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JAL-98 ProfilesI container for profiles for columns
[jalview.git]
/
src
/
jalview
/
api
/
AlignViewportI.java
diff --git
a/src/jalview/api/AlignViewportI.java
b/src/jalview/api/AlignViewportI.java
index
8343f0b
..
8b80531
100644
(file)
--- a/
src/jalview/api/AlignViewportI.java
+++ b/
src/jalview/api/AlignViewportI.java
@@
-26,6
+26,7
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
@@
-53,6
+54,18
@@
public interface AlignViewportI extends ViewStyleI
*/
public int calcPanelHeight();
*/
public int calcPanelHeight();
+ /**
+ * Answers true if the viewport has at least one column selected
+ *
+ * @return
+ */
+ boolean hasSelectedColumns();
+
+ /**
+ * Answers true if the viewport has at least one hidden column
+ *
+ * @return
+ */
boolean hasHiddenColumns();
boolean isValidCharWidth();
boolean hasHiddenColumns();
boolean isValidCharWidth();
@@
-69,7
+82,7
@@
public interface AlignViewportI extends ViewStyleI
ColumnSelection getColumnSelection();
ColumnSelection getColumnSelection();
- Hashtable[] getSequenceConsensusHash();
+ ProfilesI getSequenceConsensusHash();
/**
* Get consensus data table for the cDNA complement of this alignment (if any)
/**
* Get consensus data table for the cDNA complement of this alignment (if any)
@@
-110,6
+123,11
@@
public interface AlignViewportI extends ViewStyleI
boolean isClosed();
/**
boolean isClosed();
/**
+ * Dispose of all references or resources held by the viewport
+ */
+ void dispose();
+
+ /**
* get the associated calculation thread manager for the view
*
* @return
* get the associated calculation thread manager for the view
*
* @return
@@
-127,7
+145,7
@@
public interface AlignViewportI extends ViewStyleI
*
* @param hconsensus
*/
*
* @param hconsensus
*/
- void setSequenceConsensusHash(Hashtable[] hconsensus);
+ void setSequenceConsensusHash(ProfilesI hconsensus);
/**
* Set the cDNA complement consensus for the viewport
/**
* Set the cDNA complement consensus for the viewport
@@
-243,7
+261,7
@@
public interface AlignViewportI extends ViewStyleI
* @return String[]
*/
String[] getViewAsString(boolean selectedRegionOnly);
* @return String[]
*/
String[] getViewAsString(boolean selectedRegionOnly);
-
+
/**
* 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
/**
* 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
@@
-258,7
+276,8
@@
public interface AlignViewportI extends ViewStyleI
*
* @return String[]
*/
*
* @return String[]
*/
- String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
+ String[] getViewAsString(boolean selectedRegionOnly,
+ boolean isExportHiddenSeqs);
void setSelectionGroup(SequenceGroup sg);
void setSelectionGroup(SequenceGroup sg);
@@
-395,6
+414,13
@@
public interface AlignViewportI extends ViewStyleI
*/
void setFollowHighlight(boolean b);
*/
void setFollowHighlight(boolean b);
-
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+ /**
+ * check if current selection group is defined on the view, or is simply a
+ * temporary group.
+ *
+ * @return true if group is defined on the alignment
+ */
+ boolean isSelectionDefinedGroup();
}
}