X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=3ae0a52d367cfaffcb4a24429365f2265f8fd97e;hb=767cd5214b7f096cd6c3ba46c99bdec39eb2b799;hp=43f6aff8aa90fc53922e5c2d479806102b5e7ac5;hpb=59a81cfb8e64c68d882182601663d82016f1a866;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
old mode 100755
new mode 100644
index 43f6aff..8225237
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,447 +1,1313 @@
-package jalview.gui;
-
-import java.awt.*;
-import jalview.analysis.*;
-import jalview.analysis.NJTree;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.util.*;
-
-public class AlignViewport
-{
- int startRes;
- int endRes;
-
- int startSeq;
- int endSeq;
-
- boolean showFullId = false;
- boolean showText=true;
- boolean showColourText=false;
- boolean showBoxes=true;
- boolean wrapAlignment=false;
- boolean renderGaps = true;
- boolean showSequenceFeatures = false;
- boolean showAnnotation = true;
-
- boolean colourAppliesToAllGroups = true;
- ColourSchemeI globalColourScheme = null;
- boolean conservationColourSelected = false;
- boolean abovePIDThreshold = false;
-
- SequenceGroup selectionGroup = new SequenceGroup();
-
- RendererI renderer = new SequenceRenderer(this);
-
- int charHeight;
- int charWidth;
- int chunkWidth;
- int chunkHeight;
-
- Font font = new Font("SansSerif",Font.PLAIN,10);
- AlignmentI alignment;
-
- ColumnSelection colSel = new ColumnSelection();
-
- int threshold;
- int increment;
-
- NJTree currentTree = null;
-
-
- public AlignViewport(AlignmentI al,
- boolean showText,
- boolean showBoxes,
- boolean wrapAlignment) {
-
- this.startRes = 0;
- this.endRes = al.getWidth()-1;
- this.startSeq = 0;
- this.endSeq = al.getHeight()-1;
- this.showText = showText;
- this.showBoxes = showBoxes;
- this.wrapAlignment = wrapAlignment;
-
- setAlignment(al);
- setFont( font );
- }
-
- public void showSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
-
- AlignmentAnnotation consensus;
- AlignmentAnnotation conservation;
- public void updateConservation()
- {
- Annotation [] annotations = new Annotation[alignment.getWidth()];
-
- Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0,
- alignment.getWidth());
- cons.calculate();
- cons.verdict(false, 100);
- cons.findQuality();
- String sequence = cons.getConsSequence().getSequence();
- float minR,minG,minB, maxR,maxG,maxB;
- minR = 0.3f;
- minG = 0f;
- minB = 0f;
- maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring
- float min = cons.qualityRange[0].floatValue();
- float max = cons.qualityRange[1].floatValue();
-
- for (int i = 0; i < alignment.getWidth(); i++)
- {
- float value = 0;
- try
- {
- //value = Integer.parseInt(sequence.charAt(i) + "");
- value = ((Double) cons.quality.get(i)).floatValue();
- }
- catch (Exception ex)
- {
- if (sequence.charAt(i) == '*') value = 10;
- }
- float vprop = value-min;
- vprop/=max;
- annotations[i] = new Annotation(sequence.charAt(i) + "",
- "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minB+maxB*vprop, minB+maxB*vprop));
- }
-
- if(conservation==null)
- {
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment",
- annotations,
- cons.qualityRange[0].floatValue(),
- cons.qualityRange[1].floatValue(), 1);
- alignment.addAnnotation(conservation);
- }
- else
- conservation.annotations = annotations;
-
- }
-
- public void updateConsensus()
- {
- Annotation [] annotations = new Annotation[alignment.getWidth()];
-
- Vector cons = alignment.getAAFrequency();
- Hashtable hash = null;
- for (int i = 0; i < alignment.getWidth(); i++)
- {
- hash = (Hashtable) cons.elementAt(i);
- float value = Float.parseFloat(hash.get("maxCount").toString());
- value /= Float.parseFloat(hash.get("size").toString());
-
- value *= 100;
- String maxRes = hash.get("maxResidue")+" ";
- String mouseOver = hash.get("maxResidue")+" ";
- if(maxRes.length()>2)
- {
- mouseOver = "["+maxRes+"] ";
- maxRes = "+ ";
- }
-
- mouseOver += (int)value+"%";
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-
- }
-
- if(consensus==null)
- {
- consensus = new AlignmentAnnotation("% Identity",
- "PID", annotations, 0f, 100f, 1);
- alignment.addAnnotation(consensus);
- }
- else
- consensus.annotations = annotations;
-
- }
-
- public String getVisibleConsensus()
- {
- return visibleConsensus;
- }
-
- String visibleConsensus;
- Vector consensusV = new Vector();
- public Vector getConsensus(boolean recalculate)
- {
- if(recalculate || consensusV.size()<1)
- {
- consensusV = alignment.getAAFrequency();
- StringBuffer sb = new StringBuffer();
- Hashtable hash = null;
- for (int i = 0; i < consensusV.size(); i++)
- {
- hash = (Hashtable) consensusV.elementAt(i);
