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JAL-2668 add tests for HMMER commands, annotation and io
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
e0efa7c
..
3be48d6
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-22,7
+22,7
@@
package jalview.gui;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
@@
-35,6
+35,7
@@
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
@@
-46,7
+47,6
@@
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
@@
-57,6
+57,7
@@
import jalview.ws.params.AutoCalcSetting;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
+import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
@@
-72,11
+73,11
@@
import javax.swing.JInternalFrame;
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, CommandListener
+ SelectionSource
{
Font font;
{
Font font;
- NJTree currentTree = null;
+ TreeModel currentTree = null;
boolean cursorMode = false;
boolean cursorMode = false;
@@
-105,7
+106,7
@@
public class AlignViewport extends AlignmentViewport implements
*/
public AlignViewport(AlignmentI al)
{
*/
public AlignViewport(AlignmentI al)
{
- setAlignment(al);
+ super(al);
init();
}
init();
}
@@
-123,6
+124,7
@@
public class AlignViewport extends AlignmentViewport implements
public AlignViewport(AlignmentI al, String seqsetid, String viewid)
{
public AlignViewport(AlignmentI al, String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
@@
-135,8
+137,8
@@
public class AlignViewport extends AlignmentViewport implements
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
init();
init();
+
}
/**
}
/**
@@
-147,12
+149,12
@@
public class AlignViewport extends AlignmentViewport implements
* @param hiddenColumns
* ColumnSelection
*/
* @param hiddenColumns
* ColumnSelection
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
{
{
- setAlignment(al);
+ super(al);
if (hiddenColumns != null)
{
if (hiddenColumns != null)
{
- colSel = hiddenColumns;
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
}
init();
}
@@
-165,7
+167,7
@@
public class AlignViewport extends AlignmentViewport implements
* @param seqsetid
* (may be null)
*/
* @param seqsetid
* (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid)
{
this(al, hiddenColumns, seqsetid, null);
String seqsetid)
{
this(al, hiddenColumns, seqsetid, null);
@@
-181,9
+183,10
@@
public class AlignViewport extends AlignmentViewport implements
* @param viewid
* (may be null)
*/
* @param viewid
* (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid, String viewid)
{
String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
@@
-196,10
+199,10
@@
public class AlignViewport extends AlignmentViewport implements
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
+
if (hiddenColumns != null)
{
if (hiddenColumns != null)
{
- colSel = hiddenColumns;
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
}
init();
}
@@
-238,10
+241,6
@@
public class AlignViewport extends AlignmentViewport implements
void init()
{
void init()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@
-282,8
+281,12
@@
public class AlignViewport extends AlignmentViewport implements
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
}
initAutoAnnotation();
+ initInformation();
+
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
@@
-351,23
+354,19
@@
public class AlignViewport extends AlignmentViewport implements
boolean validCharWidth;
/**
boolean validCharWidth;
/**
- * update view settings with the given font. You may need to call
- * alignPanel.fontChanged to update the layout geometry
- *
- * @param setGrid
- * when true, charWidth/height is set according to font mentrics
+ * {@inheritDoc}
*/
*/
+ @Override
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
- .getCharHeight();
if (setGrid)
{
if (setGrid)
{
+ FontMetrics fm = c.getFontMetrics(font);
+ int ww = fm.charWidth('M');
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
@@
-494,7
+493,7
@@
public class AlignViewport extends AlignmentViewport implements
* @param tree
* DOCUMENT ME!
*/
* @param tree
* DOCUMENT ME!
*/
- public void setCurrentTree(NJTree tree)
+ public void setCurrentTree(TreeModel tree)
{
currentTree = tree;
}
{
currentTree = tree;
}
@@
-504,7
+503,7
@@
public class AlignViewport extends AlignmentViewport implements
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public NJTree getCurrentTree()
+ public TreeModel getCurrentTree()
{
return currentTree;
}
{
return currentTree;
}
@@
-530,7
+529,7
@@
public class AlignViewport extends AlignmentViewport implements
{
end = alignment.getWidth();
}
{
end = alignment.getWidth();
}
- viscontigs = colSel.getVisibleContigs(start, end);
+ viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
return viscontigs;
}
return viscontigs;
}
@@
-600,7
+599,9
@@
public class AlignViewport extends AlignmentViewport implements
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(Desktop.instance).sendSelection(
new SequenceGroup(getSelectionGroup()),
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(Desktop.instance).sendSelection(
new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ new ColumnSelection(getColumnSelection()),
+ new HiddenColumns(getAlignment().getHiddenColumns()),
+ this);
}
/**
}
/**
@@
-653,10
+654,10
@@
public class AlignViewport extends AlignmentViewport implements
*/
public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
*/
public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
- List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ List<SequenceI[]> seqvectors = new ArrayList<>();
for (PDBEntry pdb : pdbEntries)
{
for (PDBEntry pdb : pdbEntries)
{
- List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
+ List<SequenceI> choosenSeqs = new ArrayList<>();
for (SequenceI sq : alignment.getSequences())
{
Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
for (SequenceI sq : alignment.getSequences())
{
Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
@@
-704,11
+705,17
@@
public class AlignViewport extends AlignmentViewport implements
return normaliseSequenceLogo;
}
return normaliseSequenceLogo;
}
+
public void setNormaliseSequenceLogo(boolean state)
{
normaliseSequenceLogo = state;
}
public void setNormaliseSequenceLogo(boolean state)
{
normaliseSequenceLogo = state;
}
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ normaliseHMMSequenceLogo = state;
+ }
+
/**
*
* @return true if alignment characters should be displayed
/**
*
* @return true if alignment characters should be displayed
@@
-719,7
+726,7
@@
public class AlignViewport extends AlignmentViewport implements
return validCharWidth;
}
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
@@
-855,7
+862,7
@@
public class AlignViewport extends AlignmentViewport implements
}
}
}
}
- setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight());
firePropertyChange("alignment", null, getAlignment().getSequences());
}
firePropertyChange("alignment", null, getAlignment().getSequences());
}
@@
-1050,8
+1057,9
@@
public class AlignViewport extends AlignmentViewport implements
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
- complementPanel.setDontScrollComplement(true);
+ complementPanel.setToScrollComplementPanel(false);
complementPanel.scrollToCentre(sr, verticalOffset);
complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
}
}
}
}
@@
-1149,4
+1157,12
@@
public class AlignViewport extends AlignmentViewport implements
fr.setTransparency(featureSettings.getTransparency());
}
fr.setTransparency(featureSettings.getTransparency());
}
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return normaliseHMMSequenceLogo;
+ }
+
+
+
}
}