X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=9f879c0d459de738fb5498dd865cff5033cea766;hb=e657ed3c87bbdbaef21efe142d8123f29617d357;hp=387596d8b6dc5fc161d3f04d6bfda1e7d955e144;hpb=5b1e100f2def37f936bfc48a541261648c533aa6;p=jalview.git
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 387596d..9f879c0 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,5 +1,24 @@
-package jalview.io;
-
+/*
+* 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;
+
+
/**
* Title:
* PileUpfile
@@ -10,239 +29,248 @@ package jalview.io;
* 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 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());
-}
-}
-
-
-
-
-
-
-
+ **/
+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());
+ }
+}