- sb.append(hash.get("maxResidue").toString().charAt(0));
- }
- visibleConsensus = sb.toString();
- }
-
-
- return consensusV;
- }
-
-
- public SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
- }
-
- public void setSelectionGroup(SequenceGroup sg)
- {
- selectionGroup = sg;
- }
-
-
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
-
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
- }
-
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- public void setAbovePIDThreshold(boolean b)
- {
- abovePIDThreshold = b;
- }
-
- public int getStartRes() {
- return startRes;
- }
-
- public int getEndRes() {
- return endRes;
- }
-
- public int getStartSeq() {
- return startSeq;
- }
-
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
-
- public void setStartRes(int res) {
- this.startRes = res;
- }
- public void setStartSeq(int seq) {
- this.startSeq = seq;
- }
- public void setEndRes(int res) {
- if (res > alignment.getWidth()-1) {
- System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
- res = alignment.getWidth() -1;
- }
- if (res < 0) {
- res = 0;
- }
- this.endRes = res;
- }
- public void setEndSeq(int seq) {
- if (seq > alignment.getHeight()) {
- seq = alignment.getHeight();
- }
- if (seq < 0) {
- seq = 0;
- }
- this.endSeq = seq;
- }
- public int getEndSeq() {
- return endSeq;
- }
-
- public void setFont(Font f) {
- font = f;
- javax.swing.JFrame temp = new javax.swing.JFrame();
- temp.addNotify();
- java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);
- setCharHeight(fm.getHeight());
- setCharWidth(fm.charWidth('M'));
- }
-
- public Font getFont() {
- return font;
- }
- public void setCharWidth(int w) {
- this.charWidth = w;
- }
- public int getCharWidth() {
- return charWidth;
- }
- public void setCharHeight(int h) {
- this.charHeight = h;
- }
- public int getCharHeight() {
- return charHeight;
- }
- public void setChunkWidth(int w) {
- this.chunkWidth = w;
- }
- public int getChunkWidth() {
- return chunkWidth;
- }
- public void setChunkHeight(int h) {
- this.chunkHeight = h;
- }
- public int getChunkHeight() {
- return chunkHeight;
- }
- public AlignmentI getAlignment() {
- return alignment;
- }
- public void setAlignment(AlignmentI align) {
- this.alignment = align;
- }
-
- public void setWrapAlignment(boolean state) {
- wrapAlignment = state;
- }
- public void setShowText(boolean state) {
- showText = state;
- }
-
- public void setRenderGaps(boolean state){
- renderGaps = state;
- if(renderer instanceof SequenceRenderer)
- {
- SequenceRenderer sr = (SequenceRenderer)renderer;
- sr.renderGaps(state);
- }
- }
-
-
- public boolean getColourText()
- {
- return showColourText;
- }
-
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- public void setShowBoxes(boolean state) {
- showBoxes = state;
- }
-
- public boolean getWrapAlignment() {
- return wrapAlignment;
- }
- public boolean getShowText() {
- return showText;
- }
- public boolean getShowBoxes() {
- return showBoxes;
- }
-
- public char getGapCharacter() {
- return getAlignment().getGapCharacter();
- }
- public void setGapCharacter(char gap) {
- if (getAlignment() != null) {
- getAlignment().setGapCharacter(gap);
- }
- }
- public void setThreshold(int thresh) {
- threshold = thresh;
- }
- public int getThreshold() {
- return threshold;
- }
- public void setIncrement(int inc) {
- increment = inc;
- }
- public int getIncrement() {
- return increment;
- }
- public int getIndex(int y) {
- int y1 = 0;
- int starty = getStartSeq();
- int endy = getEndSeq();
-
- for (int i = starty; i <= endy; i++) {
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {
- int y2 = y1 + getCharHeight();
-
- if (y>=y1 && y <=y2) {
- return i;
- }
- y1 = y2;
- } else {
- return -1;
- }
- }
- return -1;
- }
-
- public ColumnSelection getColumnSelection() {
- return colSel;
- }
-
- public void resetSeqLimits(int height) {
- setEndSeq(height/getCharHeight());
- }
- public void setCurrentTree(NJTree tree) {
- currentTree = tree;
- }
- public NJTree getCurrentTree() {
- return currentTree;
- }
-
- public void setRenderer(RendererI rend) {
- this.renderer = rend;
- }
-
- public RendererI getRenderer() {
- return renderer;
- }
-
- public void setColourAppliesToAllGroups(boolean b)
- { colourAppliesToAllGroups = b; }
-
- public boolean getColourAppliesToAllGroups()
- {return colourAppliesToAllGroups; }
-
- public boolean getShowFullId()
- {
- return showFullId;
- }
-
- public void setShowFullId(boolean b)
- {
- showFullId = b;
- }
-
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
-}
+/*
+ * 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
+ *
+ * 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 .
