/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AlignmentUtils.MappingResult;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.OOMHandlerI;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.util.StringUtils;
import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.AlignCalcManager;
-import jalview.workers.ConsensusThread;
-import jalview.workers.ConservationThread;
-import jalview.workers.StrucConsensusThread;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.Deque;
+import java.util.Hashtable;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
+public class AlignViewport extends AlignmentViewport implements
+ SelectionSource, VamsasSource, AlignViewportI, CommandListener
{
- private static final int RIGHT_JUSTIFY = 1;
-
int startRes;
int endRes;
boolean showAnnotation = true;
+ SequenceAnnotationOrder sortAnnotationsBy = null;
+
int charHeight;
int charWidth;
boolean seqNameItalics;
-
NJTree currentTree = null;
boolean scaleAboveWrapped = false;
boolean gatherViewsHere = false;
- Stack historyList = new Stack();
+ private Deque<CommandI> historyList = new ArrayDeque<CommandI>();
- Stack redoList = new Stack();
-
- Hashtable sequenceColours;
+ private Deque<CommandI> redoList = new ArrayDeque<CommandI>();
int thresholdTextColour = 0;
{
if (!alignment.isNucleotide())
{
- showConservation=Cache.getDefault("SHOW_CONSERVATION", true);
- showQuality=Cache.getDefault("SHOW_QUALITY", true);
+ showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+ showQuality = Cache.getDefault("SHOW_QUALITY", true);
showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
false);
- }
+ }
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
- normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
+ normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+ false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- showConsensus=Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
+ showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
}
initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
}
}
- wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
- false);
- sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
- followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
- true);
+ wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
+ showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+ Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
}
/**
Desktop.instance).removeMappings(alignment.getCodonFrames());
}
this.alignment = align;
- if (alignment!=null && alignment.getCodonFrames() != null)
+ if (alignment != null && alignment.getCodonFrames() != null)
{
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).addMappings(alignment.getCodonFrames());
scaleRightWrapped = b;
}
-
public void setDataset(boolean b)
{
isDataset = b;
return isDataset;
}
-
-
public boolean getShowHiddenMarkers()
{
return showHiddenMarkers;
showHiddenMarkers = show;
}
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
- }
-
/**
* returns the visible column regions of the alignment
*
*/
public long[] getUndoRedoHash()
{
+ // TODO: JAL-1126
if (historyList == null || redoList == null)
+ {
return new long[]
{ -1, -1 };
+ }
return new long[]
{ historyList.hashCode(), this.redoList.hashCode() };
}
centreColumnLabels = centrecolumnlabels;
}
- public void updateSequenceIdColours()
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
- for (SequenceGroup sg:alignment.getGroups())
- {
- if (sg.idColour != null)
- {
- for (SequenceI s:sg.getSequences(getHiddenRepSequences()))
- {
- sequenceColours.put(s, sg.idColour);
- }
- }
- }
- }
-
/**
* enable or disable the display of Database Cross References in the sequence
* ID tooltip
boolean showSeqFeaturesHeight;
+ /**
+ * Send the current selection to be broadcast to any selection listeners.
+ */
public void sendSelection()
{
jalview.structure.StructureSelectionManager
{
AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
.getSequenceSetId());
- AlignmentPanel ap = null;
for (int p = 0; aps != null && p < aps.length; p++)
{
if (aps[p].av == this)
Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
.getPDBId();
if (pdbs == null)
+ {
continue;
+ }
SequenceI sq;
for (int p = 0; p < pdbs.size(); p++)
{
if (p1.getId().equals(pdb.getId()))
{
if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ {
seqs.add(sq);
+ }
continue;
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
-
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
normaliseSequenceLogo = state;
}
-
/**
*
- * @return true if alignment characters should be displayed
+ * @return true if alignment characters should be displayed
*/
public boolean isValidCharWidth()
{
return validCharWidth;
}
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+
+ private boolean showAutocalculatedAbove;
+
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
+ {
+ return calcIdParams.get(calcId);
+ }
+
+ public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+ boolean needsUpdate)
+ {
+ calcIdParams.put(calcId, settings);
+ // TODO: create a restart list to trigger any calculations that need to be
+ // restarted after load
+ // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+ if (needsUpdate)
+ {
+ Cache.log.debug("trigger update for " + calcId);
+ }
+ }
+
+ protected SequenceAnnotationOrder getSortAnnotationsBy()
+ {
+ return sortAnnotationsBy;
+ }
+
+ protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ {
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
+
+ protected boolean isShowAutocalculatedAbove()
+ {
+ return showAutocalculatedAbove;
+ }
+
+ protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
+ }
+
+ /**
+ * Method called when another alignment's edit (or possibly other) command is
+ * broadcast to here.
+ *
+ * To allow for sequence mappings (e.g. protein to cDNA), we have to first
+ * 'unwind' the command on the source sequences (in simulation, not in fact),
+ * and then for each edit in turn:
+ * <ul>
+ * <li>compute the equivalent edit on the mapped sequences</li>
+ * <li>apply the mapped edit</li>
+ * <li>'apply' the source edit to the working copy of the source sequences</li>
+ * </ul>
+ *
+ * @param command
+ * @param undo
+ * @param ssm
+ */
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
+ {
+ /*
+ * ...work in progress... do nothing unless we are a 'complement' of the
+ * source May replace this with direct calls not via SSM.
