-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.io;
-
-/**
- * <p>Title: </p>
- * PileUpfile
- * <p>Description: </p>
- *
- * Read and write PileUp style MSF Files.
- * This used to be the MSFFile class, and was written according to the EBI's idea
- * of a subset of the MSF alignment format. But, that was updated to reflect current
- * GCG style IO fashion, as found in Emboss (thanks David Martin!)
- *
- **/
-
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-import java.io.*;
-import java.util.*;
-
-
-public class PileUpfile
- extends AlignFile
-{
-
-public PileUpfile()
-{}
-
-public PileUpfile(String inStr) {
- super(inStr);
-}
-
-public PileUpfile(String inFile, String type) throws IOException {
- super(inFile,type);
-}
-
-public void parse() {
-
- int i = 0;
- boolean seqFlag = false;
- String key = new String();
- Vector headers = new Vector();
- Hashtable seqhash = new Hashtable();
- String line;
-
- try {
- while ((line = nextLine()) != null) {
-
- StringTokenizer str = new StringTokenizer(line);
-
- while (str.hasMoreTokens()) {
-
- String inStr = str.nextToken();
-
- //If line has header information add to the headers vector
- if (inStr.indexOf("Name:") != -1) {
- key = str.nextToken();
- headers.addElement(key);
- }
-
- //if line has // set SeqFlag to 1 so we know sequences are coming
- if (inStr.indexOf("//") != -1) {
- seqFlag = true;
- }
-
- //Process lines as sequence lines if seqFlag is set
- if (( inStr.indexOf("//") == -1) && (seqFlag == true)) {
- //seqeunce id is the first field
- key = inStr;
- StringBuffer tempseq;
-
- //Get sequence from hash if it exists
- if (seqhash.containsKey(key)) {
- tempseq = (StringBuffer)seqhash.get(key);
- } else {
- tempseq = new StringBuffer();
- seqhash.put(key,tempseq);
- }
-
- //loop through the rest of the words
- while (str.hasMoreTokens()) {
- //append the word to the sequence
- tempseq.append(str.nextToken());
- }
- }
- }
- }
- } catch (IOException e) {
- System.err.println("Exception parsing PileUpfile " + e);
- e.printStackTrace();
- }
-
- this.noSeqs = headers.size();
-
- //Add sequences to the hash
- for (i = 0; i < headers.size(); i++ ) {
-
- if ( seqhash.get(headers.elementAt(i)) != null) {
- String head = headers.elementAt(i).toString();
- String seq = seqhash.get(head).toString();
-
- int start = 1;
- int end = seq.length();
-
- if (maxLength < head.length() ) {
- maxLength = head.length();
- }
-
- if (head.indexOf("/") > 0 ) {
-
- StringTokenizer st = new StringTokenizer(head,"/");
-
- if (st.countTokens() == 2) {
-
- head = st.nextToken();
- String tmp = st.nextToken();
- st = new StringTokenizer(tmp,"-");
- if (st.countTokens() == 2) {
- start = Integer.valueOf(st.nextToken()).intValue();
- end = Integer.valueOf(st.nextToken()).intValue();
- }
- }
- }
-
- Sequence newSeq = new Sequence(head,seq,start,end);
-
- seqs.addElement(newSeq);
-
- } else {
- System.err.println("PileUpfile Parser: Can't find sequence for " + headers.elementAt(i));
- }
- }
-
-}
-
-public static int checkSum(String seq) {
- //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
- int check = 0;
-
- String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
- index += "--------------------------------------------------------------------------------------------------------------------------------";
-
- for(int i = 0; i < seq.length(); i++) {
- try {
- if (i <seq.length()) {
- int pos = index.indexOf(seq.substring(i,i+1));
- if (!index.substring(pos,pos+1).equals("_")) {
- check += ((i % 57) + 1) * pos;
- }
- }
- } catch (Exception e) {
- System.err.println("Exception during MSF Checksum calculation");
- e.printStackTrace();
- }
- }
- return check % 10000;
-}
-
-public static String print(SequenceI[] s) {
- StringBuffer out = new StringBuffer("PileUp\n\n");
-
- int max = 0;
- int maxid = 0;
-
- int i = 0;
- String big = "";
- while (i < s.length && s[i] != null) {
- big += s[i].getSequence();
- i++;
- }
- i = 0;
- int bigcheck = checkSum(big);
-
- out.append(" MSF: " + s[0].getSequence().length() + " Type: P Check: " + bigcheck + " ..\n\n\n");
-
- while (i < s.length && s[i] != null) {
- String seq = s[i].getSequence();
- String name = s[i].getName()+ "/" + s[i].getStart() + "-" + s[i].getEnd();
- int check = checkSum(s[i].getSequence());
- out.append(" Name: " + name + " oo Len: " + s[i].getSequence().length() + " Check: " + check + " Weight: 1.00\n");
- if (seq.length() > max) {
- max = seq.length();
- }
- if (name.length() > maxid) {
- maxid = name.length();
- }
- i++;
- }
-
- if (maxid < 10) {
- maxid = 10;
- }
- maxid++;
- out.append( "\n\n//\n\n");
-
- int len = 50;
-
- int nochunks = max / len + 1;
- if (max%len == 0) {
- nochunks--;
- }
- for (i = 0; i < nochunks; i++) {
- int j = 0;
- while (j < s.length && s[j] != null) {
- String name = s[j].getName();
- out.append( new Format("%-" + maxid + "s").form(name + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
- for (int k = 0; k < 5; k++) {
-
- int start = i*50 + k*10;
- int end = start + 10;
-
- if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
- out.append(s[j].getSequence().substring(start,end));
- if (k < 4) {
- out.append(" ");
- } else {
- out.append("\n");
- }
- } else {
- if (start < s[j].getSequence().length()) {
- out.append(s[j].getSequence().substring(start));
- out.append("\n");
- } else {
- if (k == 0) {
- out.append("\n");
- }
- }
- }
- }
- j++;
- }
- out.append("\n");
-
- }
- return out.toString();
-}
-public String print() {
- return print(getSeqsAsArray());
-}
-}
-
-
-
-
-
-
-
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
+/**\r
+ * <p>Title: </p>\r
+ * PileUpfile\r
+ * <p>Description: </p>\r
+ *\r
+ * Read and write PileUp style MSF Files.\r
+ * This used to be the MSFFile class, and was written according to the EBI's idea\r
+ * of a subset of the MSF alignment format. But, that was updated to reflect current\r
+ * GCG style IO fashion, as found in Emboss (thanks David Martin!)\r
+ *\r
+ **/\r
+import java.io.*;\r
+import java.util.*;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.util.*;\r
+\r
+public class PileUpfile\r
+ extends AlignFile\r
+{\r
+ public PileUpfile()\r
+ {\r
+ }\r
+\r
+ public PileUpfile(String inStr)\r
+ {\r
+ super(inStr);\r
+ }\r
+\r
+ public PileUpfile(String inFile, String type)\r
+ throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public void parse()\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 PileUpfile " + e);\r
+ e.printStackTrace();\r
+ }\r
+\r
+ this.noSeqs = headers.size();\r
+\r
+ //Add sequences to the hash\r
+ for (i = 0; i < headers.size(); i++)\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
+\r
+ int start = 1;\r
+ int end = -1;\r
+\r
+ if (maxLength < head.length())\r
+ {\r
+ maxLength = head.length();\r
+ }\r
+\r
+ if (head.indexOf("/") > 0)\r
+ {\r
+ StringTokenizer st = new StringTokenizer(head, "/");\r
+\r
+ if (st.countTokens() == 2)\r
+ {\r
+ head = st.nextToken();\r
+\r
+ String tmp = st.nextToken();\r
+ st = new StringTokenizer(tmp, "-");\r
+\r
+ if (st.countTokens() == 2)\r
+ {\r
+ start = Integer.valueOf(st.nextToken()).intValue();\r
+ end = Integer.valueOf(st.nextToken()).intValue();\r
+ }\r
+ }\r
+ }\r
+\r
+ Sequence newSeq = new Sequence(head, seq, start, end);\r
+\r
+ seqs.addElement(newSeq);\r
+ }\r
+ else\r
+ {\r
+ System.err.println(\r
+ "PileUpfile Parser: Can't find sequence for " +\r
+ headers.elementAt(i));\r
+ }\r
+ }\r
+ }\r
+\r
+ public static int checkSum(String seq)\r
+ {\r
+\r
+ int check = 0;\r
+\r
+ String sequence = seq.toUpperCase();\r
+\r
+ for (int i = 0; i < sequence.length(); i++)\r
+ {\r
+ if (i < sequence.length())\r
+ {\r
+ int value = sequence.charAt(i);\r
+ if (value != -1)\r
+ {\r
+ check += (i % 57 + 1) * value;\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ return check % 10000;\r
+ }\r
+\r
+ public static String print(SequenceI[] s)\r
+ {\r
+ StringBuffer out = new StringBuffer("PileUp\n\n");\r
+\r
+ int max = 0;\r
+ int maxid = 0;\r
+\r
+ int i = 0;\r
+ int bigChecksum = 0;\r
+ int[] checksums = new int[s.length];\r
+ while (i < s.length)\r
+ {\r
+ checksums[i] = checkSum(s[i].getSequence());\r
+ bigChecksum += checksums[i];\r
+ i++;\r
+ }\r
+\r
+ out.append(" MSF: " + s[0].getSequence().length() +\r
+ " Type: P Check: " + bigChecksum%10000 + " ..\n\n\n");\r
+\r
+ i=0;\r
+ while ( (i < s.length) && (s[i] != null))\r
+ {\r
+ String seq = s[i].getSequence();\r
+ out.append(" Name: " + s[i].getName() + " oo Len: " +\r
+ s[i].getSequence().length() + " Check: " + checksums[i] +\r
+ " Weight: 1.00\n");\r
+\r
+ if (seq.length() > max)\r
+ {\r
+ max = seq.length();\r
+ }\r
+\r
+ if (s[i].getName().length() > maxid)\r
+ {\r
+ maxid = s[i].getName().length();\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ if (maxid < 10)\r
+ {\r
+ maxid = 10;\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
+ while ( (j < s.length) && (s[j] != null))\r
+ {\r
+ String name = s[j].getName();\r
+ out.append(new Format("%-" + maxid + "s").form(name) + " ");\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().substring(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].getSequence().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
+ }\r
+\r
+ out.append("\n");\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ public String print()\r
+ {\r
+ return print(getSeqsAsArray());\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff