X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=57273862f82f9bbd2e03e515f8cb45059e77992b;hb=7423fd27a25ace181a99c20b307d54b860d0fbc2;hp=831fd5a184461ba5dcab7a7602f01779cafde4f9;hpb=b32b824388dea3107cd1598d63f8759f00b75e1f;p=jalview.git diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java index 831fd5a..5727386 100644 --- a/src/jalview/gui/AppJmolBinding.java +++ b/src/jalview/gui/AppJmolBinding.java @@ -3,7 +3,7 @@ */ package jalview.gui; -import java.util.Vector; +import java.util.BitSet; import jalview.bin.Cache; import jalview.datamodel.PDBEntry; @@ -11,7 +11,7 @@ import jalview.datamodel.SequenceI; import org.jmol.popup.JmolPopup; -class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding +public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding { /** @@ -20,12 +20,14 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding private AppJmol appJmolWindow; public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry, - SequenceI[] seq, String[] chains, String protocol) + SequenceI[][] sequenceIs, String[][] chains, String protocol) { - super(pdbentry, seq, chains, protocol); + super(pdbentry, sequenceIs, chains, protocol); appJmolWindow = appJmol; } - FeatureRenderer fr=null; + + FeatureRenderer fr = null; + @Override public jalview.api.FeatureRenderer getFeatureRenderer() { @@ -37,7 +39,7 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding } fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas - .getFeatureRenderer()); + .getFeatureRenderer()); } return fr; @@ -59,10 +61,9 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding public void sendConsoleMessage(String strStatus) { - if (appJmolWindow.scriptWindow!=null && strStatus != null - ) - // && !strStatus.equals("Script completed")) - // should we squash the script completed string ? + if (appJmolWindow.scriptWindow != null && strStatus != null) + // && !strStatus.equals("Script completed")) + // should we squash the script completed string ? { appJmolWindow.scriptWindow.sendConsoleMessage(strStatus); } @@ -71,39 +72,46 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding @Override public void showUrl(String url, String target) { - try { + try + { jalview.util.BrowserLauncher.openURL(url); - } catch (Exception e) { + } catch (Exception e) + { Cache.log.error("Failed to launch Jmol-associated url " + url, e); // TODO: 2.6 : warn user if browser was not configured. } } @Override - public void updateUI() + public void refreshGUI() { // appJmolWindow.repaint(); - appJmolWindow.updateTitleAndMenus(); + javax.swing.SwingUtilities.invokeLater(new Runnable() { + public void run() { + appJmolWindow.updateTitleAndMenus(); + appJmolWindow.revalidate(); + }}); } public void updateColours(Object source) { AlignmentPanel ap = (AlignmentPanel) source; - if (appJmolWindow.ap.alignFrame.getCurrentView()!=ap.av) + if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av) return; - + colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); } public void notifyScriptTermination(String strStatus, int msWalltime) { if (appJmolWindow.scriptWindow != null) - appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, msWalltime); + appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, + msWalltime); } public void showUrl(String url) { - showUrl(url,"jmol"); + showUrl(url, "jmol"); } public void newJmolPopup(boolean translateLocale, String menuName, @@ -113,18 +121,37 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName, asPopup); } - public synchronized void addSequence(SequenceI[] seq) + + public void selectionChanged(BitSet arg0) { - Vector v = new Vector(); - for (int i = 0; i < sequence.length; i++) - v.addElement(sequence[i]); + // TODO Auto-generated method stub - for (int i = 0; i < seq.length; i++) - if (!v.contains(seq[i])) - v.addElement(seq[i]); + } + + public void refreshPdbEntries() + { + // TODO Auto-generated method stub - SequenceI[] tmp = new SequenceI[v.size()]; - v.copyInto(tmp); - sequence = tmp; } + + + /** + * add the given sequences to the mapping scope for the given pdb file handle + * + * @param pdbFile + * - pdbFile identifier + * @param seq + * - set of sequences it can be mapped to + */ + public void addSequenceForStructFile(String pdbFile, SequenceI[] seq) + { + for (int pe = 0; pe < pdbentry.length; pe++) + { + if (pdbentry[pe].getFile().equals(pdbFile)) + { + addSequence(pe, seq); + } + } + } + } \ No newline at end of file