X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=b15c3cc1bf650a1c01bc1a8df0a1f01f196c5f8c;hb=6f04e0a80f3c3ba8087a1ad316debd395d0a4db0;hp=211cff0e27a7a817e0a28324b463a3d35bc3d7e9;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index 211cff0..b15c3cc 100644 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -26,6 +26,9 @@ import jalview.appletgui.FeatureRenderer; import jalview.appletgui.SequenceRenderer; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.io.StructureFile; +import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; @@ -49,8 +52,8 @@ import java.io.PrintStream; import java.util.List; import java.util.Vector; -public class AppletPDBCanvas extends Panel implements MouseListener, - MouseMotionListener, StructureListener +public class AppletPDBCanvas extends Panel + implements MouseListener, MouseMotionListener, StructureListener { MCMatrix idmat = new MCMatrix(3, 3); @@ -67,7 +70,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, int my = 0; - public PDBfile pdb; + public StructureFile pdb; PDBEntry pdbentry; @@ -127,7 +130,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, PDBChain mainchain; - Vector highlightRes; + Vector highlightRes; boolean pdbAction = false; @@ -144,7 +147,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, StructureSelectionManager ssm; public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq, - String[] chains, AlignmentPanel ap, String protocol) + String[] chains, AlignmentPanel ap, DataSourceType protocol) { this.ap = ap; @@ -156,11 +159,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener, try { - pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol); + pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null); - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (protocol == DataSourceType.PASTE) { - pdbentry.setFile("INLINE" + pdb.id); + pdbentry.setFile("INLINE" + pdb.getId()); } } catch (Exception ex) @@ -169,13 +172,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, return; } - pdbentry.setId(pdb.id); + pdbentry.setId(pdb.getId()); ssm.addStructureViewerListener(this); colourBySequence(); - int max = -10; + float max = -10; int maxchain = -1; int pdbstart = 0; int pdbend = 0; @@ -185,33 +188,34 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // JUST DEAL WITH ONE SEQUENCE FOR NOW SequenceI sequence = seq[0]; - for (int i = 0; i < pdb.chains.size(); i++) + for (int i = 0; i < pdb.getChains().size(); i++) { mappingDetails.append("\n\nPDB Sequence is :\nSequence = " - + pdb.chains.elementAt(i).sequence + + pdb.getChains().elementAt(i).sequence .getSequenceAsString()); mappingDetails.append("\nNo of residues = " - + pdb.chains.elementAt(i).residues.size() - + "\n\n"); + + pdb.getChains().elementAt(i).residues.size() + "\n\n"); // Now lets compare the sequences to get // the start and end points. // Align the sequence to the pdb // TODO: DNa/Pep switch AlignSeq as = new AlignSeq(sequence, - pdb.chains.elementAt(i).sequence, - pdb.chains.elementAt(i).isNa ? AlignSeq.DNA + pdb.getChains().elementAt(i).sequence, + pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP); as.calcScoreMatrix(); as.traceAlignment(); PrintStream ps = new PrintStream(System.out) { + @Override public void print(String x) { mappingDetails.append(x); } + @Override public void println() { mappingDetails.append("\n"); @@ -235,7 +239,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend); } - mainchain = pdb.chains.elementAt(maxchain); + mainchain = pdb.getChains().elementAt(maxchain); mainchain.pdbstart = pdbstart; mainchain.pdbend = pdbend; @@ -270,6 +274,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { doKeyPressed(evt); @@ -284,19 +289,19 @@ 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++) + for (int ii = 0; ii < pdb.getChains().size(); ii++) { - if (pdb.chains.elementAt(ii).isVisible) + if (pdb.getChains().elementAt(ii).isVisible) { - Vector tmp = pdb.chains.elementAt(ii).bonds; + Vector tmp = pdb.getChains().elementAt(ii).bonds; for (int i = 0; i < tmp.size(); i++) { @@ -323,16 +328,14 @@ public class AppletPDBCanvas extends Panel implements MouseListener, min[1] = (float) 1e30; min[2] = (float) 1e30; - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (int ii = 0; ii < pdb.getChains().size(); ii++) { - if (pdb.chains.elementAt(ii).isVisible) + if (pdb.getChains().elementAt(ii).isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.getChains().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]; @@ -453,24 +456,19 @@ public class AppletPDBCanvas extends Panel implements MouseListener, int bsize = 0; // Find centre coordinate - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (int ii = 0; ii < pdb.getChains().size(); ii++) { - if (pdb.chains.elementAt(ii).isVisible) + if (pdb.getChains().elementAt(ii).isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.getChains().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]; } } } @@ -480,6 +478,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, centre[2] = ztot / (2 * (float) bsize); } + @Override public void paint(Graphics g) { @@ -489,9 +488,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, g.fillRect(0, 0, getSize().width, getSize().height); g.setColor(Color.black); g.setFont(new Font("Verdana", Font.BOLD, 14)); - g.drawString( - MessageManager.getString("label.error_loading_pdb_data"), 50, - getSize().height / 2); + g.drawString(MessageManager.getString("label.error_loading_pdb_data"), + 50, getSize().height / 2); return; } @@ -579,16 +577,18 @@ public class AppletPDBCanvas extends Panel implements MouseListener, showFeatures = true; } + FeatureColourFinder finder = new FeatureColourFinder(fr); + PDBChain chain; if (bysequence && pdb != null) { - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (int ii = 0; ii < pdb.getChains().size(); ii++) { - chain = pdb.chains.elementAt(ii); + chain = pdb.getChains().