import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.Alcodon;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
*/
public class Jalview2XML
{
-
- private class ViewerData
- {
-
- private int x;
-
- private int y;
-
- private int width;
-
- private int height;
-
- private boolean alignWithPanel;
-
- private boolean colourWithAlignPanel;
-
- private boolean colourByViewer;
-
- private String stateData = "";
-
- // todo: java bean in place of Object []
- private Map<File, Object[]> fileData = new HashMap<File, Object[]>();
-
- public ViewerData(int x, int y, int width, int height,
- boolean alignWithPanel, boolean colourWithAlignPanel,
- boolean colourByViewer)
- {
- this.x = x;
- this.y = y;
- this.width = width;
- this.height = height;
- this.alignWithPanel = alignWithPanel;
- this.colourWithAlignPanel = colourWithAlignPanel;
- this.colourByViewer = colourByViewer;
- }
-
- }
-
/*
* SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
* of sequence objects are created.
boolean storeDS, JarOutputStream jout)
{
initSeqRefs();
+ List<String> viewIds = new ArrayList<String>();
List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
AlignViewport av = ap.av;
pdb.setType(entry.getType());
/*
- * Store any JMol or Chimera views associated with this sequence. This
+ * Store any structure views associated with this sequence. This
* section copes with duplicate entries in the project, so a dataset
* only view *should* be coped with sensibly.
*/
- List<String> viewIds = new ArrayList<String>();
// This must have been loaded, is it still visible?
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
String matchedFile = null;
view.setFontSize(av.font.getSize());
view.setFontStyle(av.font.getStyle());
view.setRenderGaps(av.renderGaps);
- view.setShowAnnotation(av.getShowAnnotation());
+ view.setShowAnnotation(av.isShowAnnotation());
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
view.setRightAlignIds(av.isRightAlignIds());
- view.setShowSequenceFeatures(av.showSequenceFeatures);
+ view.setShowSequenceFeatures(av.isShowSequenceFeatures());
view.setShowText(av.getShowText());
view.setShowUnconserved(av.getShowUnconserved());
view.setWrapAlignment(av.getWrapAlignment());
{
jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder;
+ String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getRenderOrder().toArray(new String[0]);
Vector settingsAdded = new Vector();
Object gstyle = null;
.getColour(renderOrder[ro]).getRGB());
}
- setting.setDisplay(av.getFeaturesDisplayed()
- .containsKey(renderOrder[ro]));
+ setting.setDisplay(av.getFeaturesDisplayed().isVisible(
+ renderOrder[ro]));
float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(renderOrder[ro]);
if (rorder > -1)
}
// Make sure we save none displayed feature settings
- Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureColours
- .keySet().iterator();
+ Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getFeatureColours().keySet().iterator();
while (en.hasNext())
{
String key = en.next().toString();
fs.addSetting(setting);
settingsAdded.addElement(key);
}
- en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups
- .keySet().iterator();
+ // is groups actually supposed to be a map here ?
+ en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().getFeatureGroups()
+ .iterator();
Vector groupsAdded = new Vector();
while (en.hasNext())
{
Group g = new Group();
g.setName(grp);
g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
- .getFeatureRenderer().featureGroups.get(grp))
+ .getFeatureRenderer().checkGroupVisibility(grp, false))
.booleanValue());
fs.addGroup(g);
groupsAdded.addElement(grp);
for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
.size(); c++)
{
- int[] region = (int[]) av.getColumnSelection()
- .getHiddenColumns().elementAt(c);
+ int[] region = av.getColumnSelection()
+ .getHiddenColumns().get(c);
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
hc.setEnd(region[1]);
an.addProperty(prop);
}
}
+
AnnotationElement ae;
if (aa[i].annotations != null)
{
protected void loadStructures(jarInputStreamProvider jprovider,
JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
{
- // run through all PDB ids on the alignment, and collect mappings between
- // jmol view ids and all sequences referring to it
- Map<String, ViewerData> jmolViewIds = new HashMap<String, ViewerData>();
+ /*
+ * Run through all PDB ids on the alignment, and collect mappings between
+ * distinct view ids and all sequences referring to that view.
