-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import jalview.io.*;\r
-import jalview.analysis.NJTree;\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
-\r
-public class AlignViewport\r
-{\r
- int startRes;\r
- int endRes;\r
-\r
- int startSeq;\r
- int endSeq;\r
-\r
- boolean showScores=false;\r
- boolean showText=true;\r
- boolean showColourText=false;\r
- boolean showBoxes=true;\r
- boolean wrapAlignment=false;\r
- boolean renderGaps = false;\r
-\r
- boolean groupEdit = false;\r
-\r
- RendererI renderer = new SequenceRenderer();\r
-\r
- int charHeight;\r
- double charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
-\r
- Color backgroundColour;\r
-\r
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
-\r
- Selection sel = new Selection();\r
- ColumnSelection colSel = new ColumnSelection();\r
-\r
- OutputGenerator og;\r
-\r
- String visibleConsensus;\r
-\r
- int threshold;\r
- int increment;\r
-\r
- NJTree currentTree = null;\r
-\r
- int window = 50;\r
- int baseline = 30;\r
-\r
- Vector kmers;\r
-\r
- public AlignViewport(AlignmentI da,\r
- boolean showScores,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
- this(0,da.getWidth()-1,0,da.getHeight()-1,showScores,\r
- showText,\r
- showBoxes,\r
- wrapAlignment);\r
-\r
- setAlignment(da);\r
- }\r
-\r
- public AlignViewport(int startRes, int endRes,\r
- int startSeq, int endSeq,\r
- boolean showScores,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
-\r
- this.startRes = startRes;\r
- this.endRes = endRes;\r
- this.startSeq = startSeq;\r
- this.endSeq = endSeq;\r
-\r
- this.showScores = showScores;\r
- this.showText = showText;\r
- this.showBoxes = showBoxes;\r
- this.wrapAlignment = wrapAlignment;\r
-\r
- // og = new AlignmentOutputGenerator(this);\r
-\r
- setFont( font );\r
- }\r
-\r
- public AlignViewport(int startRes, int endRes,\r
- int startSeq, int endSeq,\r
- boolean showScores,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment,\r
- Color backgroundColour) {\r
- this(startRes,endRes,startSeq,endSeq,showScores,showText,showBoxes,wrapAlignment);\r
-\r
- this.backgroundColour = backgroundColour;\r
- }\r
-\r
-\r
- public String getVisibleConsensus()\r
- {\r
- return visibleConsensus;\r
- }\r
-\r
- Vector consensus = new Vector();\r
- public Vector getConsensus(boolean recalculate)\r
- {\r
- if(recalculate || consensus.size()<1)\r
- {\r
- consensus = alignment.getAAFrequency();\r
- StringBuffer sb = new StringBuffer();\r
- Hashtable hash = null;\r
- for (int i = 0; i < consensus.size(); i++)\r
- {\r
- hash = (Hashtable) consensus.elementAt(i);\r
- sb.append(hash.get("maxResidue").toString().charAt(0));\r
- }\r
- visibleConsensus = sb.toString();\r
- }\r
-\r
-\r
- return consensus;\r
- }\r
-\r
-\r
- public int getStartRes() {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes() {\r
- return endRes;\r
- }\r
-\r
- public int getStartSeq() {\r
- return startSeq;\r
- }\r
-\r
-\r
- public void setStartRes(int res) {\r
- this.startRes = res;\r
- }\r
- public void setStartSeq(int seq) {\r
- this.startSeq = seq;\r
- }\r
- public void setEndRes(int res) {\r
- if (res > alignment.getWidth()-1) {\r
- System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth() -1;\r
- }\r
- if (res < 0) {\r
- res = 0;\r
- }\r
- this.endRes = res;\r
- }\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
- seq = alignment.getHeight();\r
- }\r
- if (seq < 0) {\r
- seq = 0;\r
- }\r
- this.endSeq = seq;\r
- }\r
- public int getEndSeq() {\r
- return endSeq;\r
- }\r
-\r
- public void setFont(Font f) {\r
- font = f;\r
- javax.swing.JFrame temp = new javax.swing.JFrame();\r
- temp.addNotify();\r
- java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);\r
- setCharHeight(fm.getHeight());\r
- setCharWidth(fm.charWidth('M'));\r
- }\r
-\r
- public Font getFont() {\r
- return font;\r
- }\r
- public void setCharWidth(double w) {\r
- this.charWidth = w;\r
- }\r
- public double getCharWidth() {\r
- return charWidth;\r
- }\r
