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JAL-1641 docs for ComplexAlignFile interface
[jalview.git]
/
src
/
jalview
/
api
/
ComplexAlignFile.java
diff --git
a/src/jalview/api/ComplexAlignFile.java
b/src/jalview/api/ComplexAlignFile.java
index
0d731cd
..
92243fb
100644
(file)
--- a/
src/jalview/api/ComplexAlignFile.java
+++ b/
src/jalview/api/ComplexAlignFile.java
@@
-4,14
+4,41
@@
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
+/**
+ * This interface should be implemented by complex file parser with the ability
+ * to store linked data and complex view states in addition to alingment data
+ *
+ * @author tcnofoegbu
+ *
+ */
public interface ComplexAlignFile
{
public interface ComplexAlignFile
{
+ /**
+ * Determines if Sequence features should be shown
+ *
+ * @return
+ */
public boolean isShowSeqFeatures();
public boolean isShowSeqFeatures();
+ /**
+ * Obtains the colour scheme from a complex file parser
+ *
+ * @return
+ */
public ColourSchemeI getColourScheme();
public ColourSchemeI getColourScheme();
+ /**
+ * Retrieves the Column selection/hidden column from a complex file parser
+ *
+ * @return
+ */
public ColumnSelection getColumnSelection();
public ColumnSelection getColumnSelection();
+ /**
+ * Retrieves hidden sequences from a complex file parser
+ *
+ * @return
+ */
public SequenceI[] getHiddenSequences();
}
public SequenceI[] getHiddenSequences();
}