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) @@ -606,25 +606,16 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (pos > 0) { pos = sequence[s].findIndex(pos); - tmp.startCol = sr.getResidueBoxColour(sequence[s], pos); - if (showFeatures) - { - tmp.startCol = fr.findFeatureColour(tmp.startCol, - sequence[s], pos); - } + tmp.startCol = sr.getResidueColour(sequence[s], pos, + finder); } pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1; if (pos > 0) { pos = sequence[s].findIndex(pos); - tmp.endCol = sr.getResidueBoxColour(sequence[s], pos); - if (showFeatures) - { - tmp.endCol = fr.findFeatureColour(tmp.endCol, - sequence[s], pos); - } + tmp.endCol = sr.getResidueColour(sequence[s], pos, + finder); } - } } } @@ -644,19 +635,23 @@ 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)); + xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + + (getSize().width / 2)); + ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + + (getSize().height / 2)); - xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2)); - yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getSize().height / 2)); + xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + + (getSize().width / 2)); + yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + + (getSize().height / 2)); xmid = (xend + xstart) / 2; ymid = (yend + ystart) / 2; @@ -784,6 +779,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, } } + @Override public void mousePressed(MouseEvent e) { pdbAction = true; @@ -796,23 +792,25 @@ public class AppletPDBCanvas extends Panel implements MouseListener, repaint(); if (foundchain != -1) { - PDBChain chain = pdb.chains.elementAt(foundchain); + PDBChain chain = pdb.getChains().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.removeElement(fatom.alignmentMapping + ""); + highlightRes.removeElement(atomString); } else { - highlightRes.addElement(fatom.alignmentMapping + ""); + highlightRes.addElement(atomString); } } } @@ -826,6 +824,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, dragging = false; } + @Override public void mouseMoved(MouseEvent e) { pdbAction = true; @@ -842,7 +841,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, PDBChain chain = null; if (foundchain != -1) { - chain = pdb.chains.elementAt(foundchain); + chain = pdb.getChains().elementAt(foundchain); if (chain == mainchain) { mouseOverStructure(fatom.resNumber, chain.id); @@ -868,18 +867,22 @@ public class AppletPDBCanvas extends Panel implements MouseListener, } } + @Override public void mouseClicked(MouseEvent e) { } + @Override public void mouseEntered(MouseEvent e) { } + @Override public void mouseExited(MouseEvent e) { } + @Override public void mouseDragged(MouseEvent evt) { int x = evt.getX(); @@ -901,14 +904,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, } // Alter the bonds - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.getChains()) { - 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]); @@ -933,6 +932,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, repaint(); } + @Override public void mouseReleased(MouseEvent evt) { dragging = false; @@ -942,18 +942,12 @@ public class AppletPDBCanvas extends Panel implements MouseListener, void drawLabels(Graphics g) { - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.getChains()) { - 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 +955,6 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (tmpBond.at2.isSelected) { - labelAtom(g, tmpBond, 2); } } @@ -975,8 +968,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (n == 1) { - int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getSize().width / 2)); - int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getSize().height / 2)); + int xstart = (int) (((b.start[0] - centre[0]) * scale) + + (getSize().width / 2)); + int ystart = (int) (((centre[1] - b.start[1]) * scale) + + (getSize().height / 2)); g.setColor(Color.red); g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart); @@ -984,8 +979,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (n == 2) { - int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getSize().width / 2)); - int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getSize().height / 2)); + int xstart = (int) (((b.end[0] - centre[0]) * scale) + + (getSize().width / 2)); + int ystart = (int) (((centre[1] - b.end[1]) * scale) + + (getSize().height / 2)); g.setColor(Color.red); g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); @@ -1000,25 +997,27 @@ public class AppletPDBCanvas extends Panel implements MouseListener, foundchain = -1; - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (int ii = 0; ii < pdb.getChains().size(); ii++) { - PDBChain chain = pdb.chains.elementAt(ii); + PDBChain chain = pdb.getChains().elementAt(ii); int truex; Bond tmpBond = null; if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.getChains().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)); + truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + + (getSize().width / 2)); if (Math.abs(truex - x) <= 2) { - int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2)); + int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + + (getSize().height / 2)); if (Math.abs(truey - y) <= 2) { @@ -1031,11 +1030,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // Still here? Maybe its the last bond - truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2)); + truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + + (getSize().width / 2)); if (Math.abs(truex - x) <= 2) { - int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getSize().height / 2)); + int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + + (getSize().height / 2)); if (Math.abs(truey - y) <= 2) { @@ -1049,13 +1050,14 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (fatom != null) // )&& chain.ds != null) { - chain = pdb.chains.elementAt(foundchain); + chain = pdb.getChains().elementAt(foundchain); } } return fatom; } + @Override public void update(Graphics g) { paint(g); @@ -1077,7 +1079,7 @@ 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 +1097,13 @@ 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; } @@ -1115,9 +1117,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener, public void setAllchainsVisible(boolean b) { - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (int ii = 0; ii < pdb.getChains().size(); ii++) { - PDBChain chain = pdb.chains.elementAt(ii); + PDBChain chain = pdb.getChains().elementAt(ii); chain.isVisible = b; } mainchain.isVisible = true; @@ -1127,10 +1129,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // //////////////////////////////// // /StructureListener - public String[] getPdbFile() + @Override + public String[] getStructureFiles() { - return new String[] - { pdbentry.getFile() }; + return new String[] { pdbentry.getFile() }; } String lastMessage; @@ -1187,7 +1189,7 @@ 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 +1207,13 @@ 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; } @@ -1230,6 +1232,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // return new Color(viewer.getAtomArgb(atomIndex)); } + @Override public void updateColours(Object source) { colourBySequence(); @@ -1244,4 +1247,19 @@ 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; + } }