- public void setCharHeight(int h) {\r
- this.charHeight = h;\r
- }\r
- public int getCharHeight() {\r
- return charHeight;\r
- }\r
- public void setChunkWidth(int w) {\r
- this.chunkWidth = w;\r
- }\r
- public int getChunkWidth() {\r
- return chunkWidth;\r
- }\r
- public void setChunkHeight(int h) {\r
- this.chunkHeight = h;\r
- }\r
- public int getChunkHeight() {\r
- return chunkHeight;\r
- }\r
- public AlignmentI getAlignment() {\r
- return alignment;\r
- }\r
- public void setAlignment(AlignmentI align) {\r
- this.alignment = align;\r
- }\r
- public void setShowScores(boolean state) {\r
- showScores = state;\r
- }\r
- public void setWrapAlignment(boolean state) {\r
- wrapAlignment = state;\r
- }\r
- public void setShowText(boolean state) {\r
- showText = state;\r
- }\r
-\r
- public void setRenderGaps(boolean state){\r
- renderGaps = state;\r
- if(renderer instanceof SequenceRenderer)\r
- {\r
- SequenceRenderer sr = (SequenceRenderer)renderer;\r
- sr.renderGaps(state);\r
- }\r
- }\r
-\r
-\r
- public boolean getColourText()\r
- {\r
- return showColourText;\r
- }\r
-\r
- public void setColourText(boolean state)\r
- {\r
- showColourText = state;\r
- }\r
-\r
- public void setShowBoxes(boolean state) {\r
- showBoxes = state;\r
- }\r
- public boolean getShowScores() {\r
- return showScores;\r
- }\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
- }\r
- public boolean getShowText() {\r
- return showText;\r
- }\r
- public boolean getShowBoxes() {\r
- return showBoxes;\r
- }\r
- // public CommandParser getCommandLog() {\r
- /// return log;\r
- // }\r
- public boolean getGroupEdit() {\r
- return groupEdit;\r
- }\r
- public void setGroupEdit(boolean state) {\r
- groupEdit = state;\r
- }\r
- public char getGapCharacter() {\r
- return getAlignment().getGapCharacter();\r
- }\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
- getAlignment().setGapCharacter(gap);\r
- }\r
- }\r
- public void setThreshold(int thresh) {\r
- threshold = thresh;\r
- }\r
- public int getThreshold() {\r
- return threshold;\r
- }\r
- public void setIncrement(int inc) {\r
- increment = inc;\r
- }\r
- public int getIncrement() {\r
- return increment;\r
- }\r
- public int getIndex(int y) {\r
- int y1 = 0;\r
- int starty = getStartSeq();\r
- int endy = getEndSeq();\r
-\r
- for (int i = starty; i <= endy; i++) {\r
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {\r
- int y2 = y1 + getCharHeight();\r
-\r
- if (y>=y1 && y <=y2) {\r
- return i;\r
- }\r
- y1 = y2;\r
- } else {\r
- return -1;\r
- }\r
- }\r
- return -1;\r
- }\r
- public Selection getSelection() {\r
- return sel;\r
- }\r
- public ColumnSelection getColumnSelection() {\r
- return colSel;\r
- }\r
- public OutputGenerator getOutputGenerator() {\r
- return og;\r
- }\r
- public void resetSeqLimits(int height) {\r
- setStartSeq(0);\r
- setEndSeq(height/getCharHeight());\r
- }\r
- public void setCurrentTree(NJTree tree) {\r
- currentTree = tree;\r
- }\r
- public NJTree getCurrentTree() {\r
- return currentTree;\r
- }\r
-\r
- public void setRenderer(RendererI rend) {\r
- this.renderer = rend;\r
- }\r
-\r
- public RendererI getRenderer() {\r
- return renderer;\r
- }\r
- public int getPIDWindow() {\r
- return window;\r
- }\r
- public void setPIDWindow(int window) {\r
- this.window = window;\r
- }\r
-\r
- public int getPIDBaseline() {\r
- return baseline;\r
- }\r
- public void setPIDBaseline(int baseline) {\r
- this.baseline = baseline;\r
- }\r
-\r
- public void setKmers(Vector kmers) {\r
- this.kmers = kmers;\r
- }\r
-\r
- public Vector getKmers() {\r
- return this.kmers;\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+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.viewmodel.AlignmentViewport;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+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, CommandListener
+{
+ Font font;
+
+ NJTree currentTree = null;
+
+ boolean cursorMode = false;
+
+ boolean antiAlias = false;
+
+ private Rectangle explodedGeometry;
+
+ String viewName;
+
+ /*
+ * Flag set true on the view that should 'gather' multiple views of the same
+ * sequence set id when a project is reloaded. Set false on all views when
+ * they are 'exploded' into separate windows. Set true on the current view
+ * when 'Gather' is performed, and also on the first tab when the first new
+ * view is created.
+ */
+ private boolean gatherViewsHere = false;
+
+ private AnnotationColumnChooser annotationColumnSelectionState;
+
+ /**
+ * Creates a new AlignViewport object.
+ *
+ * @param al
+ * alignment to view
+ */
+ public AlignViewport(AlignmentI al)
+ {
+ setAlignment(al);
+ init();
+ }
+
+ /**
+ * Create a new AlignViewport object with a specific sequence set ID
+ *
+ * @param al
+ * @param seqsetid
+ * (may be null - but potential for ambiguous constructor exception)
+ */
+ public AlignViewport(AlignmentI al, String seqsetid)
+ {
+ this(al, seqsetid, null);
+ }
+
+ public AlignViewport(AlignmentI al, String seqsetid, String viewid)
+ {
+ sequenceSetID = seqsetid;
+ viewId = viewid;
+ // TODO remove these once 2.4.VAMSAS release finished
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ {
+ Cache.log.debug("Setting viewport's sequence set id : "
+ + sequenceSetID);
+ }
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ {
+ Cache.log.debug("Setting viewport's view id : " + viewId);
+ }
+ setAlignment(al);
+ init();
+ }
+
+ /**
+ * Create a new AlignViewport with hidden regions
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+ {
+ setAlignment(al);
+ if (hiddenColumns != null)
+ {
+ colSel = hiddenColumns;
+ }
+ init();
+ }
+
+ /**
+ * New viewport with hidden columns and an existing sequence set id
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param seqsetid
+ * (may be null)
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid)
+ {
+ this(al, hiddenColumns, seqsetid, null);
+ }
+
+ /**
+ * New viewport with hidden columns and an existing sequence set id and viewid
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param seqsetid
+ * (may be null)
+ * @param viewid
+ * (may be null)
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid, String viewid)
+ {
+ sequenceSetID = seqsetid;
+ viewId = viewid;
+ // TODO remove these once 2.4.VAMSAS release finished
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ {
+ Cache.log.debug("Setting viewport's sequence set id : "
+ + sequenceSetID);
+ }
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ {
+ Cache.log.debug("Setting viewport's view id : " + viewId);
+ }
+ setAlignment(al);
+ if (hiddenColumns != null)
+ {
+ colSel = hiddenColumns;
+ }
+ init();
+ }
+
+ /**
+ * Apply any settings saved in user preferences
+ */
+ private void applyViewProperties()
+ {
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
+ viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+ setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+ setPadGaps(Cache.getDefault("PAD_GAPS", true));
+ setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+ viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+ viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+ viewStyle.setShowUnconserved(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);
+ viewStyle.setScaleProteinAsCdna(Cache.getDefault(
+ Preferences.SCALE_PROTEIN_TO_CDNA, true));
+ }
+
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+ applyViewProperties();
+
+ String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+ String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+ String fontSize = Cache.getDefault("FONT_SIZE", "10");
+
+ int style = 0;
+
+ if (fontStyle.equals("bold"))
+ {
+ style = 1;
+ }
+ else if (fontStyle.equals("italic"))
+ {
+ style = 2;
+ }
+
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
+
+ alignment
+ .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+
+ // We must set conservation and consensus before setting colour,
+ // as Blosum and Clustal require this to be done
