/**
* 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
{
}
/**
- *
- *
+ *
+ *
* @return flag indicating if colourchanges propagated to all groups
*/
public boolean getColourAppliesToAllGroups()
/**
* GUI state
- *
+ *
* @return true if percent identity threshold is applied to shading
*/
public boolean getAbovePIDThreshold()
/**
* GUI state
- *
- *
+ *
+ *
* @param b
* indicate if percent identity threshold is applied to shading
*/
/**
* DOCUMENT ME!
- *
+ *
* @param thresh
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getThreshold()
int increment;
/**
- *
+ *
* @param inc
* set the scalar for bleaching colourschemes according to degree of
* conservation
/**
* GUI State
- *
+ *
* @return get scalar for bleaching colourschemes by conservation
*/
public int getIncrement()
/**
* GUI state
- *
+ *
* @return true if conservation based shading is enabled
*/
public boolean getConservationSelected()
/**
* GUI state
- *
+ *
* @param b
* enable conservation based shading
*/
return;
}
if (calculator
- .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class)==null)
+ .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
{
calculator.registerWorker(new jalview.workers.ConservationThread(
this, ap));
{
return;
}
- if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class)==null)
+ if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
{
calculator.registerWorker(new ConsensusThread(this, ap));
}
{
return;
}
- if (calculator
- .getRegisteredWorkersOfClass(StrucConsensusThread.class)==null)
+ if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
{
calculator.registerWorker(new StrucConsensusThread(this, ap));
}
}
/**
- *
+ *
* @return flag to indicate if the consensus histogram should be rendered by
* default
*/
}
/**
- *
- *
+ *
+ *
* @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)
{
}
/**
- *
+ *
* @return
*/
@Override
/**
* 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)
/**
* 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
* 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
// JBPNote: in applet, this method returned references to the alignment
// sequences, and it did not honour the presence/absence of annotation
// attached to the alignment (probably!)
- if (selectionGroup == null || selectionGroup.getSize()==0)
+ if (selectionGroup == null || selectionGroup.getSize() == 0)
{
sequences = alignment.getSequencesArray();
AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
/**
* get the currently selected sequence objects or all the sequences in the
* alignment.
- *
+ *
* @return array of references to sequence objects
*/
public SequenceI[] getSequenceSelection()
* 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
* 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
/**
* 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)
/*
* (non-Javadoc)
+ *
* @see jalview.api.AlignViewportI#calcPanelHeight()
*/
public int calcPanelHeight()
// setHeight of panels
AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
int height = 0;
- int charHeight=getCharHeight();
+ int charHeight = getCharHeight();
if (aa != null)
{
boolean graphgrp[] = null;
}
}
aa[i].height = 0;
-
+
if (aa[i].hasText)
{
aa[i].height += charHeight;
}
-
+
if (aa[i].hasIcons)
{
aa[i].height += 16;
}
-
+
if (aa[i].graph > 0)
{
aa[i].height += aa[i].graphHeight;
}
-
+
if (aa[i].height == 0)
{
aa[i].height = 20;
}
-
+
height += aa[i].height;
}
}
boolean normLogo = isNormaliseSequenceLogo();
/**
- * TODO reorder the annotation rows according to group/sequence ordering on alignment
+ * TODO reorder the annotation rows according to group/sequence ordering on
+ * alignment
*/
boolean sortg = true;
git://source.jalview.org / jalview.git / blobdiff