/*
- * 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 2.5)
+ * 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;
AlignmentAnnotation conservation;
AlignmentAnnotation quality;
+
AlignmentAnnotation[] groupConsensus;
+
AlignmentAnnotation[] groupConservation;
boolean autocalculateConsensus = true;
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();
}
}
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),
hconsensus = new Hashtable[aWidth];
AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
.getWidth(), hconsensus, includeAllConsensusSymbols);
- AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation, includeAllConsensusSymbols);
-
+ 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)
return sequences;
}
+
/**
* get the currently selected sequence objects or all the sequences in the
* alignment.
*/
public SequenceI[] getSequenceSelection()
{
- SequenceI[] sequences=null;
- if (selectionGroup!=null)
+ SequenceI[] sequences = null;
+ if (selectionGroup != null)
{
sequences = selectionGroup.getSequencesInOrder(alignment);
}
}
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
seqs = selectionGroup.getSequencesInOrder(alignment);
start = selectionGroup.getStartRes();
end = selectionGroup.getEndRes(); // inclusive for start and end in
- // SeqCigar constructor
+ // SeqCigar constructor
}
else
{
* 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)
boolean centreColumnLabels;
-
public boolean getCentreColumnLabels()
{
return centreColumnLabels;
}
}
}
- public boolean followHighlight=false;
- public boolean getFollowHighlight() {
+
+ public boolean followHighlight = false;
+
+ public boolean getFollowHighlight()
+ {
return followHighlight;
}
+
/**
* 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 showUnconserved
+ * 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.
+ * 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
+ * @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))
+ 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))
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
{
- // do nothing
+ // do nothing
return;
}
- if (colSel==null)
+ if (colSel == null)
{
colSel = new ColumnSelection();
}
- for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) {
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
colSel.addElement(cspos);
}
- }
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff