-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\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
-* 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 print() {\r
- String tmp = "";\r
-\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
- return tmp;\r
- }\r
-\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
- 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
- }\r
-\r
- public void makeBond(Atom at1, Atom 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
- 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
- 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
- for (int i = 0; i < bonds.size(); i++) {\r
- try {\r
- Bond b = (Bond) bonds.elementAt(i);\r
-\r
- if (b.at1.resName.equalsIgnoreCase("ASP") ||\r
- b.at1.resName.equalsIgnoreCase("GLU")) {\r
- b.startCol = Color.red;\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.equalsIgnoreCase("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.equalsIgnoreCase("ASP") ||\r
- b.at2.resName.equalsIgnoreCase("GLU")) {\r
- b.endCol = Color.red;\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.equalsIgnoreCase("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
- }\r
-\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
- b = (Bond) bonds.elementAt(i);\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.endCol = cs.findColour(\r
- ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.\r
- get(b.at2.resName)).intValue()]\r
- );*/\r
-\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
-\r
-\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
- }\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 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 MCview;
+
+import jalview.datamodel.*;
+
+import jalview.schemes.ResidueProperties;
+
+import java.awt.*;
+
+import java.util.*;
+import jalview.analysis.AlignSeq;
+
+
+public class PDBChain {
+ /**
+ * SequenceFeature group for PDB File features added to sequences
+ */
+ private static final String PDBFILEFEATURE = "PDBFile";
+ public String id;
+ public Vector bonds = new Vector();
+ public Vector atoms = new Vector();
+ public Vector residues = new Vector();
+ public int offset;
+ public Sequence sequence;
+ public boolean isVisible = true;
+ public int pdbstart = 0;
+ public int pdbend = 0;
+ public int seqstart = 0;
+ public int seqend = 0;
+
+ public PDBChain(String id) {
+ this.id = id;
+ }
+
+ public String print() {
+ String tmp = "";
+
+ for (int i = 0; i < bonds.size(); i++) {
+ tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " +
+ ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +
+ "\n";
+ }
+
+ return tmp;
+ }
+
+ void makeExactMapping(AlignSeq as, Sequence s1)
+ {
+ int pdbpos = as.getSeq2Start()-2;
+ int alignpos = s1.getStart() + as.getSeq1Start()-3;
+
+ for(int i=0; i<as.astr1.length(); i++)
+ {
+ if (as.astr1.charAt(i) != '-')
+ {
+ alignpos++;
+ }
+
+ if (as.astr2.charAt(i) != '-')
+ {
+ pdbpos++;
+ }
+
+ if (as.astr1.charAt(i) == as.astr2.charAt(i))
+ {
+ Residue res = (Residue) residues.elementAt(pdbpos);
+ Enumeration en = res.atoms.elements();
+ while (en.hasMoreElements())
+ {
+ Atom atom = (Atom) en.nextElement();
+ atom.alignmentMapping = alignpos;
+ }
+ }
+ }
+ }
+ /**
+ * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
+ * @param seq
+ */
+ public void transferRESNUMFeatures(SequenceI seq, String status) {
+ if (seq != sequence) {
+ /** SequenceFeature[] seqsfeatures=seq.getSequenceFeatures();
+ int totfeat=seqsfeatures.length;
+ // Remove any features for this exact chain ?
+ for (int i=0; i<seqsfeatures.length; i++) {
+
+ } */
+ if (status==null)
+ status = "IEA:jalview";
+ SequenceFeature[] features = sequence.getSequenceFeatures();
+ for (int i=0; i<features.length; i++) {
+ if (features[i].getFeatureGroup().equals(PDBChain.PDBFILEFEATURE)) {
+ SequenceFeature tx = new SequenceFeature(features[i]);
+ tx.setBegin(1+((Atom)((Residue)residues.elementAt(tx.getBegin()-offset)).atoms.elementAt(0)).alignmentMapping);
+ tx.setEnd(1+((Atom)((Residue)residues.elementAt(tx.getEnd()-offset)).atoms.elementAt(0)).alignmentMapping);
+ tx.setStatus(status+((tx.getStatus()==null || tx.getStatus().length()==0) ? "" : ":"+tx.getStatus()));
+ seq.getDatasetSequence().addSequenceFeature(tx);
+ }
+ }
+
+ }
+ }
+
+ public void makeCaBondList()
+ {
+ for (int i = 0; i < (residues.size() - 1); i++)
+ {
+ Residue tmpres = (Residue) residues.elementAt(i);
+ Residue tmpres2 = (Residue) residues.elementAt(i + 1);
