r
- public void setChainColours() {\r
- for (int i = 0; i < bonds.size(); i++) {\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
-\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
+ tmp.startCol = col;\r
+ tmp.endCol = col;\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff