/*
- * 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;
AlignmentAnnotation quality;
+ AlignmentAnnotation[] groupConsensus;
+
+ AlignmentAnnotation[] groupConservation;
+
boolean autocalculateConsensus = true;
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
this.endRes = al.getWidth() - 1;
this.startSeq = 0;
this.endSeq = al.getHeight() - 1;
+ if (applet != null)
+ {
+ // get the width and height scaling factors if they were specified
+ String param = applet.getParameter("widthScale");
+ if (param != null)
+ {
+ try
+ {
+ widthScale = new Float(param).floatValue();
+ } catch (Exception e)
+ {
+ }
+ if (widthScale <= 1.0)
+ {
+ 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);
+ }
+ }
+ param = applet.getParameter("heightScale");
+ if (param != null)
+ {
+ try
+ {
+ heightScale = new Float(param).floatValue();
+ } catch (Exception e)
+ {
+ }
+ if (heightScale <= 1.0)
+ {
+ 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);
+ }
+ }
+ }
setFont(font);
MAC = new jalview.util.Platform().isAMac();
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);
-
- 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);
- }
+ .getWidth(), hconsensus, true); // always calculate the full profile
+ AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
+ ignoreGapsInConsensusCalculation,
+ includeAllConsensusSymbols);
if (globalColourScheme != null)
{
*
* @return consensus sequence as a new sequence object
*/
- /**
- * 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)
protected FeatureSettings featureSettings = null;
+ private float heightScale = 1, widthScale = 1;
+
public void setFont(Font f)
{
font = f;
}
java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
- setCharHeight(fm.getHeight());
- charWidth = 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 = 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)
}
/**
+ * 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
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 showNonconserved
+ * the showUnconserved to set
*/
public void setShowunconserved(boolean displayNonconserved)
{
this.showUnconserved = 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)
+ */
+ private boolean includeAllConsensusSymbols = false;
+
+ /**
+ * 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)
+ */
+ 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)
+ */
+ public boolean showSequenceLogo = false;
+
+ /**
+ * should consensus histograms be rendered by default
+ */
+ public boolean showConsensusHistogram = true;
+
+ /**
+ * @return the showConsensusProfile
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
+ /**
+ * @param showSequenceLogo
+ * the new value public void setShowSequenceLogo(boolean
+ * showSequenceLogo) { this.showSequenceLogo = showSequenceLogo; }
+ */
+ /**
+ * @param showGroupConsensus
+ * the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+
+ /**
+ * @return the includeAllConsensusSymbols
+ */
+ public boolean isIncludeAllConsensusSymbols()
+ {
+ return false;
+ }
+
+ /**
+ *
+ * @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);
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff