-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FastaFile extends AlignFile\r
-{\r
- /**\r
- * Creates a new FastaFile object.\r
- */\r
- public FastaFile()\r
- {\r
- }\r
-\r
- /**\r
- * Creates a new FastaFile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public FastaFile(String inFile, String type) throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public void parse() throws IOException\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- boolean firstLine = true;\r
-\r
- String line;\r
- Sequence seq = null;\r
-\r
- boolean annotation = false;\r
-\r
- while ((line = nextLine()) != null)\r
- {\r
- line = line.trim();\r
- if (line.length() > 0)\r
- {\r
- if (line.charAt(0)=='>')\r
- {\r
- if (line.startsWith(">#_"))\r
- {\r
- if (annotation)\r
- {\r
- Annotation[] anots = new Annotation[sb.length()];\r
- String anotString = sb.toString();\r
- for (int i = 0; i < sb.length(); i++)\r
- {\r
- anots[i] = new Annotation(anotString.substring(i, i+1),\r
- null,\r
- ' ', 0);\r
- }\r
- AlignmentAnnotation aa = new AlignmentAnnotation(\r
- seq.getName().substring(2), seq.getDescription(),\r
- anots);\r
-\r
- annotations.addElement(aa);\r
- }\r
- annotation = true;\r
- }\r
- else\r
- annotation = false;\r
-\r
- if (!firstLine)\r
- {\r
- if (!annotation && !isValidProteinSequence(sb.toString().toCharArray()))\r
- {\r
- throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
- +" : "+seq.getName()\r
- +" : "+invalidCharacter);\r
- }\r
-\r
- seq.setSequence(sb.toString());\r
-\r
- if (!annotation)\r
- seqs.addElement(seq);\r
- }\r
-\r
- seq = parseId(line.substring(1));\r
- firstLine = false;\r
-\r
- sb = new StringBuffer();\r
- }\r
- else\r
- {\r
- sb.append(line);\r
- }\r
- }\r
- }\r
-\r
- if (annotation)\r
- {\r
- Annotation[] anots = new Annotation[sb.length()];\r
- String anotString = sb.toString();\r
- for (int i = 0; i < sb.length(); i++)\r
- {\r
- anots[i] = new Annotation(anotString.substring(i, i + 1),\r
- null,\r
- ' ', 0);\r
- }\r
- AlignmentAnnotation aa = new AlignmentAnnotation(\r
- seq.getName().substring(2), seq.getDescription(),\r
- anots);\r
-\r
- annotations.addElement(aa);\r
- }\r
-\r
- else if (!firstLine)\r
- {\r
-\r
- if (!isValidProteinSequence(sb.toString().toCharArray()))\r
- {\r
- throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
- +" : "+seq.getName()\r
- +" : "+invalidCharacter);\r
- }\r
-\r
- seq.setSequence(sb.toString());\r
- seqs.addElement(seq);\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- * @param gaps DOCUMENT ME!\r
- * @param displayId DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print(SequenceI[] s)\r
- {\r
- int len = 72;\r
- StringBuffer out = new StringBuffer();\r
- int i = 0;\r
-\r
- while ((i < s.length) && (s[i] != null))\r
- {\r
- out.append(">" + printId(s[i]));\r
- if(s[i].getDescription()!=null)\r
- out.append(" "+s[i].getDescription());\r
-\r
- out.append("\n");\r
-\r
- int nochunks = (s[i].getLength() / len) + 1;\r
-\r
- for (int j = 0; j < nochunks; j++)\r
- {\r
- int start = j * len;\r
- int end = start + len;\r
-\r
- if (end < s[i].getLength())\r
- {\r
- out.append(s[i].getSequenceAsString(start, end) + "\n");\r
- }\r
- else if (start < s[i].getLength())\r
- {\r
- out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");\r
- }\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return out.toString();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\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.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FastaFile extends AlignFile
+{
+ /**
+ * Length of a sequence line
+ */
+ int len = 72;
+
+ StringBuffer out;
+
+ /**
+ * Creates a new FastaFile object.
+ */
+ public FastaFile()
+ {
+ }
+
+ /**
+ * Creates a new FastaFile object.
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public FastaFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public FastaFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public void parse() throws IOException
+ {
+ StringBuffer sb = new StringBuffer();
+ boolean firstLine = true;
+
+ String line, uline;
+ Sequence seq = null;
+
+ boolean annotation = false;
+
+ while ((uline = nextLine()) != null)
+ {
+ line = uline.trim();
+ if (line.length() > 0)
+ {
+ if (line.charAt(0) == '>')
+ {
+ if (line.startsWith(">#_"))
+ {
+ if (annotation)
+ {
+ annotations.addElement(makeAnnotation(seq, sb));
+ }
+ }
+ else
+ {
+ annotation = false;
+ }
+
+ if (!firstLine)
+ {
+ seq.setSequence(sb.toString());
+
+ if (!annotation)
+ {
+ seqs.addElement(seq);
+ }
+ }
+
+ seq = parseId(line.substring(1));
+ firstLine = false;
+
+ sb = new StringBuffer();
+
+ if (line.startsWith(">#_"))
+ {
+ annotation = true;
+ }
+ }
+ else
+ {
+ sb.append(annotation ? uline : line);
+ }
+ }
+ }
+
+ if (annotation)
+ {
+ annotations.addElement(makeAnnotation(seq, sb));
+ }
+
+ else if (!firstLine)
+ {
+ seq.setSequence(sb.toString());
+ seqs.addElement(seq);
+ }
+ }
+
+ private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
+ {
+ Annotation[] anots = new Annotation[sb.length()];
+ char cb;
+ for (int i = 0; i < anots.length; i++)
+ {
+ char cn = sb.charAt(i);
+ if (cn != ' ')
+ {
+ anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
+ }
+ }
+ AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
+ .substring(2), seq.getDescription(), anots);
+ return aa;
+ }
+
+ /**
+ * called by AppletFormatAdapter to generate an annotated alignment, rather
+ * than bare sequences.
+ *
+ * @param al
+ */
+ public void addAnnotations(Alignment al)
+ {
+ addProperties(al);
+ for (int i = 0; i < annotations.size(); i++)
+ {
+ AlignmentAnnotation aa = (AlignmentAnnotation) annotations
+ .elementAt(i);
+ aa.setPadGaps(true, al.getGapCharacter());
+ al.addAnnotation(aa);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param len
+ * DOCUMENT ME!
+ * @param gaps
+ * DOCUMENT ME!
+ * @param displayId
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print(SequenceI[] s)
+ {
+ out = new StringBuffer();
+ int i = 0;
+
+ while ((i < s.length) && (s[i] != null))
+ {
+ out.append(">" + printId(s[i]));
+ if (s[i].getDescription() != null)
+ {
+ out.append(" " + s[i].getDescription());
+ }
+
+ out.append(newline);
+
+ int nochunks = (s[i].getLength() / len) + 1;
+
+ for (int j = 0; j < nochunks; j++)
+ {
+ int start = j * len;
+ int end = start + len;
+
+ if (end < s[i].getLength())
+ {
+ out.append(s[i].getSequenceAsString(start, end) + newline);
+ }
+ else if (start < s[i].getLength())
+ {
+ out.append(s[i].getSequenceAsString(start, s[i].getLength())
+ + newline);
+ }
+ }
+
+ i++;
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+}
git://source.jalview.org / jalview.git / blobdiff