+ if (hconsensus == null && !isDataset)
+ {
+ if (!alignment.isNucleotide())
+ {
+ 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);
+ showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
+ showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+ }
+ initAutoAnnotation();
+ String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT;
+ String propertyValue = Cache.getProperty(colourProperty);
+ if (propertyValue == null)
+ {
+ // fall back on this property for backwards compatibility
+ propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ }
+ if (propertyValue != null)
+ {
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ propertyValue);
+
+ if (globalColourScheme instanceof UserColourScheme)
+ {
+ globalColourScheme = UserDefinedColours.loadDefaultColours();
+ ((UserColourScheme) globalColourScheme).setThreshold(0,
+ isIgnoreGapsConsensus());
+ }
+
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+ }
+ }
+
+ /**
+ * get the consensus sequence as displayed under the PID consensus annotation
+ * row.
+ *
+ * @return consensus sequence as a new sequence object
+ */
+ public SequenceI getConsensusSeq()
+ {
+ if (consensus == null)
+ {
+ updateConsensus(null);
+ }
+ if (consensus == null)
+ {
+ return null;
+ }
+ StringBuffer seqs = new StringBuffer();
+ for (int i = 0; i < consensus.annotations.length; i++)
+ {
+ if (consensus.annotations[i] != null)
+ {
+ if (consensus.annotations[i].description.charAt(0) == '[')
+ {
+ seqs.append(consensus.annotations[i].description.charAt(1));
+ }
+ else
+ {
+ seqs.append(consensus.annotations[i].displayCharacter);
+ }
+ }
+ }
+
+ SequenceI sq = new Sequence("Consensus", seqs.toString());
+ sq.setDescription("Percentage Identity Consensus "
+ + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+ return sq;
+ }
+
+ boolean validCharWidth;
+
+ /**
+ * update view settings with the given font. You may need to call
+ * alignPanel.fontChanged to update the layout geometry
+ *
+ * @param setGrid
+ * when true, charWidth/height is set according to font mentrics
+ */
+ public void setFont(Font f, boolean setGrid)
+ {
+ font = f;
+
+ Container c = new Container();
+
+ java.awt.FontMetrics fm = c.getFontMetrics(font);
+ int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
+ .getCharHeight();
+ if (setGrid)
+ {
+ setCharHeight(fm.getHeight());
+ setCharWidth(ww);
+ }
+ viewStyle.setFontName(font.getName());
+ viewStyle.setFontStyle(font.getStyle());
+ viewStyle.setFontSize(font.getSize());
+
+ validCharWidth = true;
+ }
+
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
+ {
+ super.setViewStyle(settingsForView);
+ setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
+ viewStyle.getFontSize()), false);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont()
+ {
+ return font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ */
+ public void setAlignment(AlignmentI align)
+ {
+ replaceMappings(align);
+ this.alignment = align;
+ }
+
+ /**
+ * Replace any codon mappings for this viewport with those for the given
+ * viewport
+ *
+ * @param align
+ */
+ public void replaceMappings(AlignmentI align)
+ {
+
+ /*
+ * Deregister current mappings (if any)
+ */
+ deregisterMappings();
+
+ /*
+ * Register new mappings (if any)
+ */
+ if (align != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(align.getCodonFrames());
+ }
+
+ /*
+ * replace mappings on our alignment
+ */
+ if (alignment != null && align != null)
+ {
+ alignment.setCodonFrames(align.getCodonFrames());
+ }
+ }
+
+ protected void deregisterMappings()
+ {
+ AlignmentI al = getAlignment();
+ if (al != null)
+ {
+ Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+ if (mappings != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (noReferencesTo(acf))
+ {
+ ssm.deregisterMapping(acf);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getGapCharacter()
+ {
+ return getAlignment().getGapCharacter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gap
+ * DOCUMENT ME!
+ */
+ public void setGapCharacter(char gap)
+ {
+ if (getAlignment() != null)
+ {
+ getAlignment().setGapCharacter(gap);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ColumnSelection getColumnSelection()
+ {
+ return colSel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
+ */
+ public void setCurrentTree(NJTree tree)
+ {
+ currentTree = tree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NJTree getCurrentTree()
+ {
+ return currentTree;
+ }
+
+ /**
+ * returns the visible column regions of the alignment
+ *
+ * @param selectedRegionOnly
+ * true to just return the contigs intersecting with the selected
+ * area
+ * @return
+ */
+ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int[] viscontigs = null;
+ int start = 0, end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ viscontigs = colSel.getVisibleContigs(start, end);
+ return viscontigs;
+ }
+
+ /**
+ * get hash of undo and redo list for the alignment
+ *
+ * @return long[] { historyList.hashCode, redoList.hashCode };
+ */
+ public long[] getUndoRedoHash()
+ {
+ // TODO: JAL-1126
+ if (historyList == null || redoList == null)
+ {
+ return new long[] { -1, -1 };
+ }
+ return new long[] { historyList.hashCode(), this.redoList.hashCode() };
+ }
+
+ /**
+ * test if a particular set of hashcodes are different to the hashcodes for
+ * the undo and redo list.
+ *
+ * @param undoredo
+ * the stored set of hashcodes as returned by getUndoRedoHash
+ * @return true if the hashcodes differ (ie the alignment has been edited) or
+ * the stored hashcode array differs in size
+ */
+ public boolean isUndoRedoHashModified(long[] undoredo)
+ {
+ if (undoredo == null)
+ {
+ return true;
+ }
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length != undoredo.length)
+ {
+ return true;
+ }
+
+ for (int i = 0; i < cstate.length; i++)
+ {
+ if (cstate[i] != undoredo[i])
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public boolean followSelection = true;
+
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
+ {
+ return followSelection;
+ }
+
+ /**
+ * Send the current selection to be broadcast to any selection listeners.
+ */
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
+
+ /**
+ * return the alignPanel containing the given viewport. Use this to get the
+ * components currently handling the given viewport.
+ *
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame
+ * reference
+ */
+ public AlignmentPanel getAlignPanel()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+ .getSequenceSetId());
+ for (int p = 0; aps != null && p < aps.length; p++)
+ {
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
+ }
+ return null;
+ }
+
+ public boolean getSortByTree()
+ {
+ return sortByTree;
+ }
+
+ public void setSortByTree(boolean sort)
+ {
+ sortByTree = sort;
+ }
+
+ /**
+ * synthesize a column selection if none exists so it covers the given
+ * selection group. if wholewidth is false, no column selection is made if the
+ * selection group covers the whole alignment width.
+ *
+ * @param sg
+ * @param wholewidth
+ */
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+ {
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
+ {
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
+ }
+ }
+ }
+
+ /**
+ * Returns the (Desktop) instance of the StructureSelectionManager
+ */
+ @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<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ for (PDBEntry pdb : pdbEntries)
+ {
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (SequenceI sq : alignment.getSequences())
+ {
+ Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
+ if (pdbs == null)
+ {
+ continue;
+ }
+ for (PDBEntry p1 : pdbs)
+ {
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq))
+ {
+ seqs.add(sq);
+ continue;
+ }
+ }
+ }
+ }
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+ }
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ /**
+ *
+ * @return true if alignment characters should be displayed
+ */
+ public boolean isValidCharWidth()
+ {
+ return validCharWidth;
+ }
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+
+ 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);
+ }
+ }
+
+ /**
+ * 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)
+ {
+ /*
+ * 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();
+ }
+ }
+
+ /**
+ * 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
+
+ // JBPComment: title is a largely redundant parameter at the moment
+ // JBPComment: this really should be an 'insert/pre/append' controller
+ // JBPComment: but the DNA/Protein check makes it a bit more complex
+
+ // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+ // this comment:
+ // TODO: create undo object for this JAL-1101
+
+ /*
+ * If any cDNA/protein mappings can be made between the alignments, offer to
+ * open a linked alignment with split frame option.