+ */
+/*
+ * 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.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+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.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Stack;
+import java.util.Vector;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.141 $
+ */
+public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
+{
+ int startRes;
+
+ int endRes;
+
+ int startSeq;
+
+ int endSeq;
+
+ boolean showJVSuffix = true;
+
+ boolean showText = true;
+
+ boolean showColourText = false;
+
+ boolean showBoxes = true;
+
+ boolean wrapAlignment = false;
+
+ boolean renderGaps = true;
+
+ boolean showSequenceFeatures = false;
+
+ boolean showAnnotation = true;
+
+ int charHeight;
+
+ int charWidth;
+
+ boolean validCharWidth;
+
+ int wrappedWidth;
+
+ Font font;
+
+ boolean seqNameItalics;
+
+
+ NJTree currentTree = null;
+
+ boolean scaleAboveWrapped = false;
+
+ boolean scaleLeftWrapped = true;
+
+ boolean scaleRightWrapped = true;
+
+ boolean showHiddenMarkers = true;
+
+ boolean cursorMode = false;
+
+ /**
+ * Keys are the feature types which are currently visible. Note: Values are
+ * not used!
+ */
+ Hashtable featuresDisplayed = null;
+
+ boolean antiAlias = false;
+
+ Rectangle explodedPosition;
+
+ String viewName;
+
+ boolean gatherViewsHere = false;
+
+ Stack historyList = new Stack();
+
+ Stack redoList = new Stack();
+
+ Hashtable sequenceColours;
+
+ int thresholdTextColour = 0;
+
+ Color textColour = Color.black;
+
+ Color textColour2 = Color.white;
+
+ boolean rightAlignIds = false;
+
+ /**
+ * 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)
+ {
+ this.colSel = hiddenColumns;
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
+ {
+ hasHiddenColumns = true;
+ }
+ else
+ {
+ hasHiddenColumns = false;
+ }
+ }
+ 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)
+ {
+ this.colSel = hiddenColumns;
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
+ {
+ hasHiddenColumns = true;
+ }
+ else
+ {
+ hasHiddenColumns = false;
+ }
+ }
+ init();
+ }
+
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+ showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+
+ rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+ centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+ setPadGaps(Cache.getDefault("PAD_GAPS", true));
+ shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
+ showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+
+ String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+ String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+ String fontSize = Cache.getDefault("FONT_SIZE", "10");
+
+ seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
+ int style = 0;
+
+ if (fontStyle.equals("bold"))
+ {
+ style = 1;
+ }
+ else if (fontStyle.equals("italic"))
+ {
+ style = 2;
+ }
+
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+
+ 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);
+ consensus = new AlignmentAnnotation("Consensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
+ }
+ initAutoAnnotation();
+ if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+ {
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+
+ if (globalColourScheme instanceof UserColourScheme)
+ {
+ globalColourScheme = UserDefinedColours.loadDefaultColours();
+ ((UserColourScheme) globalColourScheme).setThreshold(0,
+ getIgnoreGapsConsensus());
+ }
+
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+ }
+
+ 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);
+ }
+
+ /**
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
+ */
+ public void setShowSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+
+ public boolean getShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ /**
+ * centre columnar annotation labels in displayed alignment annotation TODO:
+ * add to jalviewXML and annotation display settings
+ */
+ boolean centreColumnLabels = false;
+
+ private boolean showdbrefs;
+
+ private boolean shownpfeats;
+
+ // --------END Structure Conservation
+
+ /**
+ * 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartSeq()
+ {
+ return startSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param res
+ * DOCUMENT ME!
+ */
+ public void setStartRes(int res)
+ {
+ this.startRes = res;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ */
+ public void setStartSeq(int seq)
+ {
+ this.startSeq = seq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param res
+ * DOCUMENT ME!
+ */
+ public void setEndRes(int res)
+ {
+ if (res > (alignment.getWidth() - 1))
+ {
+ // log.System.out.println(" Corrected res from " + res + " to maximum " +
+ // (alignment.getWidth()-1));
+ res = alignment.getWidth() - 1;
+ }
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ this.endRes = res;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ */
+ public void setEndSeq(int seq)
+ {
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+
+ this.endSeq = seq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
+ */
+ public void setFont(Font f)
+ {
+ font = f;
+
+ Container c = new Container();
+
+ java.awt.FontMetrics fm = c.getFontMetrics(font);
+ setCharHeight(fm.getHeight());
+ setCharWidth(fm.charWidth('M'));
+ validCharWidth = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont()
+ {
+ return font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ public void setCharWidth(int w)
+ {
+ this.charWidth = w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCharWidth()
+ {
+ return charWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param h
+ * DOCUMENT ME!
