* 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;
-
+*/\r
+package jalview.io;\r
+\r
+\r
/**
* <p>Title: </p>
* PileUpfile
* 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
+import jalview.datamodel.*;\r
+\r
+import jalview.util.*;\r
+\r
+import java.io.*;\r
+\r
+import java.util.*;\r
+\r
+\r
+public class PileUpfile extends AlignFile {\r
+ public PileUpfile() {\r
+ }\r
+\r
+ public PileUpfile(String inStr) {\r
+ super(inStr);\r
+ }\r
+\r
+ public PileUpfile(String inFile, String type) throws IOException {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public void parse() {\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
+ while ((line = nextLine()) != null) {\r
+ StringTokenizer str = new StringTokenizer(line);\r
+\r
+ while (str.hasMoreTokens()) {\r
+ String inStr = str.nextToken();\r
+\r
+ //If line has header information add to the headers vector\r
+ if (inStr.indexOf("Name:") != -1) {\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
+ seqFlag = true;\r
+ }\r
+\r
+ //Process lines as sequence lines if seqFlag is set\r
+ if ((inStr.indexOf("//") == -1) && (seqFlag == true)) {\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
+ tempseq = (StringBuffer) seqhash.get(key);\r
+ } else {\r
+ tempseq = new StringBuffer();\r
+ seqhash.put(key, tempseq);\r
+ }\r
+\r
+ //loop through the rest of the words\r
+ while (str.hasMoreTokens()) {\r
+ //append the word to the sequence\r
+ tempseq.append(str.nextToken());\r
+ }\r
+ }\r
+ }\r
+ }\r
+ } catch (IOException e) {\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
+ if (seqhash.get(headers.elementAt(i)) != null) {\r
+ String head = headers.elementAt(i).toString();\r
+ String seq = seqhash.get(head).toString();\r
+\r
+ int start = 1;\r
+ int end = seq.length();\r
+\r
+ if (maxLength < head.length()) {\r
+ maxLength = head.length();\r
+ }\r
+\r
+ if (head.indexOf("/") > 0) {\r
+ StringTokenizer st = new StringTokenizer(head, "/");\r
+\r
+ if (st.countTokens() == 2) {\r
+ head = st.nextToken();\r
+\r
+ String tmp = st.nextToken();\r
+ st = new StringTokenizer(tmp, "-");\r
+\r
+ if (st.countTokens() == 2) {\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
+ } else {\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
+ //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";\r
+ int check = 0;\r
+\r
+ String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";\r
+ index += "--------------------------------------------------------------------------------------------------------------------------------";\r
+\r
+ for (int i = 0; i < seq.length(); i++) {\r
+ try {\r
+ if (i < seq.length()) {\r
+ int pos = index.indexOf(seq.substring(i, i + 1));\r
+\r
+ if (!index.substring(pos, pos + 1).equals("_")) {\r
+ check += (((i % 57) + 1) * pos);\r
+ }\r
+ }\r
+ } catch (Exception e) {\r
+ System.err.println("Exception during MSF Checksum calculation");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ return check % 10000;\r
+ }\r
+\r
+ public static String print(SequenceI[] s) {\r
+ StringBuffer out = new StringBuffer("PileUp\n\n");\r
+\r
+ int max = 0;\r
+ int maxid = 0;\r
+\r
+ int i = 0;\r
+ String big = "";\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ big += s[i].getSequence();\r
+ i++;\r
+ }\r
+\r
+ i = 0;\r
+\r
+ int bigcheck = checkSum(big);\r
+\r
+ out.append(" MSF: " + s[0].getSequence().length() +\r
+ " Type: P Check: " + bigcheck + " ..\n\n\n");\r
+\r
+ while ((i < s.length) && (s[i] != null)) {\r
+ String seq = s[i].getSequence();\r
+ String name = s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd();\r
+ int check = checkSum(s[i].getSequence());\r
+ out.append(" Name: " + name + " oo Len: " +\r
+ s[i].getSequence().length() + " Check: " + check +\r
+ " Weight: 1.00\n");\r
+\r
+ if (seq.length() > max) {\r
+ max = seq.length();\r
+ }\r
+\r
+ if (name.length() > maxid) {\r
+ maxid = name.length();\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ if (maxid < 10) {\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
+ nochunks--;\r
+ }\r
+\r
+ for (i = 0; i < nochunks; i++) {\r
+ int j = 0;\r
+\r
+ while ((j < s.length) && (s[j] != null)) {\r
+ String name = s[j].getName();\r
+ out.append(new Format("%-" + maxid + "s").form(name + "/" +\r
+ s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+\r
+ for (int k = 0; k < 5; k++) {\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
+ out.append(s[j].getSequence().substring(start, end));\r
+\r
+ if (k < 4) {\r
+ out.append(" ");\r
+ } else {\r
+ out.append("\n");\r
+ }\r
+ } else {\r
+ if (start < s[j].getSequence().length()) {\r
+ out.append(s[j].getSequence().substring(start));\r
+ out.append("\n");\r
+ } else {\r
+ if (k == 0) {\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
+ return print(getSeqsAsArray());\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff