/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
/**
* @author $author$
* @version $Revision$
*/
-public class AlignViewport
+public class AlignViewport implements SelectionSource
{
+ private static final int RIGHT_JUSTIFY = 1;
+
int startRes;
int endRes;
AlignmentAnnotation conservation;
AlignmentAnnotation quality;
-
+ AlignmentAnnotation[] groupConsensus;
+ AlignmentAnnotation[] groupConservation;
+
boolean autoCalculateConsensus = true;
/** DOCUMENT ME!! */
Hashtable hiddenRepSequences;
+ boolean sortByTree;
+
/**
* Creates a new AlignViewport object.
*
- * @param al
- * DOCUMENT ME!
+ * @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
}
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)
+ {
+ hasHiddenColumns = true;
+ }
+ }
+ init();
+ }
void init()
{
alignment.addAnnotation(quality);
}
}
-
+ // TODO: add menu option action that nulls or creates consensus object depending on if the user wants to see the annotation or not in a specific alignment
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
consensus.hasText = true;
}
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);
}
/**
- * DOCUMENT ME!
+ * set the flag
*
* @param b
- * DOCUMENT ME!
+ * features are displayed if true
*/
public void setShowSequenceFeatures(boolean b)
{
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.paintAlignment(false);
- }
- 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)
- {
- new OOMWarning("calculating conservation", error);
-
- conservation = null;
- quality = null;
-
- }
-
- UPDATING_CONSERVATION = false;
- updatingConservation = false;
-
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
-
- }
- }
-
ConservationThread conservationThread;
ConsensusThread consensusThread;
*/
public void updateConservation(final AlignmentPanel ap)
{
- if (alignment.isNucleotide() || conservation == null)
+ // see note in mantis : issue number 8585
+ if (alignment.isNucleotide() || conservation == null || !autoCalculateConsensus)
{
return;
}
- conservationThread = new ConservationThread(ap);
+ conservationThread = new ConservationThread(this, ap);
conservationThread.start();
}
*/
public void updateConsensus(final AlignmentPanel ap)
{
+ // see note in mantis : issue number 8585
+ if (consensus == null || !autoCalculateConsensus)
+ {
+ return;
+ }
consensusThread = new ConsensusThread(ap);
consensusThread.start();
}
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);
- }
-
+ AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation);
+
if (globalColourScheme != null)
{
globalColourScheme.setConsensus(hconsensus);
*/
public void setSelectionGroup(SequenceGroup sg)
{
- selectionGroup = sg;
+ selectionGroup = sg;
}
/**
seqs[index++] = sg.getSequenceAt(i);
}
}
-
+ sg.setSeqrep(repSequence);
+ sg.setHidereps(true);
hideSequence(seqs);
}
selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
}
firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
}
if (alignment.getHiddenSequences().getSize() < 1)
selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
}
firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
hasHiddenRows = false;
hiddenRepSequences = null;
}
*/
public SequenceI[] getSequenceSelection()
{
- SequenceI[] sequences;
- if (selectionGroup == null)
+ SequenceI[] sequences=null;
+ if (selectionGroup!=null)
{
- sequences = alignment.getSequencesArray();
+ sequences = selectionGroup.getSequencesInOrder(alignment);
}
- else
+ if (sequences == null)
{
- sequences = selectionGroup.getSequencesInOrder(alignment);
+ sequences = alignment.getSequencesArray();
}
return sequences;
}
return sequenceSetID;
}
+ /**
+ * unique viewId for synchronizing state with stored Jalview Project
+ *
+ */
+ private String viewId=null;
+
+ public String getViewId()
+ {
+ if (viewId==null)
+ {
+ viewId = this.getSequenceSetId()+"."+this.hashCode()+"";
+ }
+ return viewId;
+ }
+
public void alignmentChanged(AlignmentPanel ap)
{
if (padGaps)
{
alignment.padGaps();
}
-
if (hconsensus != null && autoCalculateConsensus)
{
- updateConsensus(ap);
updateConservation(ap);
}
+ if (autoCalculateConsensus)
+ {
+ updateConsensus(ap);
+ }
// Reset endRes of groups if beyond alignment width
int alWidth = alignment.getWidth();
{
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;
+ }
+ private long sgrouphash=-1,colselhash=-1;
+
+ boolean showSeqFeaturesHeight;
+ /**
+ * checks current SelectionGroup against record of last hash value, and updates record.
+ * @return true if SelectionGroup changed since last call
+ */
+ boolean isSelectionGroupChanged() {
+ int hc=(selectionGroup==null) ? -1 : selectionGroup.hashCode();
+ if (hc!=sgrouphash)
+ {
+ sgrouphash = hc;
+ return true;
+ }
+ return false;
+ }
+ /**
+ * checks current colsel against record of last hash value, and updates record.
+ * @return true if colsel changed since last call
+ */
+ boolean isColSelChanged() {
+ int hc=(colSel==null) ? -1 : colSel.hashCode();
+ if (hc!=colselhash)
+ {
+ colselhash = hc;
+ return true;
+ }
+ return false;
+ }
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager().sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this);
+ }
+ public void setShowSequenceFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+ }
+ public boolean getShowSequenceFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
+ }
+ boolean showUnconserved=false;
+ public boolean getShowUnconserved()
+ {
+ return showUnconserved;
+ }
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ showUnconserved=showunconserved;
+ }
+ /**
+ * 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;
+ }
+ /**
+ * should conservation rows be shown for groups
+ */
+ boolean showGroupConservation = false;
+ /**
+ * should consensus rows be shown for groups
+ */
+ boolean showGroupConsensus = false;
+
+ /**
+ * @return the showGroupConservation
+ */
+ public boolean isShowGroupConservation()
+ {
+ return showGroupConservation;
+ }
+ /**
+ * @param showGroupConservation the showGroupConservation to set
+ */
+ public void setShowGroupConservation(boolean showGroupConservation)
+ {
+ this.showGroupConservation = showGroupConservation;
+ }
+ /**
+ * @return the showGroupConsensus
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return showGroupConsensus;
+ }
+ /**
+ * @param showGroupConsensus the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff