-/*\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
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class AMSAFile\r
- extends jalview.io.FastaFile\r
-{\r
-\r
- AlignmentI al;\r
- /**\r
- * Creates a new AMSAFile object for output.\r
- */\r
- public AMSAFile(AlignmentI al)\r
- {\r
- this.al = al;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- super.print(getSeqsAsArray());\r
-\r
- AlignmentAnnotation aa;\r
- if (al.getAlignmentAnnotation() != null)\r
- {\r
-\r
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
- {\r
- aa = al.getAlignmentAnnotation()[i];\r
-\r
-\r
- if (aa.autoCalculated || !aa.visible)\r
- {\r
- continue;\r
- }\r
-\r
- out.append(">#_" + aa.label);\r
- if (aa.description != null)\r
- {\r
- out.append(" " + aa.description);\r
- }\r
-\r
- out.append("\n");\r
-\r
- int nochunks = Math.min(aa.annotations.length, al.getWidth())\r
- / len + 1;\r
-\r
- for (int j = 0; j < nochunks; j++)\r
- {\r
- int start = j * len;\r
- int end = start + len;\r
- if (end > aa.annotations.length)\r
- {\r
- end = aa.annotations.length;\r
- }\r
-\r
- String ch;\r
- for (int k = start; k < end; k++)\r
- {\r
- if (aa.annotations[k] == null)\r
- {\r
- ch = " ";\r
- }\r
- else\r
- {\r
- ch = aa.annotations[k].displayCharacter;\r
- }\r
-\r
- out.append(ch);\r
-\r
- }\r
- out.append("\n");\r
- }\r
- }\r
- }\r
- return out.toString();\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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 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 Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+
+public class AMSAFile extends jalview.io.FastaFile
+{
+
+ AlignmentI al;
+
+ /**
+ * Creates a new AMSAFile object for output.
+ */
+ public AMSAFile(AlignmentI al)
+ {
+ this.al = al;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ super.print(getSeqsAsArray());
+
+ AlignmentAnnotation aa;
+ if (al.getAlignmentAnnotation() != null)
+ {
+
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+ {
+ aa = al.getAlignmentAnnotation()[i];
+
+ if (aa.autoCalculated || !aa.visible)
+ {
+ continue;
+ }
+
+ out.append(">#_" + aa.label);
+ if (aa.description != null)
+ {
+ out.append(" " + aa.description);
+ }
+
+ out.append(newline);
+
+ int nochunks = Math.min(aa.annotations.length, al.getWidth()) / len
+ + 1;
+
+ for (int j = 0; j < nochunks; j++)
+ {
+ int start = j * len;
+ int end = start + len;
+ if (end > aa.annotations.length)
+ {
+ end = aa.annotations.length;
+ }
+
+ String ch;
+ for (int k = start; k < end; k++)
+ {
+ if (aa.annotations[k] == null)
+ {
+ ch = " ";
+ }
+ else
+ {
+ ch = aa.annotations[k].displayCharacter;
+ }
+ if (ch.length() > 1)
+ {
+ this.warningMessage = "Truncated column annotation to first letter.";
+ ch = ch.substring(0, 1);
+ }
+ out.append(ch);
+
+ }
+ out.append(newline);
+ }
+ }
+ }
+ return out.toString();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff