X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=58650cbc3768d7d7545c8b615cb820b3c7c6befc;hb=27f51f19a31e2d2cb3543ae858b248c91c1e9428;hp=c9819a235b5eb4188df68fe7308e901452ca77ed;hpb=5d972bc514ac9c78173432433b0404fda9730a75;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index c9819a2..58650cb 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -28,6 +28,7 @@ import java.awt.dnd.*; import java.awt.event.*; import java.awt.print.*; import javax.swing.*; +import javax.swing.event.MenuEvent; import jalview.analysis.*; import jalview.commands.*; @@ -141,7 +142,7 @@ public class AlignFrame } setMenusFromViewport(viewport); - + buildSortByAnnotationScoresMenu(); if (viewport.wrapAlignment) { wrapMenuItem_actionPerformed(null); @@ -911,7 +912,8 @@ public class AlignFrame new AnnotationExporter().exportAnnotations( alignPanel, viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null, - viewport.alignment.getGroups() + viewport.alignment.getGroups(), + ((Alignment)viewport.alignment).alignmentProperties ); } @@ -1309,7 +1311,7 @@ public class AlignFrame { return; } - + // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation) SequenceI [] seqs = viewport.getSelectionAsNewSequence(); String[] omitHidden = null; @@ -1473,6 +1475,7 @@ public class AlignFrame sequences = alignment.getSequencesArray(); } + int alwidth=0; if (newAlignment) { @@ -1487,12 +1490,14 @@ public class AlignFrame // new dataset is constructed alignment.setDataset(null); } + alwidth = alignment.getWidth()+1; } else { AlignmentI pastedal = alignment; // preserve pasted alignment object // Add pasted sequences and dataset into existing alignment. alignment = viewport.getAlignment(); + alwidth = alignment.getWidth()+1; // decide if we need to import sequences from an existing dataset boolean importDs = Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[1] != alignment.getDataset(); @@ -1544,7 +1549,9 @@ public class AlignFrame { annotationAdded=true; if (alann[i].sequenceRef==null && !alann[i].autoCalculated) { - alignment.addAnnotation(new AlignmentAnnotation(alann[i])); + AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); + newann.padAnnotation(alwidth); + alignment.addAnnotation(newann); } } } @@ -1571,6 +1578,7 @@ public class AlignFrame { annotationAdded=true; sequences[i].getAnnotation()[a].adjustForAlignment(); + sequences[i].getAnnotation()[a].padAnnotation(alwidth); alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a); } @@ -1584,6 +1592,7 @@ public class AlignFrame if (annotationAdded) { alignPanel.annotationPanel.adjustPanelHeight(); + buildSortByAnnotationScoresMenu(); } viewport.firePropertyChange("alignment", null, alignment.getSequences()); } else { @@ -2260,6 +2269,65 @@ public class AlignFrame alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); } + public void alignmentProperties() + { + JEditorPane editPane = new JEditorPane("text/html",""); + editPane.setEditable(false); + StringBuffer contents = new StringBuffer(""); + + float avg = 0; + int min=Integer.MAX_VALUE, max=0; + for(int i=0; imax) + max = size; + if(sizeSequences: "+ viewport.alignment.getHeight()); + contents.append("
Minimum Sequence Length: "+min); + contents.append("
Maximum Sequence Length: "+max); + contents.append("
Average Length: "+(int)avg); + + if (((Alignment)viewport.alignment).getProperties() != null) + { + Hashtable props = ((Alignment)viewport.alignment).getProperties(); + Enumeration en = props.keys(); + contents.append("

"); + while(en.hasMoreElements()) + { + String key = en.nextElement().toString(); + StringBuffer val = new StringBuffer(); + String vals = props.get(key).toString(); + int pos=0, npos; + do { + npos = vals.indexOf("\n",pos); + if (npos==-1) + { + val.append(vals.substring(pos)); + } else { + val.append(vals.substring(pos, npos)); + val.append("
"); + } + pos = npos+1; + } while (npos!=-1); + contents.append(""); + } + contents.append("
"+key+""+val+"