+ */
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
+ {
+ if (al.getDataset() == null)
+ {
+ // need to create ds seqs
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() == null)
+ {
+ sq.createDatasetSequence();
+ }
+ }
+ }
+ if (AlignmentUtils.isMappable(al, getAlignment()))
+ {
+ if (openLinkedAlignment(al, title))
+ {
+ return;
+ }
+ }
+ }
+
+ /*
+ * No mappings, or offer declined - add sequences to this alignment
+ */
+ // TODO: JAL-407 regardless of above - identical sequences (based on ID and
+ // provenance) should share the same dataset sequence
+
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ getAlignment().addSequence(al.getSequenceAt(i));
+ }
+
+ setEndSeq(getAlignment().getHeight());
+ firePropertyChange("alignment", null, getAlignment().getSequences());
+ }
+
+ /**
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment, either as a standalone alignment or in a split frame. Returns
+ * true if the new alignment was opened, false if not, because the user
+ * declined the offer.
+ *
+ * @param al
+ * @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_split_window?"));
+ int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ MessageManager.getString("label.open_split_window"),
+ 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);
+
+ /*
+ * 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();
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ /*
+ * Map sequences. At least one should get mapped as we have already passed
+ * the test for 'mappability'. Any mappings made will be added to the
+ * protein alignment. Note creating dataset sequences on the new alignment
+ * is a pre-requisite for building mappings.
+ */
+ al.setDataset(null);
+ AlignmentUtils.mapProteinToCdna(protein, cdna);
+
+ /*
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(title);
+ 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
+ {
+ newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+
+ if (openSplitPane)
+ {
+ al.alignAs(thisAlignment);
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
+ }
+
+ return true;
+ }
+
+ /**
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
+ *
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param complement
+ * cdna/protein complement alignment to show in the other split half
+ * @return the protein alignment in the split frame
+ */
+ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+ AlignmentI complement)
+ {
+ /*
+ * Make a new frame with a copy of the alignment we are adding to. If this
+ * is protein, the mappings to cDNA will be registered with
+ * StructureSelectionManager as a side-effect.
+ */
+ AlignFrame copyMe = new AlignFrame(complement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ return proteinFrame.viewport.getAlignment();
+ }
+
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
+ {
+ return annotationColumnSelectionState;
+ }
+
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+ }
+
+ @Override
+ public void setIdWidth(int i)
+ {
+ super.setIdWidth(i);
+ AlignmentPanel ap = getAlignPanel();
+ if (ap != null)
+ {
+ // modify GUI elements to reflect geometry change
+ Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
+ .getPreferredSize();
+ idw.width = i;
+ getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+ }
+ }
+
+ public Rectangle getExplodedGeometry()
+ {
+ return explodedGeometry;
+ }
+
+ public void setExplodedGeometry(Rectangle explodedPosition)
+ {
+ this.explodedGeometry = explodedPosition;
+ }
+
+ public boolean isGatherViewsHere()
+ {
+ return gatherViewsHere;
+ }
+
+ public void setGatherViewsHere(boolean gatherViewsHere)
+ {
+ this.gatherViewsHere = gatherViewsHere;
+ }
+
+ /**
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
+ */
+ public void scrollComplementaryAlignment()
+ {
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResults sr = new SearchResults();
+ int verticalOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
+ {
+ // TODO would like next line without cast but needs more refactoring...
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, verticalOffset);
+ }
+ }
+
+ /**
+ * Answers true if no alignment holds a reference to the given mapping
+ *
+ * @param acf
+ * @return
+ */
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
+ {
+ return true;
+ }
+ for (AlignFrame af : frames)
+ {
+ if (!af.isClosed())
+ {
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ AlignmentI al = ap.getAlignment();
+ if (al != null && al.getCodonFrames().contains(acf))
+ {
+ return false;
+ }
+ }
+ }
+ }
+ return true;
+ }
+
+}