X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=36da772b567362a643d270d4c6964362227182e9;hb=0b9d0f8eba1cec46c0b31fdd402a826e26244ff5;hp=fc96f62df9e4865a9f98ad184901cd6f49cf7007;hpb=f2b6ee8c1feb4f6a7e229ee94741ef93f0bd453d;p=jalview.git
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index fc96f62..36da772 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,22 +1,23 @@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* 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
+ * 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
+ *
+ * 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 .
*/
package jalview.viewmodel;
+import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
@@ -27,25 +28,29 @@ import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.workers.AlignCalcManager;
import jalview.workers.ConsensusThread;
-import jalview.workers.ConservationThread;
import jalview.workers.StrucConsensusThread;
import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
import java.util.Vector;
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
- *
+ *
* @author jimp
- *
+ *
*/
public abstract class AlignmentViewport implements AlignViewportI
{
@@ -62,7 +67,7 @@ public abstract class AlignmentViewport implements AlignViewportI
*/
protected boolean isDataset = false;
- private Hashtable hiddenRepSequences;
+ private Map hiddenRepSequences;
protected ColumnSelection colSel = new ColumnSelection();
@@ -74,12 +79,195 @@ public abstract class AlignmentViewport implements AlignViewportI
protected ColourSchemeI globalColourScheme = null;
+ /**
+ * gui state - changes to colour scheme propagated to all groups
+ */
+ private boolean colourAppliesToAllGroups;
+
+ /**
+ * @param value
+ * indicating if subsequent colourscheme changes will be propagated
+ * to all groups
+ */
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ colourAppliesToAllGroups = b;
+ }
+
+ /**
+ *
+ *
+ * @return flag indicating if colourchanges propagated to all groups
+ */
+ public boolean getColourAppliesToAllGroups()
+ {
+ return colourAppliesToAllGroups;
+ }
+
+ boolean abovePIDThreshold = false;
+
+ /**
+ * GUI state
+ *
+ * @return true if percent identity threshold is applied to shading
+ */
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ /**
+ * GUI state
+ *
+ *
+ * @param b
+ * indicate if percent identity threshold is applied to shading
+ */
+ public void setAbovePIDThreshold(boolean b)
+ {
+ abovePIDThreshold = b;
+ }
+
+ int threshold;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thresh
+ * DOCUMENT ME!
+ */
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ int increment;
+
+ /**
+ *
+ * @param inc
+ * set the scalar for bleaching colourschemes according to degree of
+ * conservation
+ */
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ /**
+ * GUI State
+ *
+ * @return get scalar for bleaching colourschemes by conservation
+ */
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ boolean conservationColourSelected = false;
+
+ /**
+ * GUI state
+ *
+ * @return true if conservation based shading is enabled
+ */
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ /**
+ * GUI state
+ *
+ * @param b
+ * enable conservation based shading
+ */
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+ @Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
+ // TODO: logic refactored from AlignFrame changeColour -
+ // autorecalc stuff should be changed to rely on the worker system
+ // check to see if we should implement a changeColour(cs) method rather than
+ // put th logic in here
+ // - means that caller decides if they want to just modify state and defer
+ // calculation till later or to do all calculations in thread.
+ // via changecolour
globalColourScheme = cs;
+ if (getColourAppliesToAllGroups())
+ {
+ for (SequenceGroup sg : getAlignment().getGroups())
+ {
+ if (cs == null)
+ {
+ sg.cs = null;
+ continue;
+ }
+ if (cs instanceof ClustalxColourScheme)
+ {
+ sg.cs = new ClustalxColourScheme(sg, getHiddenRepSequences());
+ }
+ else
+ {
+ try
+ {
+ sg.cs = cs.getClass().newInstance();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ sg.cs = cs;
+ }
+ }
+
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(getHiddenRepSequences()), 0,
+ sg.getWidth()));
+ }
+ else
+ {
+ sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+
+ if (getConservationSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(getHiddenRepSequences()), 0,
+ getAlignment().getWidth() - 1);
+ c.calculate();
+ c.verdict(false, getConsPercGaps());
+ sg.cs.setConservation(c);
+ }
+ else
+ {
+ sg.cs.setConservation(null);
+ sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+
+ }
+ }
+
}
+ @Override
public ColourSchemeI getGlobalColourScheme()
{
return globalColourScheme;
@@ -114,10 +302,12 @@ public abstract class AlignmentViewport implements AlignViewportI
*/
int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+ @Override
public int getConsPercGaps()
{
return ConsPercGaps;
}
+
@Override
public void setSequenceConsensusHash(Hashtable[] hconsensus)
{
@@ -231,6 +421,7 @@ public abstract class AlignmentViewport implements AlignViewportI
return calculator.isWorking();
}
+ @Override
public boolean isCalculationInProgress(
AlignmentAnnotation alignmentAnnotation)
{
@@ -272,10 +463,12 @@ public abstract class AlignmentViewport implements AlignViewportI
* should consensus profile be rendered by default
*/
protected boolean showSequenceLogo = false;
+
/**
* should consensus profile be rendered normalised to row height
*/
protected boolean normaliseSequenceLogo = false;
+
/**
* should consensus histograms be rendered by default
*/
@@ -284,6 +477,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* @return the showConsensusProfile
*/
+ @Override
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
@@ -350,10 +544,11 @@ public abstract class AlignmentViewport implements AlignViewportI
}
/**
- *
+ *
* @return flag to indicate if the consensus histogram should be rendered by
* default
*/
+ @Override
public boolean isShowConsensusHistogram()
{
return this.showConsensusHistogram;
@@ -364,7 +559,6 @@ public abstract class AlignmentViewport implements AlignViewportI
*/
protected boolean showUnconserved = false;
-
/**
* when set, updateAlignment will always ensure sequences are of equal length
*/
@@ -395,8 +589,8 @@ public abstract class AlignmentViewport implements AlignViewportI
}
/**
- *
- *
+ *
+ *
* @return null or the currently selected sequence region
*/
public SequenceGroup getSelectionGroup()
@@ -406,10 +600,10 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* Set the selection group for this window.
- *
+ *
* @param sg
* - group holding references to sequences in this alignment view
- *
+ *
*/
public void setSelectionGroup(SequenceGroup sg)
{
@@ -425,6 +619,7 @@ public abstract class AlignmentViewport implements AlignViewportI
}
}
+ @Override
public ColumnSelection getColumnSelection()
{
return colSel;
@@ -434,14 +629,24 @@ public abstract class AlignmentViewport implements AlignViewportI
{
this.colSel = colSel;
}
- public Hashtable getHiddenRepSequences()
+
+ /**
+ *
+ * @return
+ */
+ @Override
+ public Map getHiddenRepSequences()
{
return hiddenRepSequences;
}
- public void setHiddenRepSequences(Hashtable hiddenRepSequences)
+
+ @Override
+ public void setHiddenRepSequences(
+ Map hiddenRepSequences)
{
this.hiddenRepSequences = hiddenRepSequences;
}
+
protected boolean hasHiddenColumns = false;
public void updateHiddenColumns()
@@ -480,7 +685,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* unique viewId for synchronizing state (e.g. with stored Jalview Project)
- *
+ *
*/
protected String viewId = null;
@@ -513,10 +718,10 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* checks current SelectionGroup against record of last hash value, and
* updates record.
- *
+ *
* @param b
* update the record of last hash value
- *
+ *
* @return true if SelectionGroup changed since last call (when b is true)
*/
public boolean isSelectionGroupChanged(boolean b)
@@ -537,7 +742,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* checks current colsel against record of last hash value, and optionally
* updates record.
- *
+ *
* @param b
* update the record of last hash value
* @return true if colsel changed since last call (when b is true)
@@ -557,6 +762,7 @@ public abstract class AlignmentViewport implements AlignViewportI
return false;
}
+ @Override
public boolean getIgnoreGapsConsensus()
{
return ignoreGapsInConsensusCalculation;
@@ -565,7 +771,7 @@ public abstract class AlignmentViewport implements AlignViewportI
// / property change stuff
// JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
this);
protected boolean showConservation = true;
@@ -574,10 +780,9 @@ public abstract class AlignmentViewport implements AlignViewportI
protected boolean showConsensus = true;
-
/**
* Property change listener for changes in alignment
- *
+ *
* @param listener
* DOCUMENT ME!
*/
@@ -589,7 +794,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* DOCUMENT ME!
- *
+ *
* @param listener
* DOCUMENT ME!
*/
@@ -601,7 +806,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* Property change listener for changes in alignment
- *
+ *
* @param prop
* DOCUMENT ME!
* @param oldvalue
@@ -616,7 +821,6 @@ public abstract class AlignmentViewport implements AlignViewportI
}
// common hide/show column stuff
-
public void hideSelectedColumns()
{
@@ -660,7 +864,6 @@ public abstract class AlignmentViewport implements AlignViewportI
hasHiddenColumns = false;
}
-
// common hide/show seq stuff
public void showAllHiddenSeqs()
{
@@ -715,8 +918,6 @@ public abstract class AlignmentViewport implements AlignViewportI
}
}
-
-
public void hideAllSelectedSeqs()
{
if (selectionGroup == null || selectionGroup.getSize() < 1)
@@ -730,7 +931,6 @@ public abstract class AlignmentViewport implements AlignViewportI
setSelectionGroup(null);
}
-
public void hideSequence(SequenceI[] seq)
{
@@ -804,7 +1004,6 @@ public abstract class AlignmentViewport implements AlignViewportI
* broadcast selection to any interested parties
*/
public abstract void sendSelection();
-
public void invertColumnSelection()
{
@@ -815,7 +1014,7 @@ public abstract class AlignmentViewport implements AlignViewportI
* This method returns an array of new SequenceI objects derived from the
* whole alignment or just the current selection with start and end points
* adjusted
- *
+ *
* @note if you need references to the actual SequenceI objects in the
* alignment or currently selected then use getSequenceSelection()
* @return selection as new sequenceI objects
@@ -851,7 +1050,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* get the currently selected sequence objects or all the sequences in the
* alignment.
- *
+ *
* @return array of references to sequence objects
*/
public SequenceI[] getSequenceSelection()
@@ -868,13 +1067,12 @@ public abstract class AlignmentViewport implements AlignViewportI
return sequences;
}
-
/**
* This method returns the visible alignment as text, as seen on the GUI, ie
* if columns are hidden they will not be returned in the result. Use this for
* calculating trees, PCA, redundancy etc on views which contain hidden
* columns.
- *
+ *
* @return String[]
*/
public jalview.datamodel.CigarArray getViewAsCigars(
@@ -888,7 +1086,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* return a compact representation of the current alignment selection to pass
* to an analysis function
- *
+ *
* @param selectedOnly
* boolean true to just return the selected view
* @return AlignmentView
@@ -902,7 +1100,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* return a compact representation of the current alignment selection to pass
* to an analysis function
- *
+ *
* @param selectedOnly
* boolean true to just return the selected view
* @param markGroups
@@ -918,13 +1116,12 @@ public abstract class AlignmentViewport implements AlignViewportI
hasHiddenColumns, selectedOnly, markGroups);
}
-
/**
* This method returns the visible alignment as text, as seen on the GUI, ie
* if columns are hidden they will not be returned in the result. Use this for
* calculating trees, PCA, redundancy etc on views which contain hidden
* columns.
- *
+ *
* @return String[]
*/
public String[] getViewAsString(boolean selectedRegionOnly)
@@ -965,7 +1162,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* return visible region boundaries within given column range
- *
+ *
* @param min
* first column (inclusive, from 0)
* @param max
@@ -1015,6 +1212,7 @@ public abstract class AlignmentViewport implements AlignViewportI
return startEnd;
}
+
/**
* @return the padGaps
*/
@@ -1035,7 +1233,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* apply any post-edit constraints and trigger any calculations needed after
* an edit has been performed on the alignment
- *
+ *
* @param ap
*/
public void alignmentChanged(AlignmentViewPanel ap)
@@ -1059,12 +1257,11 @@ public abstract class AlignmentViewport implements AlignViewportI
// Reset endRes of groups if beyond alignment width
int alWidth = alignment.getWidth();
- Vector groups = alignment.getGroups();
+ List groups = alignment.getGroups();
if (groups != null)
{
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg : groups)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
if (sg.getEndRes() > alWidth)
{
sg.setEndRes(alWidth - 1);
@@ -1082,7 +1279,6 @@ public abstract class AlignmentViewport implements AlignViewportI
// alignment.adjustSequenceAnnotations();
}
-
/**
* reset scope and do calculations for all applied colourschemes on alignment
*/
@@ -1091,13 +1287,7 @@ public abstract class AlignmentViewport implements AlignViewportI
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
- cs.alignmentChanged(alignment);
- // TODO: fold all recalc events for clustalX into alignmentChanged
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
- alignment.getWidth());
- }
+ cs.alignmentChanged(alignment, null);
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
@@ -1108,16 +1298,13 @@ public abstract class AlignmentViewport implements AlignViewportI
}
}
- int s, sSize = alignment.getGroups().size();
- for (s = 0; s < sSize; s++)
+ for (SequenceGroup sg : alignment.getGroups())
{
- SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
- if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+ if (sg.cs != null)
{
- ((ClustalxColourScheme) sg.cs).resetClustalX(sg
- .getSequences(hiddenRepSequences), sg.getWidth());
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
+ sg.recalcConservation();
}
- sg.recalcConservation();
}
}