+ */
+ public void setCharHeight(int h)
+ {
+ this.charHeight = h;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCharHeight()
+ {
+ return charHeight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ public void setWrappedWidth(int w)
+ {
+ this.wrappedWidth = w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWrappedWidth()
+ {
+ return wrappedWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ */
+ public void setAlignment(AlignmentI align)
+ {
+ if (alignment != null && alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).removeMappings(alignment.getCodonFrames());
+ }
+ this.alignment = align;
+ if (alignment!=null && alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).addMappings(alignment.getCodonFrames());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean state)
+ {
+ wrapAlignment = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setShowText(boolean state)
+ {
+ showText = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setRenderGaps(boolean state)
+ {
+ renderGaps = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setColourText(boolean state)
+ {
+ showColourText = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setShowBoxes(boolean state)
+ {
+ showBoxes = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getWrapAlignment()
+ {
+ return wrapAlignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowText()
+ {
+ return showText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowBoxes()
+ {
+ return showBoxes;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowJVSuffix()
+ {
+ return showJVSuffix;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setShowJVSuffix(boolean b)
+ {
+ showJVSuffix = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleAboveWrapped()
+ {
+ return scaleAboveWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleLeftWrapped()
+ {
+ return scaleLeftWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleRightWrapped()
+ {
+ return scaleRightWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleAboveWrapped(boolean b)
+ {
+ scaleAboveWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleLeftWrapped(boolean b)
+ {
+ scaleLeftWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleRightWrapped(boolean b)
+ {
+ scaleRightWrapped = b;
+ }
+
+
+ public void setDataset(boolean b)
+ {
+ isDataset = b;
+ }
+
+ public boolean isDataset()
+ {
+ return isDataset;
+ }
+
+
+
+ public boolean getShowHiddenMarkers()
+ {
+ return showHiddenMarkers;
+ }
+
+ public void setShowHiddenMarkers(boolean show)
+ {
+ 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
+ *
+ * @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 getCentreColumnLabels()
+ {
+ return centreColumnLabels;
+ }
+
+ public void setCentreColumnLabels(boolean centrecolumnlabels)
+ {
+ 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
+ */
+ public void setShowDbRefs(boolean show)
+ {
+ showdbrefs = show;
+ }
+
+ /**
+ *
+ * @return true if Database References are to be displayed on tooltips.
+ */
+ public boolean isShowDbRefs()
+ {
+ return showdbrefs;
+ }
+
+ /**
+ *
+ * @return true if Non-positional features are to be displayed on tooltips.
+ */
+ public boolean isShowNpFeats()
+ {
+ return shownpfeats;
+ }
+
+ /**
+ * enable or disable the display of Non-Positional sequence features in the
+ * sequence ID tooltip
+ *
+ * @param show
+ */
+ public void setShowNpFeats(boolean show)
+ {
+ shownpfeats = show;
+ }
+
+ /**
+ *
+ * @return true if view has hidden rows
+ */
+ public boolean hasHiddenRows()
+ {
+ return hasHiddenRows;
+ }
+
+ /**
+ *
+ * @return true if view has hidden columns
+ */
+ public boolean hasHiddenColumns()
+ {
+ return hasHiddenColumns;
+ }
+
+ /**
+ * when set, view will scroll to show the highlighted position
+ */
+ public boolean followHighlight = true;
+
+ /**
+ * @return true if view should scroll to show the highlighted region of a
+ * sequence
+ * @return
+ */
+ public boolean getFollowHighlight()
+ {
+ return followHighlight;
+ }
+
+ public boolean followSelection = true;
+
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
+ {
+ return followSelection;
+ }
+
+ boolean showSeqFeaturesHeight;
+
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
+
+ public void setShowSequenceFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+ }
+
+ public boolean getShowSequenceFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
+ }
+
+ /**
+ * 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());
+ AlignmentPanel ap = null;
+ 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);
+ }
+ }
+ }
+
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ }
+
+ /**
+ *
+ * @param pdbEntries
+ * @return a series of SequenceI arrays, one for each PDBEntry, listing which
+ * sequence in the alignment holds a reference to it
+ */
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+ {
+ ArrayList seqvectors = new ArrayList();
+ for (PDBEntry pdb : pdbEntries)
+ {
+ ArrayList seqs = new ArrayList();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
+ .getPDBId();
+ if (pdbs == null)
+ continue;
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
+ {
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ 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 calcIdParams=new Hashtable();
+ 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);
+ }
+ }
+}