X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=76bf59bb3aca3b1e713f800898860845ce06464f;hb=c777b335d0332979123446f431b7f0c160eb4880;hp=f6e64270135d0c1a501ca39a241023e5d6c1e57a;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index f6e6427..76bf59b 100644 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -20,18 +20,37 @@ */ package MCview; -import java.io.*; -import java.util.*; - +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Event; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.Graphics2D; // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.gui.*; -import jalview.structure.*; +import java.awt.Image; +import java.awt.RenderingHints; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.io.PrintStream; +import java.util.List; +import java.util.Vector; + +import javax.swing.JPanel; +import javax.swing.ToolTipManager; + +import jalview.analysis.AlignSeq; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignmentPanel; +import jalview.gui.FeatureRenderer; +import jalview.gui.SequenceRenderer; +import jalview.structure.AtomSpec; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListener, StructureListener @@ -104,7 +123,7 @@ public class PDBCanvas extends JPanel implements MouseListener, PDBChain mainchain; - Vector highlightRes; + Vector highlightRes; boolean pdbAction = false; @@ -134,7 +153,9 @@ public class PDBCanvas extends JPanel implements MouseListener, pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol); if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + { pdbentry.setFile("INLINE" + pdb.id); + } } catch (Exception ex) { @@ -167,17 +188,17 @@ public class PDBCanvas extends JPanel implements MouseListener, { mappingDetails.append("\n\nPDB Sequence is :\nSequence = " - + ((PDBChain) pdb.chains.elementAt(i)).sequence + + pdb.chains.elementAt(i).sequence .getSequenceAsString()); mappingDetails.append("\nNo of residues = " - + ((PDBChain) pdb.chains.elementAt(i)).residues.size() + + pdb.chains.elementAt(i).residues.size() + "\n\n"); // Now lets compare the sequences to get // the start and end points. // Align the sequence to the pdb AlignSeq as = new AlignSeq(sequence, - ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep"); + pdb.chains.elementAt(i).sequence, "pep"); as.calcScoreMatrix(); as.traceAlignment(); PrintStream ps = new PrintStream(System.out) @@ -210,7 +231,7 @@ public class PDBCanvas extends JPanel implements MouseListener, mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend); } - mainchain = (PDBChain) pdb.chains.elementAt(maxchain); + mainchain = pdb.chains.elementAt(maxchain); mainchain.pdbstart = pdbstart; mainchain.pdbend = pdbend; @@ -244,23 +265,21 @@ 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 (((PDBChain) pdb.chains.elementAt(ii)).isVisible) + if (chain.isVisible) { - Vector tmp = ((PDBChain) 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); } } } @@ -284,16 +303,12 @@ 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 (((PDBChain) pdb.chains.elementAt(ii)).isVisible) + if (chain.isVisible) { - Vector bonds = ((PDBChain) 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]; @@ -362,9 +377,9 @@ public class PDBCanvas extends JPanel implements MouseListener, * System.out.println("zmax " + max[2] + " min " + min[2]); */ - width[0] = (float) Math.abs(max[0] - min[0]); - width[1] = (float) Math.abs(max[1] - min[1]); - width[2] = (float) Math.abs(max[2] - min[2]); + width[0] = Math.abs(max[0] - min[0]); + width[1] = Math.abs(max[1] - min[1]); + width[2] = Math.abs(max[2] - min[2]); maxwidth = width[0]; @@ -419,24 +434,17 @@ 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 (((PDBChain) pdb.chains.elementAt(ii)).isVisible) + if (chain.isVisible) { - Vector bonds = ((PDBChain) 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]; } } } @@ -537,11 +545,11 @@ public class PDBCanvas extends JPanel implements MouseListener, { for (int ii = 0; ii < pdb.chains.size(); ii++) { - chain = (PDBChain) pdb.chains.elementAt(ii); + chain = pdb.chains.elementAt(ii); 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) @@ -597,13 +605,13 @@ 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)); @@ -751,23 +759,25 @@ public