+ */
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
+ {
+ // ok to continue;
+ }
+ else
+ {
+ return;
+ }
+
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
+ {
+ AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
+ mappedCommand.doCommand(views);
+ getAlignPanel().alignmentChanged();
+ }
+ }
+
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ return this;
+ }
+
+ /**
+ * Add one command to the command history list.
+ *
+ * @param command
+ */
+ public void addToHistoryList(CommandI command)
+ {
+ if (this.historyList != null)
+ {
+ this.historyList.push(command);
+ broadcastCommand(command, false);
+ }
+ }
+
+ protected void broadcastCommand(CommandI command, boolean undo)
+ {
+ getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
+ }
+
+ /**
+ * Add one command to the command redo list.
+ *
+ * @param command
+ */
+ public void addToRedoList(CommandI command)
+ {
+ if (this.redoList != null)
+ {
+ this.redoList.push(command);
+ }
+ broadcastCommand(command, true);
+ }
+
+ /**
+ * Clear the command redo list.
+ */
+ public void clearRedoList()
+ {
+ if (this.redoList != null)
+ {
+ this.redoList.clear();
+ }
+ }
+
+ public void setHistoryList(Deque<CommandI> list)
+ {
+ this.historyList = list;
+ }
+
+ public Deque<CommandI> getHistoryList()
+ {
+ return this.historyList;
+ }
+
+ public void setRedoList(Deque<CommandI> list)
+ {
+ this.redoList = list;
+ }
+
+ public Deque<CommandI> getRedoList()
+ {
+ return this.redoList;
+ }
+
+ /**
+ * Add the sequences from the given alignment to this viewport. Optionally,
+ * may give the user the option to open a new frame, or split panel, with cDNA
+ * and protein linked.
+ *
+ * @param al
+ * @param title
+ */
+ public void addAlignment(AlignmentI al, String title)
+ {
+ // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
+
+ // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+ // this comment:
+ // TODO: create undo object for this JAL-1101
+
+ /*
+ * If one alignment is protein and one nucleotide, with at least one
+ * sequence name in common, offer to open a linked alignment.
+ */
+ if (getAlignment().isNucleotide() != al.isNucleotide())
+ {
+ final Set<String> sequenceNames = getAlignment().getSequenceNames();
+ sequenceNames.retainAll(al.getSequenceNames());
+ if (!sequenceNames.isEmpty()) // at least one sequence name in both
+ {
+ if (openLinkedAlignment(al, title))
+ {
+ return;
+ }
+ }
+ }
+
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ getAlignment().addSequence(al.getSequenceAt(i));
+ }
+ // TODO this call was done by SequenceFetcher but not FileLoader or
+ // CutAndPasteTransfer. Is it needed?
+ setEndSeq(getAlignment().getHeight());
+ firePropertyChange("alignment", null, getAlignment().getSequences());
+ }
+
+ /**
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment. Returns true if the new alignment was opened, false if not,
+ * because the user declined the offer.
+ *
+ * @param title
+ */
+ protected boolean 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_linked_alignment?"));
+ int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ MessageManager.getString("label.open_linked_alignment"),
+ JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+
+ if (response != 1 && response != 2)
+ {
+ return false;
+ }
+ final boolean openSplitPane = (response == 1);
+ final boolean openInNewWindow = (response == 2);
+
+ /*
+ * Create the AlignFrame first (which creates the new alignment's datasets),
+ * before attempting sequence mapping.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(title);
+
+ /*
+ * Identify protein and dna alignments. Make a copy of this one if opening
+ * in a new split pane.
+ */
+ AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ : getAlignment();
+ final AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new Object[]
+ { title }));
+
+ // TODO if we want this (e.g. to enable reload of the alignment from file),
+ // we will need to add parameters to the stack.
+ // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
+
+ if (openInNewWindow)
+ {
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /*
+ * Try to find mappings for at least one sequence.
+ */
+ MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna);
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (mapped == MappingResult.Mapped)
+ {
+
+ /*
+ * Register the mappings (held on the protein alignment) with the
+ * StructureSelectionManager (for mouseover linking).
+ */
+ ssm.addMappings(protein.getCodonFrames());
+ }
+ else
+ {
+
+ /*
+ * No mapping possible - warn the user, but leave window open.
+ */
+ final String msg = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.mapping_failed"));
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ MessageManager.getString("label.no_mappings"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ try
+ {
+ newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN",
+ false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+
+ if (openSplitPane)
+ {
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ AlignFrame copyMe = new AlignFrame(thisAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
+ : copyMe;
+
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String proteinShortName = StringUtils.getLastToken(
+ proteinFrame.getTitle(), "/");
+ String dnaShortName = StringUtils.getLastToken(cdnaFrame.getTitle(),
+ "/");
+ String linkedTitle = MessageManager.formatMessage(
+ "label.linked_view_title", dnaShortName, proteinShortName);
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ /*
+ * Set the frames to listen for each other's edit and sort commands.
+ */
+ ssm.addCommandListener(cdnaFrame.getViewport());
+ ssm.addCommandListener(proteinFrame.getViewport());
+
+ /*
+ * 'Coding complement' (dna/protein) views will mirror each others' edits,
+ * selections, sorting etc as decided from time to time by the relevant
+ * authorities.
+ */
+ proteinFrame.getViewport().setCodingComplement(cdnaFrame.getViewport());
+ }
+
+ return true;
+ }
}
git://source.jalview.org / jalview.git / blobdiff