/*\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
+ * 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
-import jalview.util.*;\r
-\r
import java.io.*;\r
-\r
import java.util.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.util.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class MSFfile extends AlignFile\r
+public class MSFfile\r
+ extends AlignFile\r
{\r
\r
-\r
- /**\r
- * Creates a new MSFfile object.\r
- */\r
- public MSFfile()\r
- {\r
- }\r
-\r
-\r
- /**\r
- * Creates a new MSFfile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public MSFfile(String inFile, String type) throws IOException\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ */\r
+ public MSFfile()\r
+ {\r
+ }\r
+\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public MSFfile(String inFile, String type)\r
+ throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void parse()\r
+ throws IOException\r
+ {\r
+ int i = 0;\r
+ boolean seqFlag = false;\r
+ String key = new String();\r
+ Vector headers = new Vector();\r
+ Hashtable seqhash = new Hashtable();\r
+ String line;\r
+\r
+ try\r
{\r
- super(inFile, type);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void parse() throws IOException\r
- {\r
- int i = 0;\r
- boolean seqFlag = false;\r
- String key = new String();\r
- Vector headers = new Vector();\r
- Hashtable seqhash = new Hashtable();\r
- String line;\r
-\r
- try\r
- {\r
- while ((line = nextLine()) != null)\r
- {\r
- StringTokenizer str = new StringTokenizer(line);\r
-\r
- while (str.hasMoreTokens())\r
- {\r
- String inStr = str.nextToken();\r
-\r
- //If line has header information add to the headers vector\r
- if (inStr.indexOf("Name:") != -1)\r
- {\r
- key = str.nextToken();\r
- headers.addElement(key);\r
- }\r
-\r
- //if line has // set SeqFlag to 1 so we know sequences are coming\r
- if (inStr.indexOf("//") != -1)\r
- {\r
- seqFlag = true;\r
- }\r
-\r
- //Process lines as sequence lines if seqFlag is set\r
- if ((inStr.indexOf("//") == -1) && (seqFlag == true))\r
- {\r
- //seqeunce id is the first field\r
- key = inStr;\r
-\r
- StringBuffer tempseq;\r
-\r
- //Get sequence from hash if it exists\r
- if (seqhash.containsKey(key))\r
- {\r
- tempseq = (StringBuffer) seqhash.get(key);\r
- }\r
- else\r
- {\r
- tempseq = new StringBuffer();\r
- seqhash.put(key, tempseq);\r
- }\r
-\r
- //loop through the rest of the words\r
- while (str.hasMoreTokens())\r
- {\r
- //append the word to the sequence\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
- }\r
- catch (IOException e)\r
- {\r
- System.err.println("Exception parsing MSFFile " + e);\r
- e.printStackTrace();\r
- }\r
-\r
- this.noSeqs = headers.size();\r
+ while ( (line = nextLine()) != null)\r
+ {\r
+ StringTokenizer str = new StringTokenizer(line);\r
\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++)\r
+ while (str.hasMoreTokens())\r
{\r
- if (seqhash.get(headers.elementAt(i)) != null)\r
- {\r
- String head = headers.elementAt(i).toString();\r
- String seq = seqhash.get(head).toString();\r
+ String inStr = str.nextToken();\r
\r
- if (maxLength < head.length())\r
- {\r
- maxLength = head.length();\r
- }\r
+ //If line has header information add to the headers vector\r
+ if (inStr.indexOf("Name:") != -1)\r
+ {\r
+ key = str.nextToken();\r
+ headers.addElement(key);\r
+ }\r
\r
- // Replace ~ with a sensible gap character\r
