X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=4b1220b1ab98bb4d23e31c3106c0c5b473ec5ef2;hb=48a66195bf4aee8b2c479d3bbbf4c1fb8b824f5a;hp=2e61f9d6001a9dd17529baae7d6bbf5ef6a09c94;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2e61f9d..4b1220b 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -5,22 +5,21 @@
* 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 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
- * PURPOSE. See the GNU General License for more details.
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General License
+ * You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -48,15 +47,29 @@ public interface AlignmentI extends AnnotatedCollectionI
/**
*
- * Calculates the maximum width of the alignment, including gaps.
+ * Answers the width of the alignment, including gaps, that is, the length of
+ * the longest sequence, or -1 if there are no sequences. Avoid calling this
+ * method repeatedly where possible, as it has to perform a calculation. Note
+ * that this width includes any hidden columns.
*
- * @return Greatest sequence length within alignment, or -1 if no sequences
- * present
+ * @return
+ * @see AlignmentI#getVisibleWidth()
*/
@Override
int getWidth();
/**
+ *
+ * Answers the visible width of the alignment, including gaps, that is, the
+ * length of the longest sequence, excluding any hidden columns. Answers -1 if
+ * there are no sequences. Avoid calling this method repeatedly where
+ * possible, as it has to perform a calculation.
+ *
+ * @return
+ */
+ int getVisibleWidth();
+
+ /**
* Calculates if this set of sequences (visible and invisible) are all the
* same length
*
@@ -389,7 +402,7 @@ public interface AlignmentI extends AnnotatedCollectionI
*
* @return hashtable of alignment properties (or null if none are defined)
*/
- Hashtable getProperties();
+ Map