X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewer.java;h=6cef66575ed5ac76d6407611360c1a4db32ea981;hb=c4820a850ccb7171fd29206655bc327af7226e6b;hp=b7767facf7580fd0e26a03ce02c54dfeb2d18dea;hpb=b927b6af7e5654e0df7e2dbaa337322f2b52940f;p=jalview.git diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java index b7767fa..6cef665 100644 --- a/src/jalview/gui/StructureViewer.java +++ b/src/jalview/gui/StructureViewer.java @@ -20,14 +20,6 @@ */ package jalview.gui; -import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.datamodel.StructureViewerModel; -import jalview.structure.StructureSelectionManager; - -import java.awt.Rectangle; import java.util.ArrayList; import java.util.HashMap; import java.util.LinkedHashMap; @@ -35,6 +27,14 @@ import java.util.List; import java.util.Map; import java.util.Map.Entry; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.datamodel.StructureViewerModel; +import jalview.structure.StructureSelectionManager; + /** * A proxy for handling structure viewers, that orchestrates adding selected * structures, associated with sequences in Jalview, to an existing viewer, or @@ -49,9 +49,24 @@ public class StructureViewer StructureSelectionManager ssm; + /** + * decide if new structures are aligned to existing ones + */ + private boolean superposeAdded = true; + + /** + * whether to open structures in their own thread or not + */ + private boolean async = true; + + public void setAsync(boolean b) + { + async = b; + } + public enum ViewerType { - JMOL, CHIMERA + JMOL, CHIMERA, CHIMERAX, PYMOL }; /** @@ -59,7 +74,8 @@ public class StructureViewer * * @param structureSelectionManager */ - public StructureViewer(StructureSelectionManager structureSelectionManager) + public StructureViewer( + StructureSelectionManager structureSelectionManager) { ssm = structureSelectionManager; } @@ -85,7 +101,12 @@ public class StructureViewer } return "New View"; } - public ViewerType getViewerType() + + /** + * + * @return ViewerType for currently configured structure viewer + */ + public static ViewerType getViewerType() { String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name()); @@ -108,6 +129,12 @@ public class StructureViewer public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs, SequenceI[] seqs, AlignmentPanel ap) { + return viewStructures(pdbs, seqs, ap, null); + } + + public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs, + SequenceI[] seqs, AlignmentPanel ap, ViewerType viewerType) + { JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap); if (viewer != null) { @@ -117,17 +144,20 @@ public class StructureViewer return viewer; } - ViewerType viewerType = getViewerType(); + if (viewerType == null) + viewerType = getViewerType(); Map seqsForPdbs = getSequencesForPdbs(pdbs, seqs); - PDBEntry[] pdbsForFile = seqsForPdbs.keySet().toArray( - new PDBEntry[seqsForPdbs.size()]); - SequenceI[][] theSeqs = seqsForPdbs.values().toArray( - new SequenceI[seqsForPdbs.size()][]); + PDBEntry[] pdbsForFile = seqsForPdbs.keySet() + .toArray(new PDBEntry[seqsForPdbs.size()]); + SequenceI[][] theSeqs = seqsForPdbs.values() + .toArray(new SequenceI[seqsForPdbs.size()][]); if (sview != null) { - new Thread(new Runnable() + sview.setAlignAddedStructures(superposeAdded); + + Runnable viewRunnable = new Runnable() { @Override public void run() @@ -146,21 +176,39 @@ public class StructureViewer sview.updateTitleAndMenus(); } - }).start(); + }; + if (async) + { + new Thread(viewRunnable).start(); + } + else + { + viewRunnable.run(); + } return sview; } if (viewerType.equals(ViewerType.JMOL)) { - sview = new AppJmol(ap, pdbsForFile, theSeqs); + sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs); } else if (viewerType.equals(ViewerType.CHIMERA)) { - sview = new ChimeraViewFrame(pdbsForFile, theSeqs, ap); + sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs, + ap); + } + else if (viewerType.equals(ViewerType.CHIMERAX)) + { + sview = new ChimeraXViewFrame(pdbsForFile, superposeAdded, theSeqs, + ap); + } + else if (viewerType.equals(ViewerType.PYMOL)) + { + sview = new PymolViewer(pdbsForFile, superposeAdded, theSeqs, ap); } else { - Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString()); + Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString()); } return sview; } @@ -274,19 +322,34 @@ public class StructureViewer JalviewStructureDisplayI sview = null; + public JalviewStructureDisplayI getJalviewStructureDisplay() + { + return sview; + } + public JalviewStructureDisplayI viewStructures(PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap) { + return viewStructures(pdb, seqsForPdb, ap, null); + } + + public JalviewStructureDisplayI viewStructures(PDBEntry pdb, + SequenceI[] seqsForPdb, AlignmentPanel ap, ViewerType viewerType) + { if (sview != null) { - if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdb.getId())) + sview.setAlignAddedStructures(superposeAdded); + String pdbId = pdb.getId(); + if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId)) { - sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdb.getId()); + sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId); } sview.updateTitleAndMenus(); + sview.raiseViewer(); return sview; } - ViewerType viewerType = getViewerType(); + if (viewerType == null) + viewerType = getViewerType(); if (viewerType.equals(ViewerType.JMOL)) { sview = new AppJmol(pdb, seqsForPdb, null, ap); @@ -295,50 +358,57 @@ public class StructureViewer { sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap); } + else if (viewerType.equals(ViewerType.CHIMERAX)) + { + sview = new ChimeraXViewFrame(pdb, seqsForPdb, null, ap); + } + else if (viewerType.equals(ViewerType.PYMOL)) + { + sview = new PymolViewer(pdb, seqsForPdb, null, ap); + } else { - Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString()); + Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString()); } return sview; } /** - * Create a new panel controlling a structure viewer. + * Creates a new panel controlling a structure viewer * * @param type - * @param pdbf - * @param id - * @param sq * @param alignPanel * @param viewerData - * @param fileloc - * @param rect + * @param sessionFile * @param vid * @return */ - public JalviewStructureDisplayI createView(ViewerType type, String[] pdbf, - String[] id, SequenceI[][] sq, AlignmentPanel alignPanel, - StructureViewerModel viewerData, String fileloc, Rectangle rect, - String vid) + public static JalviewStructureDisplayI createView(ViewerType type, + AlignmentPanel alignPanel, StructureViewerModel viewerData, + String sessionFile, String vid) { - final boolean useinViewerSuperpos = viewerData.isAlignWithPanel(); - final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel(); - final boolean viewerColouring = viewerData.isColourByViewer(); - + JalviewStructureDisplayI viewer = null; switch (type) { case JMOL: - sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq, - useinViewerSuperpos, viewerColouring, fileloc, rect, vid); + viewer = new AppJmol(viewerData, alignPanel, sessionFile, vid); + // todo or construct and then openSession(sessionFile)? break; case CHIMERA: - Cache.log.error( - "Unsupported structure viewer type " + type.toString()); + viewer = new ChimeraViewFrame(viewerData, alignPanel, sessionFile, + vid); + break; + case CHIMERAX: + viewer = new ChimeraXViewFrame(viewerData, alignPanel, sessionFile, + vid); + break; + case PYMOL: + viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid); break; default: - Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString()); + Console.error(UNKNOWN_VIEWER_TYPE + type.toString()); } - return sview; + return viewer; } public boolean isBusy() @@ -373,4 +443,9 @@ public class StructureViewer return sview != null && sview.isVisible(); } + public void setSuperpose(boolean alignAddedStructures) + { + superposeAdded = alignAddedStructures; + } + }