X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=7f87326d02017ed444a00329a750378f3aa0d238;hb=a31403382672ec59acdf56e095d6d0136199fb44;hp=211cff0e27a7a817e0a28324b463a3d35bc3d7e9;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index 211cff0..7f87326 100644 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -127,7 +127,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, PDBChain mainchain; - Vector highlightRes; + Vector highlightRes; boolean pdbAction = false; @@ -189,11 +189,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { mappingDetails.append("\n\nPDB Sequence is :\nSequence = " - + pdb.chains.elementAt(i).sequence - .getSequenceAsString()); + + pdb.chains.elementAt(i).sequence.getSequenceAsString()); mappingDetails.append("\nNo of residues = " - + pdb.chains.elementAt(i).residues.size() - + "\n\n"); + + pdb.chains.elementAt(i).residues.size() + "\n\n"); // Now lets compare the sequences to get // the start and end points. @@ -201,8 +199,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // TODO: DNa/Pep switch AlignSeq as = new AlignSeq(sequence, pdb.chains.elementAt(i).sequence, - pdb.chains.elementAt(i).isNa ? AlignSeq.DNA - : AlignSeq.PEP); + pdb.chains.elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP); as.calcScoreMatrix(); as.traceAlignment(); PrintStream ps = new PrintStream(System.out) @@ -284,19 +281,19 @@ public class AppletPDBCanvas extends Panel implements MouseListener, scale = findScale(); } - Vector visiblebonds; + Vector visiblebonds; void setupBonds() { seqColoursReady = false; // Sort the bonds by z coord - visiblebonds = new Vector(); + visiblebonds = new Vector(); for (int ii = 0; ii < pdb.chains.size(); ii++) { if (pdb.chains.elementAt(ii).isVisible) { - Vector tmp = pdb.chains.elementAt(ii).bonds; + Vector tmp = pdb.chains.elementAt(ii).bonds; for (int i = 0; i < tmp.size(); i++) { @@ -327,12 +324,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { if (pdb.chains.elementAt(ii).isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.chains.elementAt(ii).bonds; - for (int i = 0; i < bonds.size(); i++) + for (Bond tmp : bonds) { - Bond tmp = (Bond) bonds.elementAt(i); - if (tmp.start[0] >= max[0]) { max[0] = tmp.start[0]; @@ -457,20 +452,15 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { if (pdb.chains.elementAt(ii).isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.chains.elementAt(ii).bonds; bsize += bonds.size(); - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { - xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] - + ((Bond) bonds.elementAt(i)).end[0]; - - ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] - + ((Bond) bonds.elementAt(i)).end[1]; - - ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] - + ((Bond) bonds.elementAt(i)).end[2]; + xtot = xtot + b.start[0] + b.end[0]; + ytot = ytot + b.start[1] + b.end[1]; + ztot = ztot + b.start[2] + b.end[2]; } } } @@ -588,7 +578,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, for (int i = 0; i < chain.bonds.size(); i++) { - Bond tmp = (Bond) chain.bonds.elementAt(i); + Bond tmp = chain.bonds.elementAt(i); tmp.startCol = Color.lightGray; tmp.endCol = Color.lightGray; if (chain != mainchain) @@ -644,13 +634,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, zsort = new Zsort(); } - zsort.Zsort(visiblebonds); + zsort.sort(visiblebonds); } Bond tmpBond = null; for (int i = 0; i < visiblebonds.size(); i++) { - tmpBond = (Bond) visiblebonds.elementAt(i); + tmpBond = visiblebonds.elementAt(i); xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2)); ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2)); @@ -803,16 +793,18 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { if (highlightRes == null) { - highlightRes = new Vector(); + highlightRes = new Vector(); } - if (highlightRes.contains(fatom.alignmentMapping + "" + "")) + final String atomString = Integer + .toString(fatom.alignmentMapping); + if (highlightRes.contains(atomString)) { - highlightRes.removeElement(fatom.alignmentMapping + ""); + highlightRes.removeElement(atomString); } else { - highlightRes.addElement(fatom.alignmentMapping + ""); + highlightRes.addElement(atomString); } } } @@ -901,14 +893,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, } // Alter the bonds - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond tmpBond : chain.bonds) { - Bond tmpBond = (Bond) bonds.elementAt(i); - // Translate the bond so the centre is 0,0,0 tmpBond.translate(-centre[0], -centre[1], -centre[2]); @@ -942,18 +930,12 @@ public class AppletPDBCanvas extends Panel implements MouseListener, void drawLabels(Graphics g) { - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - PDBChain chain = pdb.chains.elementAt(ii); - if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond tmpBond : chain.bonds) { - Bond tmpBond = (Bond) bonds.elementAt(i); - if (tmpBond.at1.isSelected) { labelAtom(g, tmpBond, 1); @@ -961,7 +943,6 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (tmpBond.at2.isSelected) { - labelAtom(g, tmpBond, 2); } } @@ -1008,11 +989,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.chains.elementAt(ii).bonds; for (int i = 0; i < bonds.size(); i++) { - tmpBond = (Bond) bonds.elementAt(i); + tmpBond = bonds.elementAt(i); truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2)); @@ -1077,7 +1058,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, Bond tmpBond; for (index = 0; index < mainchain.bonds.size(); index++) { - tmpBond = (Bond) mainchain.bonds.elementAt(index); + tmpBond = mainchain.bonds.elementAt(index); if (tmpBond.at1.alignmentMapping == ii - 1) { if (highlightBond1 != null) @@ -1095,13 +1076,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (index > 0) { - highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); + highlightBond1 = mainchain.bonds.elementAt(index - 1); highlightBond1.at2.isSelected = true; } if (index != mainchain.bonds.size()) { - highlightBond2 = (Bond) mainchain.bonds.elementAt(index); + highlightBond2 = mainchain.bonds.elementAt(index); highlightBond2.at1.isSelected = true; } @@ -1129,8 +1110,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // /StructureListener public String[] getPdbFile() { - return new String[] - { pdbentry.getFile() }; + return new String[] { pdbentry.getFile() }; } String lastMessage; @@ -1187,7 +1167,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, Bond tmpBond; for (index = 0; index < mainchain.bonds.size(); index++) { - tmpBond = (Bond) mainchain.bonds.elementAt(index); + tmpBond = mainchain.bonds.elementAt(index); if (tmpBond.at1.atomIndex == atomIndex) { if (highlightBond1 != null) @@ -1205,13 +1185,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (index > 0) { - highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); + highlightBond1 = mainchain.bonds.elementAt(index - 1); highlightBond1.at2.isSelected = true; } if (index != mainchain.bonds.size()) { - highlightBond2 = (Bond) mainchain.bonds.elementAt(index); + highlightBond2 = mainchain.bonds.elementAt(index); highlightBond2.at1.isSelected = true; } @@ -1244,4 +1224,19 @@ public class AppletPDBCanvas extends Panel implements MouseListener, } + @Override + public boolean isListeningFor(SequenceI seq) + { + if (sequence != null) + { + for (SequenceI s : sequence) + { + if (s == seq) + { + return true; + } + } + } + return false; + } }