X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=81e55644b6b34e941aa0fc24f6970fd085d1dc30;hb=966e2e639242c252f4ed9e5f0e3e91b0389bd2de;hp=cfbd1863b34d8728153dcb1cf772e9e3376115af;hpb=0c3e6a10ea83dc9d3591e14b1e55bc98a33dede9;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index cfbd186..81e5564 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -34,6 +34,7 @@ import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.ws.*; +import javax.swing.event.AncestorEvent; /** * DOCUMENT ME! @@ -94,21 +95,24 @@ public class AlignFrame else if(sortby.equals("Pairwise Identity")) sortPairwiseMenuItem_actionPerformed(null); - tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel); + // remove(tabbedPane); + getContentPane().add(alignPanel, BorderLayout.CENTER); + + + + // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel); ///Dataset tab ///////////////////////// - if(al.getDataset()==null) { al.setDataset(null); } - - AlignViewport ds = new AlignViewport(al.getDataset(), true); - AlignmentPanel dap = new AlignmentPanel(this, ds); - tabbedPane.add("Dataset", dap); - viewports.add(ds); - alignPanels.add(dap); + // AlignViewport ds = new AlignViewport(al.getDataset(), true); + // AlignmentPanel dap = new AlignmentPanel(this, ds); + // tabbedPane.add("Dataset", dap); + // viewports.add(ds); + // alignPanels.add(dap); ///////////////////////// @@ -124,8 +128,11 @@ public class AlignFrame }); - if(Desktop.desktop!=null) + if (Desktop.desktop != null) + { addServiceListeners(); + setGUINucleotide(al.isNucleotide()); + } } /* Set up intrinsic listeners for dynamically generated GUI bits. */ @@ -162,6 +169,26 @@ public class AlignFrame } + public void setGUINucleotide(boolean nucleotide) + { + showTranslation.setVisible( nucleotide ); + sequenceFeatures.setVisible(!nucleotide ); + featureSettings.setVisible( !nucleotide ); + conservationMenuItem.setVisible( !nucleotide ); + modifyConservation.setVisible( !nucleotide ); + + //Deal with separators + //Remember AlignFrame always starts as protein + if(nucleotide) + { + viewMenu.remove(viewMenu.getItemCount()-2); + } + else + { + calculateMenu.remove(calculateMenu.getItemCount()-2); + } + } + /* Added so Castor Mapping file can obtain Jalview Version @@ -249,7 +276,6 @@ public class AlignFrame } viewport.showSequenceFeatures = true; - ((Alignment)viewport.alignment).featuresAdded = true; alignPanel.repaint(); @@ -384,7 +410,9 @@ public class AlignFrame */ protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(viewport); + new HTMLOutput(viewport, + alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) @@ -707,7 +735,6 @@ public class AlignFrame } FastaFile ff = new FastaFile(); - ff.addDBPrefix( viewport.showDBPrefix ); ff.addJVSuffix( viewport.showJVSuffix ); c.setContents(new StringSelection( ff.print(seqs)), this); Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()}; @@ -801,7 +828,10 @@ public class AlignFrame //!newAlignment for (int i = 0; i < sequences.length; i++) { - viewport.alignment.addSequence(sequences[i]); + Sequence newseq = new Sequence(sequences[i].getName(), + sequences[i].getSequence(), sequences[i].getStart(), + sequences[i].getEnd()); + viewport.alignment.addSequence(newseq); if(sequences[i].getDatasetSequence()==null) { //////////////////////////// @@ -811,10 +841,8 @@ public class AlignFrame AlignSeq.extractGaps("-. ", sequences[i].getSequence()), sequences[i].getStart(), sequences[i].getEnd()); - sequences[i].setDatasetSequence(ds); + newseq.setDatasetSequence(ds); viewport.alignment.getDataset().addSequence(ds); - - } } @@ -950,6 +978,7 @@ public class AlignFrame viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.annotationPanel.activeRes = null; PaintRefresher.Refresh(null, viewport.alignment); } @@ -1177,16 +1206,6 @@ public class AlignFrame if(alignPanel.overviewPanel!=null) alignPanel.overviewPanel.updateOverviewImage(); - Provenance prov = viewport.alignment.getProvenance(); - if(prov == null) - { - prov = new Provenance(); - viewport.alignment.setProvenance(prov); - } - - prov.addEntry("Me", - "Edited in Jalview", new java.util.Date(), "myID"); - alignPanel.repaint(); } @@ -1293,14 +1312,6 @@ public class AlignFrame alignPanel.repaint(); } - public void seqDBRef_actionPerformed(ActionEvent e) - { - viewport.setShowDBPrefix(seqDBRef.isSelected()); - - alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth()); - alignPanel.repaint(); - } - /** * DOCUMENT ME! @@ -1403,10 +1414,8 @@ public class AlignFrame { viewport.showSequenceFeatures(sequenceFeatures.isSelected()); - if (viewport.showSequenceFeatures && - ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded) + if (viewport.showSequenceFeatures) { - System.out.println("new fetcher"); new SequenceFeatureFetcher(viewport. alignment, alignPanel); @@ -1889,7 +1898,7 @@ public class AlignFrame { addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT)); - AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix); + AlignmentSorter.sortByID(viewport.getAlignment()); alignPanel.repaint(); } @@ -2199,7 +2208,16 @@ public class AlignFrame { SequenceI seq = null; SequenceI[] msa = null; +/* + if (predictindex==-1) { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "The alignment contains no columns or residues usable for prediction!", + "Invalid Alignment Selection", JOptionPane.WARNING_MESSAGE); + this. + return; + } +*/ if ( (viewport.getSelectionGroup() != null) && (viewport.getSelectionGroup().getSize() > 0)) { @@ -2430,7 +2448,18 @@ public class AlignFrame { public void actionPerformed(ActionEvent e) { - SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction(); + SequenceI[] msa = SeqsetUtils.getNonEmptySequenceSet(gatherSeqOrMsaForSecStrPrediction()); + if (msa==null) { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "There are no columns or residues usable for prediction!\n" + +"There must be valid residues in at least one\n" + +"of the sequences in the alignment,\n" + +"or in the currently selected region.", + "Invalid Input for Secondary Structure Prediction", + JOptionPane.WARNING_MESSAGE); + return; + } + if (msa.length == 1) { // Single Sequence prediction @@ -2440,7 +2469,7 @@ public class AlignFrame { if (msa.length > 1) { - // Single Sequence prediction + // Aligned Sequences prediction jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh, title, msa); } @@ -2467,7 +2496,7 @@ public class AlignFrame // TODO: group services by location as well as function. } - public void vamsasStore_actionPerformed(ActionEvent e) + /* public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. getProperty("LAST_DIRECTORY")); @@ -2484,7 +2513,7 @@ public class AlignFrame //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this); } - } + }*/ public void featureSettings_actionPerformed(ActionEvent e) { @@ -2495,29 +2524,20 @@ public class AlignFrame public void showTranslation_actionPerformed(ActionEvent e) { - - if(!viewport.alignment.isNucleotide()) - return; - - viewport.showTranslation(showTranslation.isSelected()); - - if(!viewport.alignment.isNucleotide()) - return; - int s, sSize = viewport.alignment.getHeight(); SequenceI [] newSeq = new SequenceI[sSize]; int res, resSize; StringBuffer protein; - SequenceI seq; + String seq; for(s=0; s