+ */
+ Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
for (int i = 0; i < jseqs.length; i++)
{
sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ "," + height;
}
- if (!jmolViewIds.containsKey(sviewid))
+ if (!structureViewers.containsKey(sviewid))
{
- jmolViewIds.put(sviewid, new ViewerData(x, y, width, height,
+ structureViewers.put(sviewid, new StructureViewerModel(x, y, width, height,
false, false, true));
// Legacy pre-2.7 conversion JAL-823 :
// do not assume any view has to be linked for colour by
// file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
// seqs_file 2}, boolean[] {
// linkAlignPanel,superposeWithAlignpanel}} from hash
- ViewerData jmoldat = jmolViewIds.get(sviewid);
- jmoldat.alignWithPanel |= structureState
- .hasAlignwithAlignPanel() ? structureState.getAlignwithAlignPanel() : false;
- // never colour by linked panel if not specified
- jmoldat.colourWithAlignPanel |= structureState
- .hasColourwithAlignPanel() ? structureState.getColourwithAlignPanel()
- : false;
- // default for pre-2.7 projects is that Jmol colouring is enabled
- jmoldat.colourByViewer &= structureState
+ StructureViewerModel jmoldat = structureViewers.get(sviewid);
+ jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
+ | (structureState.hasAlignwithAlignPanel() ? structureState
+ .getAlignwithAlignPanel() : false));
+
+ /*
+ * Default colour by linked panel to false if not specified (e.g.
+ * for pre-2.7 projects)
+ */
+ boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
+ colourWithAlignPanel |= (structureState
+ .hasColourwithAlignPanel() ? structureState
+ .getColourwithAlignPanel() : false);
+ jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
+
+ /*
+ * Default colour by viewer to true if not specified (e.g. for
+ * pre-2.7 projects)
+ */
+ boolean colourByViewer = jmoldat.isColourByViewer();
+ colourByViewer &= structureState
.hasColourByJmol() ? structureState
.getColourByJmol() : true;
+ jmoldat.setColourByViewer(colourByViewer);
- if (jmoldat.stateData.length() < structureState.getContent()
- .length())
+ if (jmoldat.getStateData().length() < structureState
+ .getContent().length())
{
{
- jmoldat.stateData = structureState.getContent();
+ jmoldat.setStateData(structureState.getContent());
}
}
if (ids[p].getFile() != null)
{
File mapkey = new File(ids[p].getFile());
- Object[] seqstrmaps = jmoldat.fileData.get(mapkey);
+ StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
if (seqstrmaps == null)
{
- jmoldat.fileData.put(mapkey,
- seqstrmaps = new Object[]
- { pdbFile, ids[p].getId(), new Vector(),
- new Vector() });
+ jmoldat.getFileData().put(
+ mapkey,
+ seqstrmaps = jmoldat.new StructureData(pdbFile,
+ ids[p].getId()));
}
- if (!((Vector) seqstrmaps[2]).contains(seq))
+ if (!seqstrmaps.getSeqList().contains(seq))
{
- ((Vector) seqstrmaps[2]).addElement(seq);
- // ((Vector)seqstrmaps[3]).addElement(n) :
- // in principle, chains
- // should be stored here : do we need to
- // TODO: store and recover seq/pdb_id :
- // chain mappings
+ seqstrmaps.getSeqList().add(seq);
+ // TODO and chains?
}
}
else
}
}
}
+ // Instantiate the associated structure views
+ for (Entry<String, StructureViewerModel> entry : structureViewers.entrySet())
+ {
+ createOrLinkStructureViewer(entry, af, ap);
+ }
+ }
+
+ /**
+ *
+ * @param viewerData
+ * @param af
+ * @param ap
+ */
+ protected void createOrLinkStructureViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
+ AlignmentPanel ap)
+ {
+ final StructureViewerModel svattrib = viewerData.getValue();
+
+ /*
+ * Search for any viewer windows already open from other alignment views
+ * that exactly match the stored structure state
+ */
+ StructureViewerBase comp = findMatchingViewer(viewerData);
+
+ if (comp != null)
{
+ linkStructureViewer(ap, comp, svattrib);
+ return;
+ }
- // Instantiate the associated Jmol views
- for (Entry<String, ViewerData> entry : jmolViewIds.entrySet())
+ /*
+ * Pending an XML element for ViewerType, just check if stateData contains
+ * "chimera" (part of the chimera session filename).
