X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=2d2d10e429ff388a042a4594d5ef280fdd7215d3;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=3ee8a34b61fab110c48b2e2d6f137ccd38c0e3d9;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 3ee8a34..2d2d10e 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -43,13 +43,12 @@ import java.awt.event.ComponentListener; import java.io.File; import java.net.URL; import java.security.AccessControlException; +import java.util.ArrayList; import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.Vector; -import javajs.awt.Dimension; - import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolSelectionListener; @@ -73,7 +72,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel Vector atomsPicked = new Vector(); - public Vector chainNames; + private List chainNames; Hashtable chainFile; @@ -93,20 +92,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel boolean loadedInline; - /** - * current set of model filenames loaded in the Jmol instance - */ - String[] modelFileNames = null; - StringBuffer resetLastRes = new StringBuffer(); public Viewer viewer; public JalviewJmolBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) { - super(ssm, pdbentry, sequenceIs, chains, protocol); + super(ssm, pdbentry, sequenceIs, protocol); /* * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), * "jalviewJmol", ap.av.applet .getDocumentBase(), @@ -171,7 +165,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { // remove listeners for all structures in viewer getSsm().removeStructureViewerListener(this, this.getPdbFile()); - viewer.dispose(); + viewer.dispose(); lastCommand = null; viewer = null; releaseUIResources(); @@ -258,8 +252,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } catch (InterruptedException i) { } - ; } + + /* + * get the distinct structure files modelled + * (a file with multiple chains may map to multiple sequences) + */ String[] files = getPdbFile(); if (!waitForFileLoad(files)) { @@ -307,6 +305,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * 'matched' array will hold 'true' for visible alignment columns where * all sequences have a residue with a mapping to the PDB structure */ + // TODO could use a BitSet for matched boolean matched[] = new boolean[alignment.getWidth()]; for (int m = 0; m < matched.length; m++) { @@ -352,6 +351,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * generate select statements to select regions to superimpose structures */ { + // TODO extract method to construct selection statements for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { String chainCd = ":" + structures[pdbfnum].chain; @@ -419,6 +419,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } } StringBuilder command = new StringBuilder(256); + // command.append("set spinFps 10;\n"); + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { if (pdbfnum == refStructure || selcom[pdbfnum] == null @@ -449,12 +451,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } if (selectioncom.length() > 0) { - System.out.println("Select regions:\n" + selectioncom.toString()); + // TODO is performing selectioncom redundant here? is done later on + // System.out.println("Select regions:\n" + selectioncom.toString()); evalStateCommand("select *; cartoons off; backbone; select (" + selectioncom.toString() + "); cartoons; "); // selcom.append("; ribbons; "); String cmdString = command.toString(); - System.out.println("Superimpose command(s):\n" + cmdString); + // System.out.println("Superimpose command(s):\n" + cmdString); evalStateCommand(cmdString); } @@ -465,7 +468,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { selectioncom.setLength(selectioncom.length() - 1); } - System.out.println("Select regions:\n" + selectioncom.toString()); + // System.out.println("Select regions:\n" + selectioncom.toString()); evalStateCommand("select *; cartoons off; backbone; select (" + selectioncom.toString() + "); cartoons; "); // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); @@ -647,15 +650,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } if (modelFileNames == null) { - String mset[] = new String[viewer.ms.mc]; - _modelFileNameMap = new int[mset.length]; + List mset = new ArrayList(); + _modelFileNameMap = new int[viewer.ms.mc]; String m = viewer.ms.getModelFileName(0); if (m != null) { - mset[0] = m; + String filePath = m; try { - mset[0] = new File(m).getAbsolutePath(); + filePath = new File(m).getAbsolutePath(); } catch (AccessControlException x) { // usually not allowed to do this in applet @@ -663,39 +666,43 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel .println("jmolBinding: Using local file string from Jmol: " + m); } - if (mset[0].indexOf("/file:") != -1) + if (filePath.indexOf("/file:") != -1) { // applet path with docroot - discard as format won't match pdbfile - mset[0] = m; + filePath = m; } + mset.add(filePath); _modelFileNameMap[0] = 0; // filename index for first model is always 0. } int j = 1; - for (int i = 1; i < mset.length; i++) + for (int i = 1; i < viewer.ms.mc; i++) { m = viewer.ms.getModelFileName(i); - mset[j] = m; + String filePath = m; if (m != null) { try { - mset[j] = new File(m).getAbsolutePath(); + filePath = new File(m).getAbsolutePath(); } catch (AccessControlException x) { // usually not allowed to do this in applet, so keep raw handle // System.err.println("jmolBinding: Using local file string from Jmol: "+m); } } - _modelFileNameMap[j] = i; // record the model index for the filename - // skip any additional models in the same file (NMR structures) - if ((mset[j] == null ? mset[j] != mset[j - 1] - : (mset[j - 1] == null || !mset[j].equals(mset[j - 1])))) + + /* + * add this model unless it is read from a structure file we have + * already seen (example: 2MJW is an NMR structure with 10 models) + */ + if (!mset.contains(filePath)) { + mset.add(filePath); + _modelFileNameMap[j] = i; // record the model index for the filename j++; } } - modelFileNames = new String[j]; - System.arraycopy(mset, 0, modelFileNames, 0, j); + modelFileNames = mset.toArray(new String[mset.size()]); } return modelFileNames; } @@ -1074,7 +1081,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel fileLoadingError = null; String[] oldmodels = modelFileNames; modelFileNames = null; - chainNames = new Vector(); + chainNames = new ArrayList(); chainFile = new Hashtable(); boolean notifyLoaded = false; String[] modelfilenames = getPdbFile(); @@ -1134,6 +1141,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel for (int pe = 0; pe < getPdbCount(); pe++) { boolean matches = false; + addSequence(pe, getSequence()[pe]); if (fileName == null) { if (false) @@ -1185,7 +1193,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String chid = new String(pdb.getId() + ":" + pdb.getChains().elementAt(i).id); chainFile.put(chid, fileName); - chainNames.addElement(chid); + chainNames.add(chid); } notifyLoaded = true; } @@ -1233,6 +1241,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel setLoadingFromArchive(false); } + @Override + public List getChainNames() + { + return chainNames; + } + public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) { notifyAtomPicked(iatom, strMeasure, null); @@ -1395,7 +1409,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } @Override - public Dimension resizeInnerPanel(String data) + public int[] resizeInnerPanel(String data) { // Jalview doesn't honour resize panel requests return null;