X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=174772cadcc1dd7d204bd34bc55e41a210a11f1e;hb=f18077aa57dea5481ae537162871045f8557e2f0;hp=8565f9f3521a81bab6f7a50e84b3b7eb81da645d;hpb=e47b85d0760b8573bbaa08f431297f6c4412c101;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 8565f9f..174772c 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,8 +20,30 @@ */ package jalview.gui; +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.Arrays; +import java.util.Collections; +import java.util.Hashtable; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; + import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; @@ -58,29 +80,6 @@ import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; import jalview.util.UrlLink; -import java.awt.Color; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.Collections; -import java.util.Hashtable; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.TreeMap; -import java.util.Vector; - -import javax.swing.ButtonGroup; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JPopupMenu; -import javax.swing.JRadioButtonMenuItem; - /** * DOCUMENT ME! * @@ -198,13 +197,15 @@ public class PopupMenu extends JPopupMenu JMenu seqHideAnnotationsMenu = new JMenu(); - JMenuItem seqAddReferenceAnnotations = new JMenuItem(); + JMenuItem seqAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenu groupShowAnnotationsMenu = new JMenu(); JMenu groupHideAnnotationsMenu = new JMenu(); - JMenuItem groupAddReferenceAnnotations = new JMenuItem(); + JMenuItem groupAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenuItem sequenceFeature = new JMenuItem(); @@ -392,7 +393,7 @@ public class PopupMenu extends JPopupMenu final String structureLine = aa[i].label + " (alignment)"; menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_structure_line", new String[] + "label.2d_rna_structure_line", new Object[] { structureLine })); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -433,7 +434,7 @@ public class PopupMenu extends JPopupMenu // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_sequence_name", new String[] + "label.2d_rna_sequence_name", new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -469,7 +470,7 @@ public class PopupMenu extends JPopupMenu && ap.av.getSelectionGroup().getSize() > 1) { menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new String[] + "label.represent_group_with", new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -538,7 +539,7 @@ public class PopupMenu extends JPopupMenu if (sg != null && sg.getSize() > 0) { groupName.setText(MessageManager.formatMessage("label.name_param", - new String[] + new Object[] { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); @@ -642,13 +643,13 @@ public class PopupMenu extends JPopupMenu if (pdbe.size() == 1) { structureMenu.add(gpdbview = new JMenuItem(MessageManager - .formatMessage("label.view_structure_for", new String[] + .formatMessage("label.view_structure_for", new Object[] { sqass.getDisplayId(false) }))); } else { structureMenu.add(gpdbview = new JMenuItem(MessageManager - .formatMessage("label.view_all_structures", new String[] + .formatMessage("label.view_all_structures", new Object[] { new Integer(pdbe.size()).toString() }))); } gpdbview.setToolTipText(MessageManager @@ -668,7 +669,7 @@ public class PopupMenu extends JPopupMenu structureMenu.add(rpdbview = new JMenuItem(MessageManager .formatMessage( "label.view_all_representative_structures", - new String[] + new Object[] { new Integer(reppdb.size()).toString() }))); rpdbview.setToolTipText(MessageManager .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); @@ -946,7 +947,7 @@ public class PopupMenu extends JPopupMenu final boolean actionIsShow) { String label = types.toString(); // [a, b, c] - label = label.substring(1, label.length() - 1); + label = label.substring(1, label.length() - 1); // a, b, c final JMenuItem item = new JMenuItem(label); item.setToolTipText(calcId); item.addActionListener(new java.awt.event.ActionListener() @@ -954,41 +955,14 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - showHideAnnotation_actionPerformed(types, forSequences, allTypes, - actionIsShow); + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types, + forSequences, allTypes, actionIsShow); + refresh(); } }); showOrHideMenu.add(item); } - /** - * Action on selecting a list of annotation type (or the 'all types' values) - * to show or hide for the specified sequences. - * - * @param types - * @param forSequences - * @param anyType - * @param doShow - */ - protected void showHideAnnotation_actionPerformed( - Collection types, List forSequences, - boolean anyType, boolean doShow) - { - for (AlignmentAnnotation aa : ap.getAlignment() - .getAlignmentAnnotation()) - { - if (anyType || types.contains(aa.label)) - { - if ((aa.sequenceRef != null) - && forSequences.contains(aa.sequenceRef)) - { - aa.visible = doShow; - } - } - } - refresh(); - } - private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) { @@ -1157,7 +1131,7 @@ public class PopupMenu extends JPopupMenu { JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( - "label.open_url_param", new String[] + "label.open_url_param", new Object[] { url })); item.addActionListener(new java.awt.event.ActionListener() { @@ -1815,68 +1789,22 @@ public class PopupMenu extends JPopupMenu protected void configureReferenceAnnotationsMenu( JMenuItem menuItem, List forSequences) { - menuItem.setText(MessageManager - .getString("label.add_reference_annotations")); menuItem.setEnabled(false); - if (forSequences == null) - { - return; - } /* * Temporary store to hold distinct calcId / type pairs for the tooltip. * Using TreeMap means calcIds are shown in alphabetical order. */ Map tipEntries = new TreeMap(); - StringBuilder tooltip = new StringBuilder(64); - tooltip.append(MessageManager.getString("label.add_annotations_for")); - - /* - * For each sequence selected in the alignment, make a list of any - * annotations on the underlying dataset sequence which are not already on - * the alignment. - * - * Build a map of { alignmentSequence, } - */ - AlignmentI al = this.ap.av.getAlignment(); final Map> candidates = new LinkedHashMap>(); - for (SequenceI seq : forSequences) - { - SequenceI dataset = seq.getDatasetSequence(); - if (dataset == null) - { - continue; - } - AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); - if (datasetAnnotations == null) - { - continue; - } - final List result = new ArrayList(); - for (AlignmentAnnotation dsann : datasetAnnotations) - { - /* - * Find matching annotations on the alignment. - */ - final Iterable matchedAlignmentAnnotations = al - .findAnnotations(seq, dsann.getCalcId(), - dsann.label); - if (!matchedAlignmentAnnotations.iterator().hasNext()) - { - result.add(dsann); - tipEntries.put(dsann.getCalcId(), dsann.label); - } - } - /* - * Save any addable annotations for this sequence - */ - if (!result.isEmpty()) - { - candidates.put(seq, result); - } - } + AlignmentI al = this.ap.av.getAlignment(); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, + tipEntries, candidates, al); if (!candidates.isEmpty()) { + StringBuilder tooltip = new StringBuilder(64); + tooltip.append(MessageManager.getString("label.add_annotations_for")); + /* * Found annotations that could be added. Enable the menu item, and * configure its tooltip and action. @@ -1911,40 +1839,10 @@ public class PopupMenu extends JPopupMenu protected void addReferenceAnnotations_actionPerformed( Map> candidates) { - /* - * Add annotations at the top of the annotation, in the same order as their - * related sequences. - */ - for (SequenceI seq : candidates.keySet()) - { - for (AlignmentAnnotation ann : candidates.get(seq)) - { - AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); - int startRes = 0; - int endRes = ann.annotations.length; - final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); - if (selectionGroup != null) - { - startRes = selectionGroup.getStartRes(); - endRes = selectionGroup.getEndRes(); - } - copyAnn.restrict(startRes, endRes); - - /* - * Add to the sequence (sets copyAnn.datasetSequence), unless the - * original annotation is already on the sequence. - */ - if (!seq.hasAnnotation(ann)) - { - seq.addAlignmentAnnotation(copyAnn); - } - // adjust for gaps - copyAnn.adjustForAlignment(); - // add to the alignment and set visible - this.ap.getAlignment().addAnnotation(copyAnn); - copyAnn.visible = true; - } - } + final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); + final AlignmentI alignment = this.ap.getAlignment(); + AlignmentUtils.addReferenceAnnotations(candidates, alignment, + selectionGroup); refresh(); } @@ -2006,7 +1904,7 @@ public class PopupMenu extends JPopupMenu + MessageManager .formatMessage( "label.create_sequence_details_report_annotation_for", - new String[] + new Object[] { seq.getDisplayId(true) }) + "

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( @@ -2023,10 +1921,10 @@ public class PopupMenu extends JPopupMenu } cap.setText("" + contents.toString() + ""); - Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage( - "label.sequece_details_for", - (sequences.length == 1 ? new String[] - { sequences[0].getDisplayId(true) } : new String[] + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.sequence_details_for", + (sequences.length == 1 ? new Object[] + { sequences[0].getDisplayId(true) } : new Object[] { MessageManager.getString("label.selection") })), 500, 400); } @@ -2190,14 +2088,14 @@ public class PopupMenu extends JPopupMenu int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); } else // remove PIDColouring { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } refresh(); @@ -2548,15 +2446,7 @@ public class PopupMenu extends JPopupMenu } int gsize = sg.getSize(); - SequenceI[] hseqs; - - hseqs = new SequenceI[gsize]; - - int index = 0; - for (int i = 0; i < gsize; i++) - { - hseqs[index++] = sg.getSequenceAt(i); - } + SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]); ap.av.hideSequence(hseqs); // refresh(); TODO: ? needed ? @@ -2580,7 +2470,8 @@ public class PopupMenu extends JPopupMenu if (sg != null) { - int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), + List startEnd = ap.av.getVisibleRegionBoundaries( + sg.getStartRes(), sg.getEndRes() + 1); String description; @@ -2619,7 +2510,7 @@ public class PopupMenu extends JPopupMenu CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new String[] + "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2638,10 +2529,10 @@ public class PopupMenu extends JPopupMenu jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", new String[] + "label.select_pdb_file_for", new Object[] { sequence.getDisplayId(false) })); chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] + "label.load_pdb_file_associate_with_sequence", new Object[] { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null);