+ */
+ if (svattrib.getStateData().indexOf("chimera") > -1)
+ {
+ createChimeraViewer(viewerData, af);
+ }
+ else
+ {
+ createJmolViewer(viewerData, af);
+ }
+ }
+
+ /**
+ * Create a new Chimera viewer.
+ *
+ * @param viewerData
+ * @param af
+ */
+ protected void createChimeraViewer(Entry<String, StructureViewerModel> viewerData,
+ AlignFrame af)
+ {
+ final StructureViewerModel data = viewerData.getValue();
+ String chimeraSession = data.getStateData();
+
+ if (new File(chimeraSession).exists())
+ {
+ Set<Entry<File, StructureData>> fileData = data.getFileData()
+ .entrySet();
+ List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
+ List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
+ for (Entry<File, StructureData> pdb : fileData)
{
- String sviewid = entry.getKey();
- ViewerData svattrib = entry.getValue();
- String state = svattrib.stateData;
- Map<File, Object[]> oldFiles = svattrib.fileData;
- final boolean useinJmolsuperpos = svattrib.alignWithPanel;
- final boolean usetoColourbyseq = svattrib.colourWithAlignPanel;
- final boolean jmolColouring = svattrib.colourByViewer;
- int x = svattrib.x;
- int y = svattrib.y;
- int width = svattrib.width;
- int height = svattrib.height;
- // collate the pdbfile -> sequence mappings from this view
- Vector<String> pdbfilenames = new Vector<String>();
- Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
- Vector<String> pdbids = new Vector<String>();
+ String filePath = pdb.getValue().getFilePath();
+ String pdbId = pdb.getValue().getPdbId();
+ pdbs.add(new PDBEntry(filePath, pdbId));
+ final List<SequenceI> seqList = pdb.getValue().getSeqList();
+ SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
+ allseqs.add(seqs);
+ }
- /*
- * Search for any Jmol windows already open from other alignment views
- * that exactly match the stored structure state
- */
- AppJmol comp = null;
- JInternalFrame[] frames = getAllFrames();
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof AppJmol)
- {
- /*
- * Post jalview 2.4 schema includes structure view id
- */
- if (sviewid != null
- && ((StructureViewerBase) frame).getViewId().equals(
- sviewid))
- {
- comp = (AppJmol) frame;
- }
- /*
- * Otherwise test for matching position and size of viewer frame
- */
- else if (frame.getX() == x && frame.getY() == y
- && frame.getHeight() == height
- && frame.getWidth() == width)
- {
- comp = (AppJmol) frame;
- }
- }
- }
+ boolean colourByChimera = data.isColourByViewer();
+ boolean colourBySequence = data.isColourWithAlignPanel();
- if (comp == null)
+ // TODO can/should this be done via StructureViewer (like Jmol)?
+ final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs
+ .size()]);
+ final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs.size()][]);
+ new ChimeraViewFrame(chimeraSession, af.alignPanel, pdbArray,
+ seqsArray,
+ colourByChimera, colourBySequence);
+ }
+ else
+ {
+ Cache.log.error("Chimera session file " + chimeraSession
+ + " not found");
+ }
+ }
+
+ /**
+ * Create a new Jmol window. First parse the Jmol state to translate filenames
+ * loaded into the view, and record the order in which files are shown in the
+ * Jmol view, so we can add the sequence mappings in same order.
+ *
+ * @param viewerData
+ * @param af
+ */
+ protected void createJmolViewer(
+ final Entry<String, StructureViewerModel> viewerData, AlignFrame af)
+ {
+ final StructureViewerModel svattrib = viewerData.getValue();
+ String state = svattrib.getStateData();
+ List<String> pdbfilenames = new ArrayList<String>();
+ List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
+ List<String> pdbids = new ArrayList<String>();
+ StringBuilder newFileLoc = new StringBuilder(64);
+ int cp = 0, ncp, ecp;
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ do
+ {
+ // look for next filename in load statement
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do
+ // filename
+ // translation differently.
+ StructureData filedat = oldFiles.get(new File(oldfilenam));
+ newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList()
+ .toArray(new SequenceI[0]));
+ newFileLoc.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
+ }
+ if (cp > 0)
+ {
+ // just append rest of state
+ newFileLoc.append(state.substring(cp));
+ }
+ else
+ {
+ System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
+ newFileLoc = new StringBuilder(state);
+ newFileLoc.append("; load append ");
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in
+ // the viewer
+ StructureData filedat = oldFiles.get(id);
+ newFileLoc.append(filedat.getFilePath());
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList()
+ .toArray(new SequenceI[0]));
+ newFileLoc.append(" \"");
+ newFileLoc.append(filedat.getFilePath());
+ newFileLoc.append("\"");
+
+ }
+ newFileLoc.append(";");
+ }
+
+ if (newFileLoc.length() > 0)
+ {
+ int histbug = newFileLoc.indexOf("history = ");
+ histbug += 10;
+ int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
+ String val = (diff == -1) ? null : newFileLoc
+ .substring(histbug, diff);
+ if (val != null && val.length() >= 4)
+ {
+ if (val.contains("e"))
{
- /*
- * Create a new Jmol window. First parse the Jmol state to translate
- * filenames loaded into the view, and record the order in which files
- * are shown in the Jmol view, so we can add the sequence mappings in
- * same order.
- */
- StringBuffer newFileLoc = null;
- int cp = 0, ncp, ecp;
- while ((ncp = state.indexOf("load ", cp)) > -1)
- {
- if (newFileLoc == null)
- {
- newFileLoc = new StringBuffer();
- }
- do
- {
- // look for next filename in load statement
- newFileLoc.append(state.substring(cp,
- ncp = (state.indexOf("\"", ncp + 1) + 1)));
- String oldfilenam = state.substring(ncp,
- ecp = state.indexOf("\"", ncp));
- // recover the new mapping data for this old filename
- // have to normalize filename - since Jmol and jalview do
- // filename
- // translation differently.
- Object[] filedat = oldFiles.get(new File(oldfilenam));
- newFileLoc.append(Platform
- .escapeString((String) filedat[0]));
- pdbfilenames.addElement((String) filedat[0]);
- pdbids.addElement((String) filedat[1]);
- seqmaps.addElement(((Vector<SequenceI>) filedat[2])
- .toArray(new SequenceI[0]));
- newFileLoc.append("\"");
- cp = ecp + 1; // advance beyond last \" and set cursor so we can
- // look for next file statement.
- } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
- }
- if (cp > 0)
+ if (val.trim().equals("true"))
{
- // just append rest of state
- newFileLoc.append(state.substring(cp));
+ val = "1";
}
else
{
- System.err
- .print("Ignoring incomplete Jmol state for PDB ids: ");
- newFileLoc = new StringBuffer(state);
- newFileLoc.append("; load append ");
- for (File id : oldFiles.keySet())
- {
- // add this and any other pdb files that should be present in
- // the viewer
- Object[] filedat = oldFiles.get(id);
- String nfilename;
- newFileLoc.append(((String) filedat[0]));
- pdbfilenames.addElement((String) filedat[0]);
- pdbids.addElement((String) filedat[1]);
- seqmaps.addElement(((Vector<SequenceI>) filedat[2])
- .toArray(new SequenceI[0]));
- newFileLoc.append(" \"");
- newFileLoc.append((String) filedat[0]);
- newFileLoc.append("\"");
-
- }
- newFileLoc.append(";");
+ val = "0";
}
+ newFileLoc.replace(histbug, diff, val);
+ }
+ }
- if (newFileLoc != null)
+ final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
+ .size()]);
+ final String[] id = pdbids.toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString();
+ final String sviewid = viewerData.getKey();
+ final AlignFrame alf = af;
+ final Rectangle rect = new Rectangle(svattrib.getX(),
+ svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
{
- int histbug = newFileLoc.indexOf("history = ");
- histbug += 10;
- int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
- histbug);
- String val = (diff == -1) ? null : newFileLoc.substring(
- histbug, diff);
- if (val != null && val.length() >= 4)
- {
- if (val.contains("e"))
- {
- if (val.trim().equals("true"))
- {
- val = "1";
- }
- else
- {
- val = "0";
- }
- newFileLoc.replace(histbug, diff, val);
- }
- }
- // TODO: assemble String[] { pdb files }, String[] { id for each
- // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
- // seqs_file 2}} from hash
- final String[] pdbf = pdbfilenames
- .toArray(new String[pdbfilenames.size()]), id = pdbids
- .toArray(new String[pdbids.size()]);
- final SequenceI[][] sq = seqmaps
- .toArray(new SequenceI[seqmaps.size()][]);
- final String fileloc = newFileLoc.toString(), vid = sviewid;
- final AlignFrame alf = af;
- final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
- width, height);
+ JalviewStructureDisplayI sview = null;
try
{
- javax.swing.SwingUtilities.invokeAndWait(new Runnable()
- {
- @Override
- public void run()
- {
- JalviewStructureDisplayI sview = null;
- try
- {
- // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera!
