/*
* 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 <http://www.gnu.org/licenses/>.
*/
package jalview.viewmodel;
/**
* 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
{
globalColourScheme = cs;
}
+ @Override
public ColourSchemeI getGlobalColourScheme()
{
return globalColourScheme;
*/
int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+ @Override
public int getConsPercGaps()
{
return ConsPercGaps;
}
+
@Override
public void setSequenceConsensusHash(Hashtable[] hconsensus)
{
return calculator.isWorking();
}
+ @Override
public boolean isCalculationInProgress(
AlignmentAnnotation alignmentAnnotation)
{
* 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
*/
/**
* @return the showConsensusProfile
*/
+ @Override
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
}
/**
- *
+ *
* @return flag to indicate if the consensus histogram should be rendered by
* default
*/
+ @Override
public boolean isShowConsensusHistogram()
{
return this.showConsensusHistogram;
*/
protected boolean showUnconserved = false;
-
/**
* when set, updateAlignment will always ensure sequences are of equal length
*/
}
/**
- *
- *
+ *
+ *
* @return null or the currently selected sequence region
*/
public SequenceGroup getSelectionGroup()
/**
* Set the selection group for this window.
- *
+ *
* @param sg
* - group holding references to sequences in this alignment view
- *
+ *
*/
public void setSelectionGroup(SequenceGroup sg)
{
}
}
+ @Override
public ColumnSelection getColumnSelection()
{
return colSel;
/**
* unique viewId for synchronizing state (e.g. with stored Jalview Project)
- *
+ *
*/
protected String viewId = null;
/**
* 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)
/**
* 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)
return false;
}
+ @Override
public boolean getIgnoreGapsConsensus()
{
return ignoreGapsInConsensusCalculation;
// / 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;
protected boolean showConsensus = true;
-
/**
* Property change listener for changes in alignment
- *
+ *
* @param listener
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param listener
* DOCUMENT ME!
*/
/**
* Property change listener for changes in alignment
- *
+ *
* @param prop
* DOCUMENT ME!
* @param oldvalue
}
// common hide/show column stuff
-
public void hideSelectedColumns()
{
hasHiddenColumns = false;
}
-
// common hide/show seq stuff
public void showAllHiddenSeqs()
{
}
}
-
-
public void hideAllSelectedSeqs()
{
if (selectionGroup == null || selectionGroup.getSize() < 1)
setSelectionGroup(null);
}
-
public void hideSequence(SequenceI[] seq)
{
* broadcast selection to any interested parties
*/
public abstract void sendSelection();
-
public void invertColumnSelection()
{
* 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
/**
* get the currently selected sequence objects or all the sequences in the
* alignment.
- *
+ *
* @return array of references to sequence objects
*/
public SequenceI[] getSequenceSelection()
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(
/**
* 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
/**
* 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
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)
/**
* return visible region boundaries within given column range
- *
+ *
* @param min
* first column (inclusive, from 0)
* @param max
return startEnd;
}
+
/**
* @return the padGaps
*/
/**
* 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)
git://source.jalview.org / jalview.git / commitdiff