X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=fdd673bb591ab486faaa97e7db1dd33bb3482cd4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=6f76a25397c214875393eb0c69ccd1fd9cce8cc8;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index 6f76a25..fdd673b 100644 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -123,7 +123,7 @@ public class PDBCanvas extends JPanel implements MouseListener, PDBChain mainchain; - Vector highlightRes; + Vector highlightRes; boolean pdbAction = false; @@ -188,11 +188,9 @@ public class PDBCanvas extends JPanel 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. @@ -265,23 +263,21 @@ public class PDBCanvas extends JPanel implements MouseListener, ToolTipManager.sharedInstance().setDismissDelay(10000); } - 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++) + for (PDBChain chain : pdb.chains) { - if (pdb.chains.elementAt(ii).isVisible) + if (chain.isVisible) { - Vector tmp = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < tmp.size(); i++) + for (Bond bond : chain.bonds) { - visiblebonds.addElement(tmp.elementAt(i)); + visiblebonds.addElement(bond); } } } @@ -305,16 +301,12 @@ public class PDBCanvas extends JPanel implements MouseListener, min[1] = (float) 1e30; min[2] = (float) 1e30; - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - if (pdb.chains.elementAt(ii).isVisible) + if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond tmp : chain.bonds) { - Bond tmp = (Bond) bonds.elementAt(i); - if (tmp.start[0] >= max[0]) { max[0] = tmp.start[0]; @@ -440,24 +432,17 @@ public class PDBCanvas extends JPanel implements MouseListener, int bsize = 0; // Find centre coordinate - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - if (pdb.chains.elementAt(ii).isVisible) + if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - bsize += bonds.size(); + bsize += chain.bonds.size(); - for (int i = 0; i < bonds.size(); i++) + for (Bond bond : chain.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 + bond.start[0] + bond.end[0]; + ytot = ytot + bond.start[1] + bond.end[1]; + ztot = ztot + bond.start[2] + bond.end[2]; } } } @@ -562,7 +547,7 @@ public class PDBCanvas extends JPanel 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) @@ -618,13 +603,13 @@ public class PDBCanvas extends JPanel 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) + (getWidth() / 2)); ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2)); @@ -779,16 +764,18 @@ public class PDBCanvas extends JPanel 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.remove(fatom.alignmentMapping + ""); + highlightRes.remove(atomString); } else { - highlightRes.add(fatom.alignmentMapping + ""); + highlightRes.add(atomString); } } } @@ -870,14 +857,10 @@ public class PDBCanvas extends JPanel 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]); @@ -911,18 +894,12 @@ public class PDBCanvas extends JPanel 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); @@ -930,7 +907,6 @@ public class PDBCanvas extends JPanel implements MouseListener, if (tmpBond.at2.isSelected) { - labelAtom(g, tmpBond, 2); } } @@ -975,11 +951,9 @@ public class PDBCanvas extends JPanel implements MouseListener, if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond bond : chain.bonds) { - tmpBond = (Bond) bonds.elementAt(i); + tmpBond = bond; truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2)); @@ -1015,7 +989,7 @@ public class PDBCanvas extends JPanel implements MouseListener, } if (fatom != null) // )&& chain.ds != null) - { + { // dead code? value of chain is either overwritten or discarded chain = pdb.chains.elementAt(foundchain); } } @@ -1041,7 +1015,7 @@ public class PDBCanvas extends JPanel 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) @@ -1059,13 +1033,13 @@ public class PDBCanvas extends JPanel 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; } @@ -1093,8 +1067,7 @@ public class PDBCanvas extends JPanel implements MouseListener, // /StructureListener public String[] getPdbFile() { - return new String[] - { pdbentry.getFile() }; + return new String[] { pdbentry.getFile() }; } String lastMessage; @@ -1153,7 +1126,7 @@ public class PDBCanvas extends JPanel 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) @@ -1171,13 +1144,13 @@ public class PDBCanvas extends JPanel 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; } @@ -1210,4 +1183,19 @@ public class PDBCanvas extends JPanel implements MouseListener, } + @Override + public boolean isListeningFor(SequenceI seq) + { + if (sequence != null) + { + for (SequenceI s : sequence) + { + if (s == seq) + { + return true; + } + } + } + return false; + } }