- sview = new StructureViewer(alf.alignPanel
- .getStructureSelectionManager()).createView(
- StructureViewer.ViewerType.JMOL, pdbf, id, sq,
- alf.alignPanel,
- useinJmolsuperpos, usetoColourbyseq,
- jmolColouring, fileloc, rect, vid);
- addNewStructureViewer(sview);
- } catch (OutOfMemoryError ex)
- {
- new OOMWarning("restoring structure view for PDB id "
- + id, (OutOfMemoryError) ex.getCause());
- if (sview != null && sview.isVisible())
- {
- sview.closeViewer();
- sview.setVisible(false);
- sview.dispose();
- }
- }
- }
- });
- } catch (InvocationTargetException ex)
+ // JAL-1333 note - we probably can't migrate Jmol views to UCSF
+ // Chimera!
+ sview = new StructureViewer(alf.alignPanel
+ .getStructureSelectionManager()).createView(
+ StructureViewer.ViewerType.JMOL, pdbf, id, sq,
+ alf.alignPanel, svattrib, fileloc, rect, sviewid);
+ addNewStructureViewer(sview);
+ } catch (OutOfMemoryError ex)
{
- warn("Unexpected error when opening Jmol view.", ex);
-
- } catch (InterruptedException e)
- {
- // e.printStackTrace();
+ new OOMWarning("restoring structure view for PDB id " + id,
+ (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
+ {
+ sview.closeViewer();
+ sview.setVisible(false);
+ sview.dispose();
+ }
}
}
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
+
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ }
+ }
+ /**
+ * Returns any open frame that matches given structure viewer data. The match
+ * is based on the unique viewId, or (for older project versions) the frame's
+ * geometry.
+ *
+ * @param viewerData
+ * @return
+ */
+ protected StructureViewerBase findMatchingViewer(
+ Entry<String, StructureViewerModel> viewerData)
+ {
+ final String sviewid = viewerData.getKey();
+ final StructureViewerModel svattrib = viewerData.getValue();
+ StructureViewerBase comp = null;
+ JInternalFrame[] frames = getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ /*
+ * Post jalview 2.4 schema includes structure view id
+ */
+ if (sviewid != null
+ && ((StructureViewerBase) frame).getViewId().equals(
+ sviewid))
+ {
+ comp = (AppJmol) frame;
+ // todo: break?
}
- else
- // if (comp != null)
+ /*
+ * Otherwise test for matching position and size of viewer frame
+ */
+ else if (frame.getX() == svattrib.getX()
+ && frame.getY() == svattrib.getY()
+ && frame.getHeight() == svattrib.getHeight()
+ && frame.getWidth() == svattrib.getWidth())
{
- linkStructureViewer(ap, comp, oldFiles, useinJmolsuperpos,
- usetoColourbyseq, jmolColouring);
+ comp = (AppJmol) frame;
+ // todo: break?
}
}
}
+ return comp;
}
/**
- * Link an AlignmentPanel to an existing JMol viewer.
+ * Link an AlignmentPanel to an existing structure viewer.
*
* @param ap
* @param viewer
* @param oldFiles
- * @param useinJmolsuperpos
+ * @param useinViewerSuperpos
* @param usetoColourbyseq
- * @param jmolColouring
+ * @param viewerColouring
*/
- protected void linkStructureViewer(AlignmentPanel ap, AppJmol viewer,
- Map<File, Object[]> oldFiles,
- final boolean useinJmolsuperpos, final boolean usetoColourbyseq,
- final boolean jmolColouring)
+ protected void linkStructureViewer(AlignmentPanel ap,
+ StructureViewerBase viewer, StructureViewerModel svattrib)
{
// NOTE: if the jalview project is part of a shared session then
// view synchronization should/could be done here.
- // add mapping for sequences in this view to an already open Jmol
- // instance
+ final boolean useinViewerSuperpos = svattrib.isAlignWithPanel();
+ final boolean usetoColourbyseq = svattrib.isColourWithAlignPanel();
+ final boolean viewerColouring = svattrib.isColourByViewer();
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
+
+ /*
+ * Add mapping for sequences in this view to an already open viewer
+ */
+ final AAStructureBindingModel binding = viewer.getBinding();
for (File id : oldFiles.keySet())
{
// add this and any other pdb files that should be present in the
// viewer
- Object[] filedat = oldFiles.get(id);
- String pdbFile = (String) filedat[0];
- SequenceI[] seq = ((Vector<SequenceI>) filedat[2])
- .toArray(new SequenceI[0]);
- viewer.jmb.getSsm().setMapping(seq, null, pdbFile,
+ StructureData filedat = oldFiles.get(id);
+ String pdbFile = filedat.getFilePath();
+ SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
+ binding.getSsm().setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
- viewer.jmb.addSequenceForStructFile(pdbFile, seq);
+ binding.addSequenceForStructFile(pdbFile, seq);
}
- // and add the AlignmentPanel's reference to the Jmol view
+ // and add the AlignmentPanel's reference to the view panel
viewer.addAlignmentPanel(ap);
- if (useinJmolsuperpos)
+ if (useinViewerSuperpos)
{
viewer.useAlignmentPanelForSuperposition(ap);
}
}
if (usetoColourbyseq)
{
- viewer.useAlignmentPanelForColourbyseq(ap, !jmolColouring);
+ viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
}
else
{
af.viewport.setColourAppliesToAllGroups(true);
- if (view.getShowSequenceFeatures())
- {
- af.viewport.showSequenceFeatures = true;
- }
+ af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
+
if (view.hasCentreColumnLabels())
{
af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
// recover featre settings
if (jms.getFeatureSettings() != null)
{
- af.viewport.setFeaturesDisplayed(new Hashtable());
+ FeaturesDisplayed fdi;
+ af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
+ Hashtable featureGroups = new Hashtable();
+ Hashtable featureColours = new Hashtable();
+ Hashtable featureOrder = new Hashtable();
+
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
gc.setColourByLabel(setting.getColourByLabel());
}
// and put in the feature colour table.
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
- setting.getType(), gc);
+ featureColours.put(setting.getType(), gc);
}
else
{
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
- setting.getType(),
+ featureColours.put(setting.getType(),
new java.awt.Color(setting.getColour()));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
{
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
- setting.getType(), setting.getOrder());
+ featureOrder.put(setting.getType(), setting.getOrder());
}
else
{
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
- setting.getType(),
- fs / jms.getFeatureSettings().getSettingCount());
+ featureOrder.put(setting.getType(), new Float(fs
+ / jms.getFeatureSettings().getSettingCount()));
}
if (setting.getDisplay())
{
- af.viewport.getFeaturesDisplayed().put(setting.getType(), new Integer(
- setting.getColour()));
+ fdi.setVisible(setting.getType());
}
}
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
- Hashtable fgtable;
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+ Hashtable fgtable = new Hashtable();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
}
+ // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+ // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
+ // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
+ FeatureRendererSettings frs = new FeatureRendererSettings(
+ renderOrder, fgtable, featureColours, 1.0f, featureOrder);
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(frs);
+
}
if (view.getHiddenColumnsCount() > 0)
{
skipList = skipList2;
}
-
}
git://source.jalview.org / jalview.git / blobdiff