X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=ff3285cad4c001f335cce178bb55fc752fb84847;hb=53b2ec17b88081e402f60deab2723750bc4867d1;hp=14c4022098d8119ce1bd38e79ad83561b465d148;hpb=0c83c631f7d7db0baad3335805c15dd40c0aed59;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 14c4022..ff3285c 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -22,7 +22,6 @@ package jalview.gui; import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; @@ -30,13 +29,13 @@ import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; import jalview.api.ViewStyleI; import jalview.bin.Cache; +import jalview.bin.Instance; import jalview.commands.CommandI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; -import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; @@ -58,11 +57,9 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Rectangle; -import java.util.ArrayList; import java.util.Hashtable; import java.util.Iterator; import java.util.List; -import java.util.Vector; import javax.swing.JInternalFrame; @@ -83,7 +80,7 @@ public class AlignViewport extends AlignmentViewport private Rectangle explodedGeometry; - String viewName; + private String viewName; /* * Flag set true on the view that should 'gather' multiple views of the same @@ -294,7 +291,7 @@ public class AlignViewport extends AlignmentViewport ResidueColourScheme.NONE); } ColourSchemeI colourScheme = ColourSchemeProperty - .getColourScheme(alignment, schemeName); + .getColourScheme(this, alignment, schemeName); residueShading = new ResidueShader(colourScheme); if (colourScheme instanceof UserColourScheme) @@ -308,6 +305,7 @@ public class AlignViewport extends AlignmentViewport { residueShading.setConsensus(hconsensus); } + setColourAppliesToAllGroups(true); } boolean validCharWidth; @@ -387,7 +385,7 @@ public class AlignViewport extends AlignmentViewport if (align != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Instance.getDesktop()); ssm.registerMappings(align.getCodonFrames()); } @@ -409,7 +407,7 @@ public class AlignViewport extends AlignmentViewport if (mappings != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Instance.getDesktop()); for (AlignedCodonFrame acf : mappings) { if (noReferencesTo(acf)) @@ -467,7 +465,8 @@ public class AlignViewport extends AlignmentViewport { end = alignment.getWidth(); } - return (alignment.getHiddenColumns().getVisContigsIterator(start, end)); + return (alignment.getHiddenColumns().getVisContigsIterator(start, end, + false)); } /** @@ -534,7 +533,7 @@ public class AlignViewport extends AlignmentViewport public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + .getStructureSelectionManager(Instance.getDesktop()) .sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), new HiddenColumns(getAlignment().getHiddenColumns()), @@ -580,59 +579,7 @@ public class AlignViewport extends AlignmentViewport public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - } - - /** - * - * @param pdbEntries - * @return an array of SequenceI arrays, one for each PDBEntry, listing which - * sequences in the alignment hold a reference to it - */ - public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) - { - List seqvectors = new ArrayList<>(); - for (PDBEntry pdb : pdbEntries) - { - List choosenSeqs = new ArrayList<>(); - for (SequenceI sq : alignment.getSequences()) - { - Vector pdbRefEntries = sq.getDatasetSequence() - .getAllPDBEntries(); - if (pdbRefEntries == null) - { - continue; - } - for (PDBEntry pdbRefEntry : pdbRefEntries) - { - if (pdbRefEntry.getId().equals(pdb.getId())) - { - if (pdbRefEntry.getChainCode() != null - && pdb.getChainCode() != null) - { - if (pdbRefEntry.getChainCode().equalsIgnoreCase( - pdb.getChainCode()) && !choosenSeqs.contains(sq)) - { - choosenSeqs.add(sq); - continue; - } - } - else - { - if (!choosenSeqs.contains(sq)) - { - choosenSeqs.add(sq); - continue; - } - } - - } - } - } - seqvectors - .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()])); - } - return seqvectors.toArray(new SequenceI[seqvectors.size()][]); + .getStructureSelectionManager(Instance.getDesktop()); } @Override @@ -762,16 +709,20 @@ public class AlignViewport extends AlignmentViewport { if (AlignmentUtils.isMappable(toAdd, getAlignment())) { - if (openLinkedAlignment(toAdd, title)) - { - return; - } + openLinkedAlignment(toAdd, title); + return; } } + addDataToAlignment(toAdd); + } - /* - * No mappings, or offer declined - add sequences to this alignment - */ + /** + * adds sequences to this alignment + * + * @param toAdd + */ + void addDataToAlignment(AlignmentI toAdd) + { // TODO: JAL-407 regardless of above - identical sequences (based on ID and // provenance) should share the same dataset sequence @@ -793,7 +744,7 @@ public class AlignViewport extends AlignmentViewport } } - ranges.setEndSeq(getAlignment().getHeight()); + ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 firePropertyChange("alignment", null, getAlignment().getSequences()); } @@ -806,30 +757,58 @@ public class AlignViewport extends AlignmentViewport * @param al * @param title */ - protected boolean openLinkedAlignment(AlignmentI al, String title) + protected void openLinkedAlignment(AlignmentI al, String title) { String[] options = new String[] { MessageManager.getString("action.no"), MessageManager.getString("label.split_window"), MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.open_split_window?")); - int response = JvOptionPane.showOptionDialog(Desktop.desktop, question, + final AlignViewport us = this; + + /* + * options No, Split Window, New Window correspond to + * dialog responses 0, 1, 2 (even though JOptionPane shows them + * in reverse order) + */ + JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane()) + .setResponseHandler(0, new Runnable() + { + @Override + public void run() + { + addDataToAlignment(al); + } + }).setResponseHandler(1, new Runnable() + { + @Override + public void run() + { + us.openLinkedAlignmentAs(al, title, true); + } + }).setResponseHandler(2, new Runnable() + { + @Override + public void run() + { + us.openLinkedAlignmentAs(al, title, false); + } + }); + dialog.showDialog(question, MessageManager.getString("label.open_split_window"), JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); + } - if (response != 1 && response != 2) + protected void openLinkedAlignmentAs(AlignmentI al, String title, + boolean newWindowOrSplitPane) { - return false; - } - final boolean openSplitPane = (response == 1); - final boolean openInNewWindow = (response == 2); - /* * Identify protein and dna alignments. Make a copy of this one if opening * in a new split pane. */ - AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment()) + AlignmentI thisAlignment = newWindowOrSplitPane + ? new Alignment(getAlignment()) : getAlignment(); AlignmentI protein = al.isNucleotide() ? thisAlignment : al; final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; @@ -850,7 +829,7 @@ public class AlignViewport extends AlignmentViewport AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); newAlignFrame.setTitle(title); - newAlignFrame.statusBar.setText(MessageManager + newAlignFrame.setStatus(MessageManager .formatMessage("label.successfully_loaded_file", new Object[] { title })); @@ -861,7 +840,7 @@ public class AlignViewport extends AlignmentViewport // alignFrame.setFileName(file, format); // } - if (openInNewWindow) + if (!newWindowOrSplitPane) { Desktop.addInternalFrame(newAlignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -875,13 +854,11 @@ public class AlignViewport extends AlignmentViewport { } - if (openSplitPane) + if (newWindowOrSplitPane) { al.alignAs(thisAlignment); protein = openSplitFrame(newAlignFrame, thisAlignment); } - - return true; } /** @@ -1087,4 +1064,14 @@ public class AlignViewport extends AlignmentViewport } fr.setTransparency(featureSettings.getTransparency()); } + + public String getViewName() + { + return viewName; + } + + public void setViewName(String viewName) + { + this.viewName = viewName; + } }