- seq = seq.replace('~', '-');\r
+ //if line has // set SeqFlag to 1 so we know sequences are coming\r
+ if (inStr.indexOf("//") != -1)\r
+ {\r
+ seqFlag = true;\r
+ }\r
\r
- Sequence newSeq = parseId(head);\r
+ //Process lines as sequence lines if seqFlag is set\r
+ if ( (inStr.indexOf("//") == -1) && (seqFlag == true))\r
+ {\r
+ //seqeunce id is the first field\r
+ key = inStr;\r
\r
- newSeq.setSequence(seq);\r
+ StringBuffer tempseq;\r
\r
- seqs.addElement(newSeq);\r
+ //Get sequence from hash if it exists\r
+ if (seqhash.containsKey(key))\r
+ {\r
+ tempseq = (StringBuffer) seqhash.get(key);\r
}\r
else\r
{\r
- System.err.println("MSFFile Parser: Can't find sequence for " +\r
- headers.elementAt(i));\r
+ tempseq = new StringBuffer();\r
+ seqhash.put(key, tempseq);\r
+ }\r
+\r
+ //loop through the rest of the words\r
+ while (str.hasMoreTokens())\r
+ {\r
+ //append the word to the sequence\r
+ tempseq.append(str.nextToken());\r
}\r
+ }\r
}\r
+ }\r
+ }\r
+ catch (IOException e)\r
+ {\r
+ System.err.println("Exception parsing MSFFile " + e);\r
+ e.printStackTrace();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int checkSum(String seq)\r
+ this.noSeqs = headers.size();\r
+\r
+ //Add sequences to the hash\r
+ for (i = 0; i < headers.size(); i++)\r
{\r
- int check = 0;\r
- String sequence = seq.toUpperCase();\r
+ if (seqhash.get(headers.elementAt(i)) != null)\r
+ {\r
+ String head = headers.elementAt(i).toString();\r
+ String seq = seqhash.get(head).toString();\r
\r
- for (int i = 0; i < sequence.length(); i++)\r
+ if (maxLength < head.length())\r
{\r
- try\r
- {\r
-\r
- int value = sequence.charAt(i);\r
- if (value!=-1)\r
- {\r
- check += (i % 57 +1) * value;\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Exception during MSF Checksum calculation");\r
- e.printStackTrace();\r
- }\r
+ maxLength = head.length();\r
}\r
\r
- return check % 10000;\r
- }\r
+ // Replace ~ with a sensible gap character\r
+ seq = seq.replace('~', '-');\r
\r
+ Sequence newSeq = parseId(head);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param is_NA DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print(SequenceI[] seqs)\r
- {\r
+ newSeq.setSequence(seq);\r
\r
- boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);\r
+ seqs.addElement(newSeq);\r
+ }\r
+ else\r
+ {\r
+ System.err.println("MSFFile Parser: Can't find sequence for " +\r
+ headers.elementAt(i));\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int checkSum(String seq)\r
+ {\r
+ int check = 0;\r
+ String sequence = seq.toUpperCase();\r
+\r
+ for (int i = 0; i < sequence.length(); i++)\r
+ {\r
+ try\r
+ {\r
\r
- SequenceI [] s = new SequenceI[seqs.length];\r
+ int value = sequence.charAt(i);\r
+ if (value != -1)\r
+ {\r
+ check += (i % 57 + 1) * value;\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ System.err.println("Exception during MSF Checksum calculation");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
\r
- StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
- "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
+ return check % 10000;\r
+ }\r
\r
- int max = 0;\r
- int maxid = 0;\r
- int i = 0;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param is_NA DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print(SequenceI[] seqs)\r
+ {\r
\r
- while ((i < seqs.length) && (seqs[i] != null))\r
- {\r
