-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AlignViewport
-{
- 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;
- boolean colourAppliesToAllGroups = true;
- ColourSchemeI globalColourScheme = null;
- boolean conservationColourSelected = false;
- boolean abovePIDThreshold = false;
- SequenceGroup selectionGroup;
- int charHeight;
- int charWidth;
- boolean validCharWidth;
- int wrappedWidth;
- Font font;
- boolean seqNameItalics;
- AlignmentI alignment;
- ColumnSelection colSel = new ColumnSelection();
- int threshold;
- int increment;
- NJTree currentTree = null;
- boolean scaleAboveWrapped = false;
- boolean scaleLeftWrapped = true;
- boolean scaleRightWrapped = true;
- boolean hasHiddenColumns = false;
- boolean hasHiddenRows = false;
- boolean showHiddenMarkers = true;
-
- boolean cursorMode = false;
-
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
- Hashtable featuresDisplayed = null;
-
-
- /** DOCUMENT ME!! */
- public Hashtable [] hconsensus;
- AlignmentAnnotation consensus;
- AlignmentAnnotation conservation;
- AlignmentAnnotation quality;
- boolean autoCalculateConsensus = true;
-
- /** DOCUMENT ME!! */
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- // JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
-
- boolean ignoreGapsInConsensusCalculation = false;
-
- boolean isDataset = false;
-
- boolean antiAlias = false;
-
- boolean padGaps = false;
-
- Rectangle explodedPosition;
-
- String viewName;
-
- String sequenceSetID;
-
- 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;
-
- Hashtable hiddenRepSequences;
-
-
- /**
- * Creates a new AlignViewport object.
- *
- * @param al DOCUMENT ME!
- */
- public AlignViewport(AlignmentI al)
- {
- 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)
- hasHiddenColumns = true;
- }
- 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);
-
- autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
- padGaps = Cache.getDefault("PAD_GAPS", 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())
- {
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " +
- ConsPercGaps + "% gaps",
- new Annotation[1], 0f,
- 11f,
- AlignmentAnnotation.BAR_GRAPH);
- conservation.hasText = true;
- conservation.autoCalculated = true;
-
-
- if (Cache.getDefault("SHOW_CONSERVATION", true))
- {
- alignment.addAnnotation(conservation);
- }
-
- if (Cache.getDefault("SHOW_QUALITY", true))
- {
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- new Annotation[1],
- 0f,
- 11f,
- AlignmentAnnotation.BAR_GRAPH);
- quality.hasText = true;
- quality.autoCalculated = true;
-
- alignment.addAnnotation(quality);
- }
- }
-
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
-
- if (Cache.getDefault("SHOW_IDENTITY", true))
- {
- alignment.addAnnotation(consensus);
- }
- }
-
- 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);
- }
-
-
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setShowSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
-
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
-
-
-
- class ConservationThread extends Thread
- {
- AlignmentPanel ap;
- public ConservationThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- public void run()
- {
- try
- {
- updatingConservation = true;
-
- while (UPDATING_CONSERVATION)
- {
- try
- {
- if (ap != null)
- {
- ap.repaint();
- }
- Thread.sleep(200);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_CONSERVATION = true;
-
-
- int alWidth = alignment.getWidth();
- if(alWidth<0)
- return;
-
- Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth -1);
-
- cons.calculate();
- cons.verdict(false, ConsPercGaps);
-
- if (quality!=null)
- {
- cons.findQuality();
- }
-
- char [] sequence = cons.getConsSequence().getSequence();
- float minR;
- float minG;
- float minB;
- float maxR;
- float maxG;
- float maxB;
- minR = 0.3f;
- minG = 0.0f;
- minB = 0f;
- maxR = 1.0f - minR;
- maxG = 0.9f - minG;
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
-
- float min = 0f;
- float max = 11f;
- float qmin = 0f;
- float qmax = 0f;
-
- char c;
-
- conservation.annotations = new Annotation[alWidth];
-
- if (quality!=null)
- {
- quality.graphMax = cons.qualityRange[1].floatValue();
- quality.annotations = new Annotation[alWidth];
- qmin = cons.qualityRange[0].floatValue();
- qmax = cons.qualityRange[1].floatValue();
- }
-
- for (int i = 0; i < alWidth; i++)
- {
- float value = 0;
-
- c = sequence[i];
-
- if (Character.isDigit(c))
- value = (int) (c - '0');
- else if (c == '*')
- value = 11;
- else if (c == '+')
- value = 10;
-
- float vprop = value - min;
- vprop /= max;
- conservation.annotations[i] =
- new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value,
- new Color(minR + (maxR * vprop),
- minG + (maxG * vprop),
- minB + (maxB * vprop)));
-
- // Quality calc
- if (quality!=null)
- {
- value = ( (Double) cons.quality.get(i)).floatValue();
- vprop = value - qmin;
- vprop /= qmax;
- quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
- value,
- new Color(minR + (maxR * vprop),
- minG + (maxG * vprop),
- minB + (maxB * vprop)));
- }
- }
- }
- catch (OutOfMemoryError error)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
-
-
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating conservation!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
- conservation = null;
- quality = null;
-
- System.out.println("Conservation calculation: " + error);
- System.gc();
-
- }
-
- UPDATING_CONSERVATION = false;
- updatingConservation = false;
-
- if(ap!=null)
- {
- ap.repaint();
- }
-
- }
- }
-
-
- ConservationThread conservationThread;
-
- ConsensusThread consensusThread;
-
- boolean consUpdateNeeded = false;
-
- static boolean UPDATING_CONSENSUS = false;
-
- static boolean UPDATING_CONSERVATION = false;
-
- boolean updatingConsensus = false;
-
- boolean updatingConservation = false;
-
- /**
- * DOCUMENT ME!
- */
- public void updateConservation(final AlignmentPanel ap)
- {
- if (alignment.isNucleotide() || conservation==null)
- return;
-
- conservationThread = new ConservationThread(ap);
- conservationThread.start();
- }
-
- /**
- * DOCUMENT ME!
- */
- public void updateConsensus(final AlignmentPanel ap)
- {
- consensusThread = new ConsensusThread(ap);
- consensusThread.start();
- }
-
-
- class ConsensusThread extends Thread
- {
- AlignmentPanel ap;
- public ConsensusThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
- public void run()
- {
- updatingConsensus = true;
- while (UPDATING_CONSENSUS)
- {
- try
- {
- if (ap != null)
- {
- ap.repaint();
- }
-
- Thread.sleep(200);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
-
- UPDATING_CONSENSUS = true;
-
- try
- {
- int aWidth = alignment.getWidth();
- if(aWidth<0)
- return;
-
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
-
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(),
- 0,
- alignment.getWidth(),
- hconsensus);
-
- for (int i = 0; i < aWidth; i++)
- {
- float value = 0;
- if (ignoreGapsInConsensusCalculation)
- value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
- floatValue();
- else
- value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
- floatValue();
-
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
- String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
-
- if (maxRes.length() > 1)
- {
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
- }
-
- mouseOver += ( (int) value + "%");
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
- }
-
-
- if (globalColourScheme != null)
- globalColourScheme.setConsensus(hconsensus);
-
- }
- catch (OutOfMemoryError error)
- {
- alignment.deleteAnnotation(consensus);
-
- consensus = null;
- hconsensus = null;
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating consensus!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
- System.out.println("Consensus calculation: " + error);
- System.gc();
- }
- UPDATING_CONSENSUS = false;
- updatingConsensus = false;
-
- if (ap != null)
- {
- ap.repaint();
- }
- }
- }
- /**
- * 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 SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param sg DOCUMENT ME!
- */
- public void setSelectionGroup(SequenceGroup sg)
- {
- selectionGroup = sg;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setAbovePIDThreshold(boolean b)
- {
- abovePIDThreshold = b;
- }
-
- /**
- * 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 cs DOCUMENT ME!
- */
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
- /**
- * 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)
- {
- this.alignment = align;
- }
-
- /**
- * 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!
- *
- * @param thresh DOCUMENT ME!
- */
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getThreshold()
- {
- return threshold;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param inc DOCUMENT ME!
- */
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getIncrement()
- {
- return increment;
- }
-
-
- /**
- * 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!
- *
- * @param b DOCUMENT ME!
- */
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.141 $
+ */
+public class AlignViewport extends AlignmentViewport
+ implements SelectionSource
+{
+ Font font;
+
+ TreeModel 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)
+ {
+ super(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)
+ {
+ super(al);
+ 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);
+ }
+ init();
+
+ }
+
+ /**
+ * Create a new AlignViewport with hidden regions
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection
+ */
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
+ {
+ super(al);
+ if (hiddenColumns != null)
+ {
+ al.setHiddenColumns(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, HiddenColumns 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, HiddenColumns hiddenColumns,
+ String seqsetid, String viewid)
+ {
+ super(al);
+ 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);
+ }
+
+ if (hiddenColumns != null)
+ {
+ al.setHiddenColumns(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()
+ {
+ 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);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
+ }
+ initAutoAnnotation();
+ String colourProperty = alignment.isNucleotide()
+ ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT;
+ String schemeName = Cache.getProperty(colourProperty);
+ if (schemeName == null)
+ {
+ // only DEFAULT_COLOUR available in Jalview before 2.9
+ schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
+ }
+ ColourSchemeI colourScheme = ColourSchemeProperty
+ .getColourScheme(alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
+
+ if (colourScheme instanceof UserColourScheme)