+ Atom at1 = tmpres.findAtom("CA");
+ Atom at2 = tmpres2.findAtom("CA");
+
+ if ((at1 != null) && (at2 != null))
+ {
+ if (at1.chain.equals(at2.chain))
+ {
+ makeBond(at1, at2);
+ }
+ }
+ else
+ System.out.println("not found "+i);
+ }
+ }
+
+ public void makeBond(Atom at1, Atom at2) {
+ float[] start = new float[3];
+ float[] end = new float[3];
+
+ start[0] = at1.x;
+ start[1] = at1.y;
+ start[2] = at1.z;
+
+ end[0] = at2.x;
+ end[1] = at2.y;
+ end[2] = at2.z;
+
+ bonds.addElement(new Bond(start, end, at1, at2));
+ }
+
+ public void makeResidueList() {
+ int count = 0;
+ StringBuffer seq = new StringBuffer();
+ Vector resFeatures=new Vector();
+ int i, iSize = atoms.size()-1;
+ int resNumber=-1;
+ for (i = 0; i <= iSize; i++)
+ {
+ Atom tmp = (Atom) atoms.elementAt(i);
+ resNumber = tmp.resNumber;
+ int res = resNumber;
+
+ if (i == 0) {
+ offset = resNumber;
+ }
+
+ Vector resAtoms = new Vector();
+ //Add atoms to a vector while the residue number
+ //remains the same as the first atom's resNumber (res)
+ while ((resNumber == res) && (i < atoms.size())) {
+ resAtoms.addElement((Atom) atoms.elementAt(i));
+ i++;
+
+ if (i < atoms.size()) {
+ resNumber = ((Atom) atoms.elementAt(i)).resNumber;
+ } else {
+ resNumber++;
+ }
+ }
+
+ //We need this to keep in step with the outer for i = loop
+ i--;
+
+ //Make a new Residue object with the new atoms vector
+ residues.addElement(new Residue(resAtoms, resNumber - 1, count));
+
+ Residue tmpres = (Residue) residues.lastElement();
+ Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
+ // Make A new SequenceFeature for the current residue numbering
+ SequenceFeature sf =
+ new SequenceFeature("RESNUM",tmpat.resName+":"+tmpat.resNumIns,
+ "",offset+count,offset+count,MCview.PDBChain.PDBFILEFEATURE);
+ resFeatures.addElement(sf);
+ // Keep totting up the sequence
+ if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+ {
+ seq.append("X") ;
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
+ } else {
+
+ seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
+ .get(tmpat.resName)).intValue()]);
+ }
+ count++;
+ }
+
+ if(id.length()<1 || id.equals(" "))
+ id = "_";
+
+ sequence = new Sequence(id, seq.toString(), offset, resNumber); // resNumber-offset ~= seq.size()
+ // System.out.println("PDB Sequence is :\nSequence = " + seq);
+ // System.out.println("No of residues = " + residues.size());
+ for (i=0,iSize=resFeatures.size(); i<iSize; i++) {
+ sequence.addSequenceFeature((SequenceFeature) resFeatures.elementAt(i));
+ resFeatures.setElementAt(null, i);
+ }
+ }
+
+ public void setChargeColours() {
+ for (int i = 0; i < bonds.size(); i++) {
+ try {
+ Bond b = (Bond) bonds.elementAt(i);
+
+ if (b.at1.resName.equalsIgnoreCase("ASP") ||
+ b.at1.resName.equalsIgnoreCase("GLU")) {
+ b.startCol = Color.red;
+ } else if (b.at1.resName.equalsIgnoreCase("LYS") ||
+ b.at1.resName.equalsIgnoreCase("ARG")) {
+ b.startCol = Color.blue;
+ } else if (b.at1.resName.equalsIgnoreCase("CYS")) {
+ b.startCol = Color.yellow;
+ } else {
+ //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
+ b.startCol = Color.lightGray;
+ }
+
+ if (b.at2.resName.equalsIgnoreCase("ASP") ||
+ b.at2.resName.equalsIgnoreCase("GLU")) {
+ b.endCol = Color.red;
+ } else if (b.at2.resName.equalsIgnoreCase("LYS") ||
+ b.at2.resName.equalsIgnoreCase("ARG")) {
+ b.endCol = Color.blue;
+ } else if (b.at2.resName.equalsIgnoreCase("CYS")) {
+ b.endCol = Color.yellow;
+ } else {
+ //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
+ b.endCol = Color.lightGray;
+ }
+ } catch (Exception e) {
+ Bond b = (Bond) bonds.elementAt(i);
+ b.startCol = Color.gray;
+ b.endCol = Color.gray;
+ }
+ }
+ }
+
+
+ public void setChainColours(jalview.schemes.ColourSchemeI cs)
+ {
+ Bond b;
+ for (int i = 0; i < bonds.size(); i++) {
+ try {
+ b = (Bond) bonds.elementAt(i);
+
+ /* ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
+ ResidueProperties.codonTranslate(
+ ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)
+ );
+
+ b.endCol = cs.findColour(
+ ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
+ get(b.at2.resName)).intValue()]
+ );*/
+
+ } catch (Exception e)
+ {
+ b = (Bond) bonds.elementAt(i);
+ b.startCol = Color.gray;
+ b.endCol = Color.gray;
+ }
+ }
+ }
+
+
+
+ public void setChainColours(Color col)
+ {
+ for (int i = 0; i < bonds.size(); i++)
+ {
+ Bond tmp = (Bond) bonds.elementAt(i);
+ tmp.startCol = col;
+ tmp.endCol = col;
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff