/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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.
+ * 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.
*
- * 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
+ * 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/>.
*/
package jalview.appletgui;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
-public class AlignViewport
+public class AlignViewport implements SelectionSource, VamsasSource
{
int startRes;
AlignmentAnnotation conservation;
AlignmentAnnotation quality;
+
AlignmentAnnotation[] groupConsensus;
+
AlignmentAnnotation[] groupConservation;
boolean autocalculateConsensus = true;
boolean ignoreGapsInConsensusCalculation = false;
- jalview.bin.JalviewLite applet;
+ public jalview.bin.JalviewLite applet;
Hashtable sequenceColours;
this.endRes = al.getWidth() - 1;
this.startSeq = 0;
this.endSeq = al.getHeight() - 1;
- if (applet!=null)
+ if (applet != null)
{
// get the width and height scaling factors if they were specified
String param = applet.getParameter("widthScale");
- if (param!=null)
+ if (param != null)
{
- try {
+ try
+ {
widthScale = new Float(param).floatValue();
} catch (Exception e)
{
}
- if (widthScale<=1.0)
+ if (widthScale <= 1.0)
{
- System.err.println("Invalid alignment character width scaling factor ("+widthScale+"). Ignoring.");
+ System.err
+ .println("Invalid alignment character width scaling factor ("
+ + widthScale + "). Ignoring.");
widthScale = 1;
}
if (applet.debug)
{
- System.err.println("Alignment character width scaling factor is now "+widthScale);
+ System.err
+ .println("Alignment character width scaling factor is now "
+ + widthScale);
}
}
param = applet.getParameter("heightScale");
- if (param!=null)
+ if (param != null)
{
- try {
+ try
+ {
heightScale = new Float(param).floatValue();
} catch (Exception e)
{
}
- if (heightScale<=1.0)
+ if (heightScale <= 1.0)
{
- System.err.println("Invalid alignment character height scaling factor ("+heightScale+"). Ignoring.");
+ System.err
+ .println("Invalid alignment character height scaling factor ("
+ + heightScale + "). Ignoring.");
heightScale = 1;
}
if (applet.debug)
{
- System.err.println("Alignment character height scaling factor is now "+heightScale);
+ System.err
+ .println("Alignment character height scaling factor is now "
+ + heightScale);
}
}
}
param = applet.getParameter("sortByTree");
if (param != null)
{
- sortByTree=Boolean.valueOf(param).booleanValue();
+ sortByTree = Boolean.valueOf(param).booleanValue();
+ }
+ param = applet.getParameter("automaticScrolling");
+ if (param!=null) {
+ followHighlight = Boolean.valueOf(param).booleanValue();
+ followSelection = followHighlight;
}
-
}
if (applet != null)
UPDATING_CONSERVATION = true;
- int alWidth = alignment.getWidth();
+ int alWidth = (alignment==null) ? -1 : alignment.getWidth();
if (alWidth < 0)
{
+ updatingConservation = false;
+ UPDATING_CONSERVATION = false;
return;
}
Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3, alignment
- .getSequences(), 0, alWidth - 1);
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth - 1);
cons.calculate();
cons.verdict(false, ConsPercGaps);
maxR = 1.0f - minR;
maxG = 0.9f - minG;
maxB = 0f - minB; // scalable range for colouring both Conservation and
- // Quality
+ // Quality
float min = 0f;
float max = 11f;
{
value = 10;
}
- // TODO - refactor to use a graduatedColorScheme to calculate the histogram colors.
+ // TODO - refactor to use a graduatedColorScheme to calculate the
+ // histogram colors.
float vprop = value - min;
vprop /= max;
conservation.annotations[i] = new Annotation(String.valueOf(c),
value = ((Double) cons.quality.elementAt(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)));
+ quality.annotations[i] = new Annotation(" ",
+ String.valueOf(value), ' ', value, new Color(minR
+ + (maxR * vprop), minG + (maxG * vprop), minB
+ + (maxB * vprop)));
}
}
} catch (OutOfMemoryError error)
try
{
- int aWidth = alignment.getWidth();
+ int aWidth = alignment==null ? -1 : alignment.getWidth();
if (aWidth < 0)
{
+ UPDATING_CONSENSUS = false;
+ updatingConsensus = false;
return;
}
consensus.annotations = new Annotation[aWidth];
hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
- .getWidth(), hconsensus, includeAllConsensusSymbols);
- AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation, includeAllConsensusSymbols);
-
+ AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ alignment.getWidth(), hconsensus, true); // always calculate the
+ // full profile
+ AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
+ ignoreGapsInConsensusCalculation,
+ includeAllConsensusSymbols);
+
if (globalColourScheme != null)
{
globalColourScheme.setConsensus(hconsensus);
protected FeatureSettings featureSettings = null;
- private float heightScale=1,widthScale=1;
+ private float heightScale = 1, widthScale = 1;
public void setFont(Font f)
{
}
java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
- setCharHeight((int)(heightScale*fm.getHeight()));
- charWidth = (int)(widthScale*fm.charWidth('M'));
+ setCharHeight((int) (heightScale * fm.getHeight()));
+ charWidth = (int) (widthScale * fm.charWidth('M'));
if (upperCasebold)
{
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
fm = nullFrame.getGraphics().getFontMetrics(f2);
- charWidth = (int)(widthScale*(fm.stringWidth("MMMMMMMMMMM") / 10));
+ charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
}
}
* Property change listener for changes in alignment
*
* @param listener
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void addPropertyChangeListener(
java.beans.PropertyChangeListener listener)
* DOCUMENT ME!
*
* @param listener
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
* Property change listener for changes in alignment
*
* @param prop
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param oldvalue
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param newvalue
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void firePropertyChange(String prop, Object oldvalue,
Object newvalue)
firePropertyChange("alignment", null, alignment.getSequences());
}
}
+ public void showSequence(int index)
+ {
+ Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ hiddenRepSequences);
+ if (tmp.size() > 0)
+ {
+ if (selectionGroup == null)
+ {
+ selectionGroup = new SequenceGroup();
+ selectionGroup.setEndRes(alignment.getWidth() - 1);
+ }
+
+ for (int t = 0; t < tmp.size(); t++)
+ {
+ selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ }
+ firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
+ }
+ if (alignment.getHiddenSequences().getSize() < 1)
+ {
+ hasHiddenRows = false;
+ }
+ }
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
firePropertyChange("alignment", null, alignment.getSequences());
hasHiddenRows = false;
hiddenRepSequences = null;
+ sendSelection();
}
}
}
/**
+ * get the currently selected sequence objects or all the sequences in the
+ * alignment.
+ *
+ * @return array of references to sequence objects
+ */
+ public SequenceI[] getSequenceSelection()
+ {
+ SequenceI[] sequences = null;
+ if (selectionGroup != null)
+ {
+ sequences = selectionGroup.getSequencesInOrder(alignment);
+ }
+ if (sequences == null)
+ {
+ sequences = alignment.getSequencesArray();
+ }
+ 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
public jalview.datamodel.CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
- CigarArray selection = null;
- SequenceI[] seqs = null;
- int i, iSize;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- iSize = selectionGroup.getSize();
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in
- // SeqCigar constructor
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth() - 1;
- }
- SeqCigar[] selseqs = new SeqCigar[iSize];
- for (i = 0; i < iSize; i++)
- {
- selseqs[i] = new SeqCigar(seqs[i], start, end);
- }
- selection = new CigarArray(selseqs);
- // now construct the CigarArray operations
- if (hasHiddenColumns)
- {
- Vector regions = colSel.getHiddenColumns();
- int[] region;
- int hideStart, hideEnd;
- int last = start;
- for (int j = 0; last < end & j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
- // edit hidden regions to selection range
- if (hideStart < last)
- {
- if (hideEnd > last)
- {
- hideStart = last;
- }
- else
- {
- continue;
- }
- }
-
- if (hideStart > end)
- {
- break;
- }
-
- if (hideEnd > end)
- {
- hideEnd = end;
- }
-
- if (hideStart > hideEnd)
- {
- break;
- }
- /**
- * form operations...
- */
- if (last < hideStart)
- {
- selection.addOperation(CigarArray.M, hideStart - last);
- }
- selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
- last = hideEnd + 1;
- }
- // Final match if necessary.
- if (last < end)
- {
- selection.addOperation(CigarArray.M, end - last + 1);
- }
- }
- else
- {
- selection.addOperation(CigarArray.M, end - start + 1);
- }
- return selection;
+ return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
}
/**
* to an analysis function
*
* @param selectedOnly
- * boolean true to just return the selected view
+ * boolean true to just return the selected view
* @return AlignmentView
*/
jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+ {
+ return getAlignmentView(selectedOnly, false);
+ }
+
+ /**
+ * 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
+ * boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true)
+ * @return AlignmentView
+ */
+ public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups)
{
- // JBPNote:
- // this is here because the AlignmentView constructor modifies the
- // CigarArray
- // object. Refactoring of Cigar and alignment view representation should
- // be done to remove redundancy.
- CigarArray aligview = getViewAsCigars(selectedOnly);
- if (aligview != null)
- {
- return new AlignmentView(aligview,
- (selectedOnly && selectionGroup != null) ? selectionGroup
- .getStartRes() : 0);
- }
- return null;
+ return new AlignmentView(alignment, colSel, selectionGroup, 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
return sequenceSetID;
}
+ /**
+ * unique viewId for synchronizing state (e.g. 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)
{
{
Alignment al = (Alignment) alignment;
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
c.verdict(false, ConsPercGaps);
SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
{
- ((ClustalxColourScheme) sg.cs).resetClustalX(sg
- .getSequences(hiddenRepSequences), sg.getWidth());
+ ((ClustalxColourScheme) sg.cs).resetClustalX(
+ sg.getSequences(hiddenRepSequences), sg.getWidth());
}
sg.recalcConservation();
}
boolean centreColumnLabels;
-
public boolean getCentreColumnLabels()
{
return centreColumnLabels;
}
}
}
- public boolean followHighlight=false;
- public boolean getFollowHighlight() {
+
+ public boolean followHighlight = false;
+
+ 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;
+
+ /**
+ * 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;
+ }
+
/**
* show non-conserved residues only
*/
- public boolean showUnconserved=false;
+ public boolean showUnconserved = false;
/**
* when set, alignment should be reordered according to a newly opened tree
*/
- public boolean sortByTree=false;
+ public boolean sortByTree = false;
/**
* @return the showUnconserved
}
/**
- * @param showUnconserved the showUnconserved to set
+ * @param showNonconserved
+ * the showUnconserved to set
*/
public void setShowunconserved(boolean displayNonconserved)
{
/**
* consensus annotation includes all percentage for all symbols in column
- * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 compatible)
+ * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1
+ * compatible)
*/
- private boolean includeAllConsensusSymbols=false;
-
+ private boolean includeAllConsensusSymbols = false;
+
/**
- * should conservation rows be shown for groups
- * DISABLED FOR 2.5 RELEASE (bug 62446)
+ * should conservation rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
+ * 62446)
*/
boolean showGroupConservation = false;
+
/**
- * should consensus rows be shown for groups
- * DISABLED FOR 2.5 RELEASE (bug 62446)
+ * should consensus rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
+ * 62446)
*/
boolean showGroupConsensus = false;
+
/**
- * should consensus profile be rendered by default
- * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 compatible)
+ * should consensus profile be rendered by default DISABLED FOR 2.5 RELEASE
+ * (bug #60064 logo rendering is not AWT 1.1 compatible)
*/
public boolean showSequenceLogo = false;
+
/**
* should consensus histograms be rendered by default
*/
public boolean showConsensusHistogram = true;
+
/**
* @return the showConsensusProfile
*/
{
return showSequenceLogo;
}
+
/**
- * @param showSequenceLogo the new value
- public void setShowSequenceLogo(boolean showSequenceLogo)
- {
- this.showSequenceLogo = showSequenceLogo;
- }
+ * @param showSequenceLogo
+ * the new value public void setShowSequenceLogo(boolean
+ * showSequenceLogo) { this.showSequenceLogo = showSequenceLogo; }
*/
/**
- * @param showGroupConsensus the showGroupConsensus to set
+ * @param showGroupConsensus
+ * the showGroupConsensus to set
*/
public void setShowGroupConsensus(boolean showGroupConsensus)
{
this.showGroupConsensus = showGroupConsensus;
}
+
/**
* @return the includeAllConsensusSymbols
*/
{
return false;
}
-
+
/**
*
- * @return flag to indicate if the consensus histogram should be rendered by default
+ * @return flag to indicate if the consensus histogram should be rendered by
+ * default
*/
public boolean isShowConsensusHistogram()
{
return this.showConsensusHistogram;
}
+
+ /**
+ * 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 void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager().sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
+
+
}
git://source.jalview.org / jalview.git / blobdiff