jmol added

[jalview.git] / src / jalview / commands / SlideSequencesCommand.java

diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java
new file mode 100644 (file)
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--- /dev/null
+++ b/src/jalview/commands/SlideSequencesCommand.java
@@ -0,0 +1,93 @@
+\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+*/\r
+\r
+package jalview.commands;\r
+\r
+import jalview.datamodel.*;\r
+\r
+public class SlideSequencesCommand extends EditCommand\r
+{\r
+  boolean gapsInsertedBegin = false;\r
+\r
+  public SlideSequencesCommand(String description,\r
+                               SequenceI[] seqsLeft,\r
+                               SequenceI[] seqsRight,\r
+                               int slideSize,\r
+                               char gapChar)\r
+  {\r
+    this.description = description;\r
+\r
+    int lSize = seqsLeft.length;\r
+    gapsInsertedBegin = false;\r
+    int i, j;\r
+    for (i = 0; i < lSize; i++)\r
+    {\r
+      for (j = 0; j < slideSize; j++)\r
+        if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))\r
+        {\r
+          gapsInsertedBegin = true;\r
+          break;\r
+        }\r
+    }\r
+\r
+    if (!gapsInsertedBegin)\r
+      edits = new Edit[]\r
+          {  new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)};\r
+    else\r
+      edits = new Edit[]\r
+          {  new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)};\r
+\r
+    performEdit(0);\r
+  }\r
+\r
+  public boolean getGapsInsertedBegin()\r
+  {\r
+    return gapsInsertedBegin;\r
+  }\r
+\r
+  public boolean appendSlideCommand(SlideSequencesCommand command)\r
+  {\r
+    boolean same = false;\r
+\r
+    if(command.edits[0].seqs.length==edits[0].seqs.length)\r
+    {\r
+      same = true;\r
+      for (int i = 0; i < command.edits[0].seqs.length; i++)\r
+      {\r
+        if (edits[0].seqs[i] != command.edits[0].seqs[i])\r
+        {\r
+          same = false;\r
+        }\r
+      }\r
+    }\r
+\r
+    if(same)\r
+    {\r
+      Edit[] temp = new Edit[command.edits.length + 1];\r
+      System.arraycopy(command.edits, 0, temp, 0, command.edits.length);\r
+      command.edits = temp;\r
+      command.edits[command.edits.length - 1] = edits[0];\r
+    }\r
+\r
+    return same;\r
+  }\r
+}\r
+\r
+\r