class PDBCanvas extends JPanel implements MouseListener, repaint(); if (foundchain != -1) { - PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain); + PDBChain chain = pdb.chains.elementAt(foundchain); if (chain == mainchain) { if (fatom.alignmentMapping != -1) { 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); } } } @@ -797,7 +807,7 @@ public class PDBCanvas extends JPanel implements MouseListener, PDBChain chain = null; if (foundchain != -1) { - chain = (PDBChain) pdb.chains.elementAt(foundchain); + chain = pdb.chains.elementAt(foundchain); if (chain == mainchain) { mouseOverStructure(fatom.resNumber, chain.id); @@ -840,23 +850,19 @@ public class PDBCanvas extends JPanel implements MouseListener, if ((evt.getModifiers() & Event.META_MASK) != 0) { - objmat.rotatez((float) ((mx - omx))); + objmat.rotatez(((mx - omx))); } else { - objmat.rotatex((float) ((my - omy))); - objmat.rotatey((float) ((omx - mx))); + objmat.rotatex(((my - omy))); + objmat.rotatey(((omx - mx))); } // Alter the bonds - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - Vector bonds = ((PDBChain) 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]); @@ -890,18 +896,12 @@ 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 = (PDBChain) pdb.chains.elementAt(ii); - if (chain.isVisible) { - Vector bonds = ((PDBChain) 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); @@ -909,7 +909,6 @@ public class PDBCanvas extends JPanel implements MouseListener, if (tmpBond.at2.isSelected) { - labelAtom(g, tmpBond, 2); } } @@ -948,17 +947,15 @@ public class PDBCanvas extends JPanel implements MouseListener, for (int ii = 0; ii < pdb.chains.size(); ii++) { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); + PDBChain chain = pdb.chains.elementAt(ii); int truex; Bond tmpBond = null; if (chain.isVisible) { - Vector bonds = ((PDBChain) 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)); @@ -994,8 +991,8 @@ public class PDBCanvas extends JPanel implements MouseListener, } if (fatom != null) // )&& chain.ds != null) - { - chain = (PDBChain) pdb.chains.elementAt(foundchain); + { // dead code? value of chain is either overwritten or discarded + chain = pdb.chains.elementAt(foundchain); } } @@ -1020,7 +1017,7 @@ 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) @@ -1038,13 +1035,13 @@ 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; } @@ -1060,7 +1057,7 @@ public class PDBCanvas extends JPanel implements MouseListener, { for (int ii = 0; ii < pdb.chains.size(); ii++) { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); + PDBChain chain = pdb.chains.elementAt(ii); chain.isVisible = b; } mainchain.isVisible = true; @@ -1081,7 +1078,9 @@ public class PDBCanvas extends JPanel implements MouseListener, public void mouseOverStructure(int pdbResNum, String chain) { if (lastMessage == null || !lastMessage.equals(pdbResNum + chain)) + { ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile()); + } lastMessage = pdbResNum + chain; } @@ -1090,24 +1089,47 @@ public class PDBCanvas extends JPanel implements MouseListener, StringBuffer eval = new StringBuffer(); - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) + /** + * Highlight the specified atoms in the structure. + * + * @param atoms + */ + @Override + public void highlightAtoms(List atoms) { if (!seqColoursReady) { return; } - if (highlightRes != null && highlightRes.contains((atomIndex - 1) + "")) + for (AtomSpec atom : atoms) { - return; + int atomIndex = atom.getAtomIndex(); + if (highlightRes != null + && highlightRes.contains((atomIndex - 1) + "")) + { + continue; + } + + highlightAtom(atomIndex); } + redrawneeded = true; + repaint(); + } + + /** + * Highlight the atom at the specified index. + * + * @param atomIndex + */ + protected void highlightAtom(int atomIndex) + { int index = -1; 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) @@ -1125,22 +1147,19 @@ 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; } break; } } - - redrawneeded = true; - repaint(); } public Color getColour(int atomIndex, int pdbResNum, String chain, @@ -1166,5 +1185,4 @@ public class PDBCanvas extends JPanel implements MouseListener, // TODO Auto-generated method stub } - }