"); + } + editPane.setText(contents.toString()+""); + JInternalFrame frame = new JInternalFrame(); + frame.getContentPane().add(new JScrollPane(editPane)); + + Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400); + } + + /** * DOCUMENT ME! * @@ -2766,7 +2834,6 @@ public class AlignFrame alignPanel.paintAlignment(true); } - /** * DOCUMENT ME! * @@ -2984,6 +3051,65 @@ public class AlignFrame } }); } + /** + * Add a new sort by annotation score menu item + * @param sort the menu to add the option to + * @param scoreLabel the label used to retrieve scores for each sequence on the alignment + */ + public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel) + { + final JMenuItem item = new JMenuItem(scoreLabel); + sort.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment()); + addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment)); + alignPanel.paintAlignment(true); + } + }); + } + /** + * last hash for alignment's annotation array - used to minimise cost of rebuild. + */ + protected int _annotationScoreVectorHash; + /** + * search the alignment and rebuild the sort by annotation score submenu + * the last alignment annotation vector hash is stored to minimize + * cost of rebuilding in subsequence calls. + * + */ + public void buildSortByAnnotationScoresMenu() + { + if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash) + { + sortByAnnotScore.removeAll(); + // almost certainly a quicker way to do this - but we keep it simple + Hashtable scoreSorts=new Hashtable(); + AlignmentAnnotation aann[]; + Enumeration sq = viewport.alignment.getSequences().elements(); + while (sq.hasMoreElements()) + { + aann = ((SequenceI) sq.nextElement()).getAnnotation(); + for (int i=0;aann!=null && i0); + scoreSorts.clear(); + } + } /** * Maintain the Order by->Displayed Tree menu. @@ -3313,7 +3439,7 @@ public class AlignFrame } wsmenu.add(secstrmenu); } - this.webService.removeAll(); + resetWebServiceMenu(); for (int i = 0, j = wsmenu.size(); i < j; i++) { webService.add( (JMenu) wsmenu.get(i)); @@ -3321,7 +3447,7 @@ public class AlignFrame } else { - this.webService.removeAll(); + resetWebServiceMenu(); this.webService.add(this.webServiceNoServices); } // TODO: add in rediscovery function @@ -3329,6 +3455,31 @@ public class AlignFrame // TODO: group services by location as well as function. } + + /** + * empty the web service menu and add any ad-hoc functions + * not dynamically discovered. + * + */ + private void resetWebServiceMenu() + { + webService.removeAll(); + // Temporary hack - DBRef Fetcher always top level ws entry. + JMenuItem rfetch = new JMenuItem("Fetch DB References"); + rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences"); + webService.add(rfetch); + rfetch.addActionListener(new ActionListener() { + + public void actionPerformed(ActionEvent e) + { + new jalview.io.DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame).fetchDBRefs(false); + } + + }); + } + /* public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. @@ -3350,13 +3501,12 @@ public class AlignFrame - public void showTranslation_actionPerformed(ActionEvent e) { /////////////////////////////// // Collect Data to be translated/transferred - SequenceI [] selection = viewport.getSelectionAsNewSequence(); + SequenceI [] selection = viewport.getSequenceSelection(); String [] seqstring = viewport.getViewAsString(true); AlignmentI al = null; try { @@ -3530,6 +3680,7 @@ public void drop(DropTargetDropEvent evt) { // (isAnnotation) alignPanel.adjustAnnotationHeight(); + buildSortByAnnotationScoresMenu(); } } @@ -3571,6 +3722,19 @@ public void drop(DropTargetDropEvent evt) { return viewport; } + + + /** + * Open the dialog for regex description parsing. + */ + protected void extractScores_actionPerformed(ActionEvent e) + { + ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment); + if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0) + { + buildSortByAnnotationScoresMenu(); + } + } } class PrintThread