- // Replace all internal gaps with . and external spaces with ~\r
- s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequenceAsString().replace('-', '.'));\r
+ boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);\r
\r
- StringBuffer sb = new StringBuffer();\r
- sb.append(s[i].getSequence());\r
+ SequenceI[] s = new SequenceI[seqs.length];\r
\r
- for (int ii = 0; ii < sb.length(); ii++)\r
- {\r
- if (sb.charAt(ii) == '.')\r
- {\r
- sb.setCharAt(ii, '~');\r
- }\r
- else\r
- break;\r
- }\r
+ StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
+ "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
\r
- for (int ii = sb.length() - 1; ii > 0; ii--)\r
- {\r
- if (sb.charAt(ii) == '.')\r
- {\r
- sb.setCharAt(ii,'~');\r
- }\r
- else\r
- break;\r
- }\r
+ int max = 0;\r
+ int maxid = 0;\r
+ int i = 0;\r
\r
- s[i].setSequence(sb.toString());\r
+ while ( (i < seqs.length) && (seqs[i] != null))\r
+ {\r
+ // Replace all internal gaps with . and external spaces with ~\r
+ s[i] = new Sequence(seqs[i].getName(),\r
+ seqs[i].getSequenceAsString().replace('-', '.'));\r
\r
- if (s[i].getSequence().length > max)\r
- {\r
- max = s[i].getSequence().length;\r
- }\r
+ StringBuffer sb = new StringBuffer();\r
+ sb.append(s[i].getSequence());\r
\r
- i++;\r
+ for (int ii = 0; ii < sb.length(); ii++)\r
+ {\r
+ if (sb.charAt(ii) == '.')\r
+ {\r
+ sb.setCharAt(ii, '~');\r
}\r
+ else\r
+ {\r
+ break;\r
+ }\r
+ }\r
\r
- Format maxLenpad = new Format("%" + (new String("" + max)).length() +\r
- "d");\r
- Format maxChkpad = new Format("%" + (new String("1" + max)).length() +\r
- "d");\r
- i = 0;\r
-\r
- int bigChecksum = 0;\r
- int [] checksums = new int[s.length];\r
- while ( i < s.length )\r
+ for (int ii = sb.length() - 1; ii > 0; ii--)\r
+ {\r
+ if (sb.charAt(ii) == '.')\r
+ {\r
+ sb.setCharAt(ii, '~');\r
+ }\r
+ else\r
{\r
- checksums[i] = checkSum(s[i].getSequenceAsString());\r
- bigChecksum += checksums[i];\r
- i++;\r
+ break;\r
}\r
+ }\r
\r
- long maxNB = 0;\r
- out.append(" MSF: " + s[0].getSequence().length + " Type: " +\r
- (is_NA ? "N" : "P") + " Check: " + (bigChecksum%10000) + " ..\n\n\n");\r
+ s[i].setSequence(sb.toString());\r
\r
- String[] nameBlock = new String[s.length];\r
- String[] idBlock = new String[s.length];\r
+ if (s[i].getSequence().length > max)\r
+ {\r
+ max = s[i].getSequence().length;\r
+ }\r
\r
- i=0;\r
- while ((i < s.length) && (s[i] != null))\r
- {\r
+ i++;\r
+ }\r
\r
- nameBlock[i] = new String(" Name: " + printId(s[i])+" ");\r
+ Format maxLenpad = new Format("%" + (new String("" + max)).length() +\r
+ "d");\r
+ Format maxChkpad = new Format("%" + (new String("1" + max)).length() +\r
+ "d");\r
+ i = 0;\r
\r
- idBlock[i] = new String("Len: " +\r
- maxLenpad.form(s[i].getSequence().length) + " Check: " +\r
- maxChkpad.form(checksums[i]) + " Weight: 1.00\n");\r
+ int bigChecksum = 0;\r
+ int[] checksums = new int[s.length];\r
+ while (i < s.length)\r
+ {\r
+ checksums[i] = checkSum(s[i].getSequenceAsString());\r
+ bigChecksum += checksums[i];\r
+ i++;\r
+ }\r
\r
- if (s[i].getName().length() > maxid)\r
- {\r
- maxid = s[i].getName().length();\r
- }\r
+ long maxNB = 0;\r
+ out.append(" MSF: " + s[0].getSequence().length + " Type: " +\r
+ (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000) +\r
+ " ..\n\n\n");\r
\r
- if (nameBlock[i].length() > maxNB)\r
- {\r
- maxNB = nameBlock[i].length();\r
- }\r
