X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=1ebf58456e8af16b30b4ea971e7e4e4e2590596f;hb=ad16d6cce49a40ea1943431b980b85a6212bb9bf;hp=c22a37dca5ee02a31678e681488f9508ac9fa23f;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index c22a37d..1ebf584 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; @@ -36,7 +35,6 @@ 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; @@ -58,10 +56,9 @@ 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; @@ -76,15 +73,13 @@ public class AlignViewport extends AlignmentViewport { Font font; - TreeModel currentTree = null; - boolean cursorMode = false; boolean antiAlias = false; private Rectangle explodedGeometry; - String viewName; + private String viewName; /* * Flag set true on the view that should 'gather' multiple views of the same @@ -295,7 +290,7 @@ 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) @@ -309,6 +304,7 @@ public class AlignViewport extends AlignmentViewport { residueShading.setConsensus(hconsensus); } + setColourAppliesToAllGroups(true); } boolean validCharWidth; @@ -387,9 +383,8 @@ public class AlignViewport extends AlignmentViewport */ if (align != null) { - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - ssm.registerMappings(align.getCodonFrames()); + Desktop.getInstance().getStructureSelectionManager() + .registerMappings(align.getCodonFrames()); } /* @@ -409,8 +404,8 @@ public class AlignViewport extends AlignmentViewport List mappings = al.getCodonFrames(); if (mappings != null) { - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + StructureSelectionManager ssm = Desktop.getInstance() + .getStructureSelectionManager(); for (AlignedCodonFrame acf : mappings) { if (noReferencesTo(acf)) @@ -448,27 +443,6 @@ public class AlignViewport extends AlignmentViewport } /** - * DOCUMENT ME! - * - * @param tree - * DOCUMENT ME! - */ - public void setCurrentTree(TreeModel tree) - { - currentTree = tree; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public TreeModel getCurrentTree() - { - return currentTree; - } - - /** * returns the visible column regions of the alignment * * @param selectedRegionOnly @@ -476,10 +450,10 @@ public class AlignViewport extends AlignmentViewport * area * @return */ - public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) + public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) { - int[] viscontigs = null; - int start = 0, end = 0; + int start = 0; + int end = 0; if (selectedRegionOnly && selectionGroup != null) { start = selectionGroup.getStartRes(); @@ -489,8 +463,8 @@ public class AlignViewport extends AlignmentViewport { end = alignment.getWidth(); } - viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end); - return viscontigs; + return (alignment.getHiddenColumns().getVisContigsIterator(start, end, + false)); } /** @@ -556,12 +530,10 @@ public class AlignViewport extends AlignmentViewport @Override public void sendSelection() { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) - .sendSelection(new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), - new HiddenColumns(getAlignment().getHiddenColumns()), - this); + Desktop.getInstance().getStructureSelectionManager().sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), this); } /** @@ -602,60 +574,7 @@ public class AlignViewport extends AlignmentViewport @Override 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()][]); + return Desktop.getInstance().getStructureSelectionManager(); } @Override @@ -679,7 +598,7 @@ public class AlignViewport extends AlignmentViewport return validCharWidth; } - private Hashtable calcIdParams = new Hashtable(); + private Hashtable calcIdParams = new Hashtable<>(); public AutoCalcSetting getCalcIdSettingsFor(String calcId) { @@ -785,16 +704,20 @@ 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 @@ -816,7 +739,7 @@ public class AlignViewport extends AlignmentViewport } } - ranges.setEndSeq(getAlignment().getHeight()); + ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 firePropertyChange("alignment", null, getAlignment().getSequences()); } @@ -829,30 +752,58 @@ 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; @@ -873,7 +824,7 @@ 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 })); @@ -884,7 +835,7 @@ public class AlignViewport extends AlignmentViewport // alignFrame.setFileName(file, format); // } - if (openInNewWindow) + if (!newWindowOrSplitPane) { Desktop.addInternalFrame(newAlignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -898,13 +849,11 @@ public class AlignViewport extends AlignmentViewport { } - if (openSplitPane) + if (newWindowOrSplitPane) { al.alignAs(thisAlignment); protein = openSplitFrame(newAlignFrame, thisAlignment); } - - return true; } /** @@ -1111,4 +1060,13 @@ public class AlignViewport extends AlignmentViewport fr.setTransparency(featureSettings.getTransparency()); } + public String getViewName() + { + return viewName; + } + + public void setViewName(String viewName) + { + this.viewName = viewName; + } }