X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=bfbc969705ac06ca93a534ae3030eb5e63201b04;hb=68ba1a55efa08e12e4381bb0e5bdcb70318e1dd5;hp=d1f3421def3f84a161e03ee273eb7ea9df9b7524;hpb=10bdbbde9cd0307e3d4c2b39c47062b59b305155;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index d1f3421..bfbc969 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -74,6 +74,7 @@ import jalview.io.JalviewFileView; import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; import jalview.io.TCoffeeScoreFile; +import jalview.io.gff.SequenceOntologyI; import jalview.jbgui.GAlignFrame; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -112,13 +113,14 @@ import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.StringSelection; import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.KeyAdapter; @@ -466,6 +468,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { formatMenu.add(vsel); } + addFocusListener(new FocusAdapter() + { + @Override + public void focusGained(FocusEvent e) + { + Jalview.setCurrentAlignFrame(AlignFrame.this); + } + }); } @@ -911,10 +921,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); showProducts.setEnabled(canShowProducts()); + setGroovyEnabled(Desktop.getGroovyConsole() != null); updateEditMenuBar(); } + /** + * Set the enabled state of the 'Run Groovy' option in the Calculate menu + * + * @param b + */ + public void setGroovyEnabled(boolean b) + { + runGroovy.setEnabled(b); + } + private IProgressIndicator progressBar; /* @@ -1276,13 +1297,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentI alignmentToExport = null; AlignExportSettingI settings = exportSettings; String[] omitHidden = null; - int[] alignmentStartEnd = new int[2]; HiddenSequences hiddenSeqs = viewport.getAlignment() .getHiddenSequences(); alignmentToExport = viewport.getAlignment(); - alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 }; boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; if (settings == null) @@ -1294,9 +1313,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) { - omitHidden = viewport.getViewAsString(false); + omitHidden = viewport.getViewAsString(false, + settings.isExportHiddenSequences()); } + int[] alignmentStartEnd = new int[2]; if (hasHiddenSeqs && settings.isExportHiddenSequences()) { alignmentToExport = hiddenSeqs.getFullAlignment(); @@ -1304,64 +1325,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { alignmentToExport = viewport.getAlignment(); - alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport - .getColumnSelection().getHiddenColumns()); } + alignmentStartEnd = alignmentToExport + .getVisibleStartAndEndIndex(viewport.getColumnSelection() + .getHiddenColumns()); AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); return ed; } - public static int[] getStartEnd(int[] aligmentStartEnd, - List hiddenCols) - { - int startPos = aligmentStartEnd[0]; - int endPos = aligmentStartEnd[1]; - - int[] lowestRange = new int[] { -1, -1 }; - int[] higestRange = new int[] { -1, -1 }; - - for (int[] hiddenCol : hiddenCols) - { - lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; - higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; - } - - if (lowestRange[0] == -1 && lowestRange[1] == -1) - { - startPos = aligmentStartEnd[0]; - } - else - { - startPos = lowestRange[1] + 1; - } - - if (higestRange[0] == -1 && higestRange[1] == -1) - { - endPos = aligmentStartEnd[1]; - } - else - { - endPos = higestRange[0] - 1; - } - - // System.out.println("Export range : " + startPos + " - " + endPos); - return new int[] { startPos, endPos }; - } - - public static void main(String[] args) - { - ArrayList hiddenCols = new ArrayList(); - hiddenCols.add(new int[] { 0, 0 }); - hiddenCols.add(new int[] { 6, 9 }); - hiddenCols.add(new int[] { 11, 12 }); - hiddenCols.add(new int[] { 33, 33 }); - hiddenCols.add(new int[] { 50, 50 }); - - int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols); - // System.out.println("Export range : " + x[0] + " - " + x[1]); - } - /** * DOCUMENT ME! * @@ -3667,8 +3639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void mousePressed(MouseEvent evt) { - if (evt.isControlDown() - || SwingUtilities.isRightMouseButton(evt)) + if (evt.isPopupTrigger()) { radioItem.removeActionListener(radioItem.getActionListeners()[0]); @@ -4172,7 +4143,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { JMenuItem tm = new JMenuItem(); ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); - if (sm.isProtein() == !viewport.getAlignment().isNucleotide()) + if (sm.isDNA() == viewport.getAlignment().isNucleotide() + || sm.isProtein() == !viewport.getAlignment() + .isNucleotide()) { String smn = MessageManager.getStringOrReturn( "label.score_model_", sm.getName()); @@ -4707,6 +4680,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return showp; } + /** + * Finds and displays cross-references for the selected sequences (protein + * products for nucleotide sequences, dna coding sequences for peptides). + * + * @param sel + * the sequences to show cross-references for + * @param dna + * true if from a nucleotide alignment (so showing proteins) + * @param source + * the database to show cross-references for + */ protected void showProductsFor(final SequenceI[] sel, final boolean dna, final String source) { @@ -4739,6 +4723,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); + if (Cache.getDefault("HIDE_INTRONS", true)) + { + newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false); + } String newtitle = String.format("%s %s %s", MessageManager.getString(dna ? "label.proteins" : "label.nucleotides"), MessageManager @@ -4773,7 +4761,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, System.err.println("Failed to make CDS alignment"); } al.getCodonFrames().clear(); - al.getCodonFrames().addAll(copyAlignment.getCodonFrames()); + al.addCodonFrames(copyAlignment.getCodonFrames()); + al.addCodonFrames(cf); /* * pending getting Embl transcripts to 'align', @@ -4791,7 +4780,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { copyAlignment = AlignmentUtils.makeCopyAlignment( sequenceSelection, xrefs.getSequencesArray()); - copyAlignment.getCodonFrames().addAll(cf); + copyAlignment.addCodonFrames(cf); + al.addCodonFrames(copyAlignment.getCodonFrames()); + al.addCodonFrames(cf); } copyAlignment.setGapCharacter(AlignFrame.this.viewport .getGapCharacter()); @@ -4866,15 +4857,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception e) { - Cache.log.error( - "Exception when finding crossreferences", e); + Cache.log.error("Exception when finding crossreferences", e); } catch (OutOfMemoryError e) { new OOMWarning("whilst fetching crossreferences", e); } catch (Throwable e) { - Cache.log.error("Error when finding crossreferences", - e); + Cache.log.error("Error when finding crossreferences", e); } finally { AlignFrame.this.setProgressBar(MessageManager.formatMessage( @@ -4952,7 +4941,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getString("label.error_when_translating_sequences_submit_bug_report"); final String errorTitle = MessageManager .getString("label.implementation_error") - + MessageManager.getString("translation_failed"); + + MessageManager.getString("label.translation_failed"); JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, JOptionPane.ERROR_MESSAGE); return; @@ -5051,49 +5040,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void drop(DropTargetDropEvent evt) { Transferable t = evt.getTransferable(); - java.util.List files = null; + java.util.List files = new ArrayList(), protocols = new ArrayList(); try { - DataFlavor uriListFlavor = new DataFlavor( - "text/uri-list;class=java.lang.String"); - if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) - { - // Works on Windows and MacOSX - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - files = (java.util.List) t - .getTransferData(DataFlavor.javaFileListFlavor); - } - else if (t.isDataFlavorSupported(uriListFlavor)) - { - // This is used by Unix drag system - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - String data = (String) t.getTransferData(uriListFlavor); - files = new java.util.ArrayList(1); - for (java.util.StringTokenizer st = new java.util.StringTokenizer( - data, "\r\n"); st.hasMoreTokens();) - { - String s = st.nextToken(); - if (s.startsWith("#")) - { - // the line is a comment (as per the RFC 2483) - continue; - } - - java.net.URI uri = new java.net.URI(s); - // check to see if we can handle this kind of URI - if (uri.getScheme().toLowerCase().startsWith("http")) - { - files.add(uri.toString()); - } - else - { - // otherwise preserve old behaviour: catch all for file objects - java.io.File file = new java.io.File(uri); - files.add(file.toString()); - } - } - } + Desktop.transferFromDropTarget(files, protocols, evt, t); } catch (Exception e) { e.printStackTrace(); @@ -5419,7 +5370,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void tabbedPane_mousePressed(MouseEvent e) { - if (SwingUtilities.isRightMouseButton(e)) + if (e.isPopupTrigger()) { String msg = MessageManager.getString("label.enter_view_name"); String reply = JOptionPane.showInternalInputDialog(this, msg, msg, @@ -5568,8 +5519,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame.this.setMenusForViewport(); } }); - dbRefFetcher - .fetchDBRefs(false); + dbRefFetcher.fetchDBRefs(false); } }).start(); @@ -6127,15 +6077,75 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, try { Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); - al = dna.reverseCdna(complement); viewport.addAlignment(al, ""); + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), + Action.PASTE, al.getSequencesArray(), 0, al.getWidth(), + viewport.getAlignment())); } catch (Exception ex) { System.err.println(ex.getMessage()); return; } } + + /** + * Try to run a script in the Groovy console, having first ensured that this + * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to + * be targeted at this alignment. + */ + @Override + protected void runGroovy_actionPerformed() + { + Jalview.setCurrentAlignFrame(this); + groovy.ui.Console console = Desktop.getGroovyConsole(); + if (console != null) + { + try + { + console.runScript(); + } catch (Exception ex) + { + System.err.println((ex.toString())); + JOptionPane + .showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("label.couldnt_run_groovy_script"), + MessageManager + .getString("label.groovy_support_failed"), + JOptionPane.ERROR_MESSAGE); + } + } + else + { + System.err.println("Can't run Groovy script as console not found"); + } + } + + /** + * Hides columns containing (or not containing) a specified feature, provided + * that would not leave all columns hidden + * + * @param featureType + * @param columnsContaining + * @return + */ + public boolean hideFeatureColumns(String featureType, + boolean columnsContaining) + { + boolean notForHiding = avc.markColumnsContainingFeatures( + columnsContaining, false, false, featureType); + if (notForHiding) + { + if (avc.markColumnsContainingFeatures(!columnsContaining, false, + false, featureType)) + { + getViewport().hideSelectedColumns(); + return true; + } + } + return false; + } } class PrintThread extends Thread