+ String[] nameBlock = new String[s.length];\r
+ String[] idBlock = new String[s.length];\r
\r
- i++;\r
- }\r
+ i = 0;\r
+ while ( (i < s.length) && (s[i] != null))\r
+ {\r
\r
- if (maxid < 10)\r
- {\r
- maxid = 10;\r
- }\r
+ nameBlock[i] = new String(" Name: " + printId(s[i]) + " ");\r
\r
- if (maxNB < 15)\r
- {\r
- maxNB = 15;\r
- }\r
+ idBlock[i] = new String("Len: " +\r
+ maxLenpad.form(s[i].getSequence().length) +\r
+ " Check: " +\r
+ maxChkpad.form(checksums[i]) + " Weight: 1.00\n");\r
\r
- Format nbFormat = new Format("%-" + maxNB + "s");\r
+ if (s[i].getName().length() > maxid)\r
+ {\r
+ maxid = s[i].getName().length();\r
+ }\r
\r
- for (i = 0; (i < s.length) && (s[i] != null); i++)\r
- {\r
- out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);\r
- }\r
+ if (nameBlock[i].length() > maxNB)\r
+ {\r
+ maxNB = nameBlock[i].length();\r
+ }\r
\r
- maxid++;\r
- out.append("\n\n//\n\n");\r
+ i++;\r
+ }\r
\r
- int len = 50;\r
+ if (maxid < 10)\r
+ {\r
+ maxid = 10;\r
+ }\r
\r
- int nochunks = (max / len) + 1;\r
+ if (maxNB < 15)\r
+ {\r
+ maxNB = 15;\r
+ }\r
\r
- if ((max % len) == 0)\r
- {\r
- nochunks--;\r
- }\r
+ Format nbFormat = new Format("%-" + maxNB + "s");\r
+\r
+ for (i = 0; (i < s.length) && (s[i] != null); i++)\r
+ {\r
+ out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);\r
+ }\r
+\r
+ maxid++;\r
+ out.append("\n\n//\n\n");\r
+\r
+ int len = 50;\r
+\r
+ int nochunks = (max / len) + 1;\r
+\r
+ if ( (max % len) == 0)\r
+ {\r
+ nochunks--;\r
+ }\r
+\r
+ for (i = 0; i < nochunks; i++)\r
+ {\r
+ int j = 0;\r
\r
- for (i = 0; i < nochunks; i++)\r
+ while ( (j < s.length) && (s[j] != null))\r
+ {\r
+ String name = printId(s[j]);\r
+\r
+ out.append(new Format("%-" + maxid + "s").form(name + " "));\r
+\r
+ for (int k = 0; k < 5; k++)\r
{\r
- int j = 0;\r
+ int start = (i * 50) + (k * 10);\r
+ int end = start + 10;\r
+\r
+ if ( (end < s[j].getSequence().length) &&\r
+ (start < s[j].getSequence().length))\r
+ {\r
+ out.append(s[j].getSequence(start, end));\r
\r
- while ((j < s.length) && (s[j] != null))\r
+ if (k < 4)\r
{\r
- String name = printId( s[j] );\r
-\r
- out.append(new Format("%-" + maxid + "s").form(name+" "));\r
-\r
-\r
- for (int k = 0; k < 5; k++)\r
- {\r
- int start = (i * 50) + (k * 10);\r
- int end = start + 10;\r
-\r
- if ((end < s[j].getSequence().length) &&\r
- (start < s[j].getSequence().length))\r
- {\r
- out.append(s[j].getSequence(start, end));\r
-\r
- if (k < 4)\r
- {\r
- out.append(" ");\r
- }\r
- else\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- else\r
- {\r
- if (start < s[j].getSequence().length)\r
- {\r
- out.append(s[j].getSequenceAsString().substring(start));\r
- out.append("\n");\r
- }\r
- else\r
- {\r
- if (k == 0)\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- }\r
- }\r
-\r
- j++;\r
+ out.append(" ");\r
}\r
-\r
- out.append("\n");\r
+ else\r
+ {\r
+ out.append("\n");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (start < s[j].getSequence().length)\r
+ {\r
+ out.append(s[j].getSequenceAsString().substring(start));\r
+ out.append("\n");\r
+ }\r
+ else\r
+ {\r
+ if (k == 0)\r
+ {\r
+ out.append("\n");\r
+ }\r
+ }\r
+ }\r
}\r
\r
- return out.toString();\r
- }\r
+ j++;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
+ out.append("\n");\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
git://source.jalview.org / jalview.git / blobdiff