From 451619e33c0a90c8130c7d79ffa38161af1c6e0f Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 21 Dec 2006 13:36:28 +0000 Subject: [PATCH] remove unnecessary import --- src/jalview/datamodel/Alignment.java | 2 - src/jalview/datamodel/AlignmentI.java | 2 - src/jalview/gui/Jalview2XML.java | 2 - src/jalview/gui/Jalview2XML_V1.java | 2 - src/jalview/gui/SequenceFetcher.java | 2 +- src/jalview/gui/VamsasClient.java | 1 - src/jalview/io/JPredFile.java | 812 +++++++++++++++---------------- src/jalview/io/JnetAnnotationMaker.java | 2 +- src/jalview/io/VamsasDatastore.java | 1 - src/jalview/util/ShiftList.java | 2 - src/jalview/ws/JPredClient.java | 5 - src/jalview/ws/JPredThread.java | 2 - src/jalview/ws/MsaWSThread.java | 3 +- 13 files changed, 409 insertions(+), 429 deletions(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index b5f31bc..9a2db89 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -20,8 +20,6 @@ package jalview.datamodel; import jalview.analysis.*; -import jalview.util.*; - import java.util.*; /** Data structure to hold and manipulate a multiple sequence alignment diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index 94dbf1b..12baabf 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -18,8 +18,6 @@ */ package jalview.datamodel; -import jalview.util.ShiftList; - import java.util.*; diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index a9763d3..f1f7db1 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -21,8 +21,6 @@ package jalview.gui; import jalview.schemes.*; -import jalview.gui.*; - import java.io.*; import java.net.*; diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index b347864..62f6df0 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -20,8 +20,6 @@ package jalview.gui; import jalview.schemes.*; -import jalview.gui.*; - import java.io.*; import java.net.*; diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 0756299..f4e289b 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -356,7 +356,7 @@ public class SequenceFetcher "\n" + ( (PDBChain) pdbfile.chains.elementAt(i)).sequence. - getSequence()); + getSequenceAsString()); } } catch (Exception ex) // Problem parsing PDB file diff --git a/src/jalview/gui/VamsasClient.java b/src/jalview/gui/VamsasClient.java index b97e181..6d9e94d 100755 --- a/src/jalview/gui/VamsasClient.java +++ b/src/jalview/gui/VamsasClient.java @@ -4,7 +4,6 @@ package jalview.gui; import java.io.File; -import java.io.FileOutputStream; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.util.Hashtable; diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index 92d5414..c431cc4 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,406 +1,406 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 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 -*/ - -/** - * PredFile.java - * JalviewX / Vamsas Project - * JPred.seq.concise reader - */ -package jalview.io; - -import java.io.*; -import java.util.*; - -import jalview.datamodel.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class JPredFile extends AlignFile -{ - Vector ids; - Vector conf; - Hashtable Scores; // Hash of names and score vectors - Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector - private int QuerySeqPosition; - - - /** - * Creates a new JPredFile object. - * - * @param inFile DOCUMENT ME! - * @param type DOCUMENT ME! - * - * @throws IOException DOCUMENT ME! - */ - public JPredFile(String inFile, String type) throws IOException - { - super(inFile, type); - } - - /** - * DOCUMENT ME! - * - * @param QuerySeqPosition DOCUMENT ME! - */ - public void setQuerySeqPosition(int QuerySeqPosition) - { - this.QuerySeqPosition = QuerySeqPosition; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getQuerySeqPosition() - { - return QuerySeqPosition; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Hashtable getScores() - { - return Scores; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Hashtable getSymscores() - { - return Symscores; - } - - /** - * DOCUMENT ME! - */ - public void initData() - { - super.initData(); - Scores = new Hashtable(); - ids = null; - conf = null; - } - - /** - * parse a JPred concise file into a sequence-alignment like object. - */ - public void parse() throws IOException - { - // JBPNote log.System.out.println("all read in "); - String line; - QuerySeqPosition = -1; - noSeqs = 0; - - Vector seq_entries = new Vector(); - Vector ids = new Vector(); - Hashtable Symscores = new Hashtable(); - - while ((line = nextLine()) != null) - { - // Concise format allows no comments or non comma-formatted data - StringTokenizer str = new StringTokenizer(line, ":"); - String id = ""; - - if (!str.hasMoreTokens()) - { - continue; - } - - id = str.nextToken(); - - String seqsym = str.nextToken(); - StringTokenizer symbols = new StringTokenizer(seqsym, ","); - - // decide if we have more than just alphanumeric symbols - int numSymbols = symbols.countTokens(); - - if (numSymbols == 0) - { - continue; - } - - if (seqsym.length() != (2 * numSymbols)) - { - // Set of scalars for some property - if (Scores.containsKey(id)) - { - int i = 1; - - while (Scores.containsKey(id + "_" + i)) - { - i++; - } - - id = id + "_" + i; - } - - Vector scores = new Vector(); - - // Typecheck from first entry - int i = 0; - String ascore = "dead"; - - try - { - // store elements as floats... - while (symbols.hasMoreTokens()) - { - ascore = symbols.nextToken(); - - Float score = new Float(ascore); - scores.addElement((Object) score); - } - - Scores.put(id, scores); - } - catch (Exception e) - { - // or just keep them as strings - i = scores.size(); - - for (int j = 0; j < i; j++) - { - scores.setElementAt( - (Object) ((Float) scores.elementAt(j)).toString(), j); - } - - scores.addElement((Object) ascore); - - while (symbols.hasMoreTokens()) - { - ascore = symbols.nextToken(); - scores.addElement((Object) ascore); - } - - Scores.put(id, scores); - } - } - else if (id.equals("jnetconf")) - { - // log.debug System.out.println("here"); - id = "Prediction Confidence"; - this.conf = new Vector(numSymbols); - - for (int i = 0; i < numSymbols; i++) - { - conf.setElementAt( symbols.nextToken(), i); - } - } - else - { - // Sequence or a prediction string (rendered as sequence) - StringBuffer newseq = new StringBuffer(); - - for (int i = 0; i < numSymbols; i++) - { - newseq.append(symbols.nextToken()); - } - - if (id.indexOf(";") > -1) - { - seq_entries.addElement(newseq); - - int i = 1; - String name = id.substring(id.indexOf(";") + 1); - - while (ids.lastIndexOf(name) > -1) - { - name = id.substring(id.indexOf(";") + 1) + "_" + ++i; - } - - ids.addElement(name); - - noSeqs++; - } - else - { - if (id.equals("JNETPRED")) - { - id = "Predicted Secondary Structure"; - } - - seq_entries.addElement(newseq.toString()); - ids.addElement(id); - Symscores.put((Object) id, - (Object) new Integer(ids.size() - 1)); - } - } - } - /* leave it to the parser user to actually check this. - if (noSeqs < 1) - { - throw new IOException( - "JpredFile Parser: No sequence in the prediction!"); - }*/ - - maxLength = seq_entries.elementAt(0).toString().length(); - - for (int i = 0; i < ids.size(); i++) - { - // Add all sequence like objects - Sequence newSeq = new Sequence(ids.elementAt(i).toString(), - seq_entries.elementAt(i).toString(), 1, - seq_entries.elementAt(i).toString().length()); - - if (!Symscores.containsKey(ids.elementAt(i)) && - !isValidProteinSequence(newSeq.getSequence())) - { - throw new IOException("JPredConcise: " - +AppletFormatAdapter.INVALID_CHARACTERS +" : " - +ids.elementAt(i).toString() + ")"); - } - - if (maxLength != seq_entries.elementAt(i).toString().length()) - { - throw new IOException("JPredConcise: Entry (" + - ids.elementAt(i).toString() + - ") has an unexpected number of columns"); - } - - if (newSeq.getName().startsWith("QUERY") && - (QuerySeqPosition == -1)) - { - QuerySeqPosition = seqs.size(); - } - - seqs.addElement(newSeq); - } - } - - /** - * print - * - * @return String - */ - public String print() - { - return "Not Supported"; - } - - /** - * DOCUMENT ME! - * - * @param args DOCUMENT ME! - */ - public static void main(String[] args) - { - try - { - JPredFile blc = new JPredFile(args[0], "File"); - - for (int i = 0; i < blc.seqs.size(); i++) - { - System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() + - "\n" + ((Sequence) blc.seqs.elementAt(i)).getSequence() + - "\n"); - } - } - catch (java.io.IOException e) - { - System.err.println("Exception " + e); - e.printStackTrace(); - } - } - Vector annotSeqs=null; - /** - * removeNonSequences - */ - public void removeNonSequences() - { - if (annotSeqs!=null) - return; - annotSeqs = new Vector(); - Vector newseqs = new Vector(); - int i=0; - int j=seqs.size(); - for (; i -1) + { + seq_entries.addElement(newseq); + + int i = 1; + String name = id.substring(id.indexOf(";") + 1); + + while (ids.lastIndexOf(name) > -1) + { + name = id.substring(id.indexOf(";") + 1) + "_" + ++i; + } + + ids.addElement(name); + + noSeqs++; + } + else + { + if (id.equals("JNETPRED")) + { + id = "Predicted Secondary Structure"; + } + + seq_entries.addElement(newseq.toString()); + ids.addElement(id); + Symscores.put((Object) id, + (Object) new Integer(ids.size() - 1)); + } + } + } + /* leave it to the parser user to actually check this. + if (noSeqs < 1) + { + throw new IOException( + "JpredFile Parser: No sequence in the prediction!"); + }*/ + + maxLength = seq_entries.elementAt(0).toString().length(); + + for (int i = 0; i < ids.size(); i++) + { + // Add all sequence like objects + Sequence newSeq = new Sequence(ids.elementAt(i).toString(), + seq_entries.elementAt(i).toString(), 1, + seq_entries.elementAt(i).toString().length()); + + if (!Symscores.containsKey(ids.elementAt(i)) && + !isValidProteinSequence(newSeq.getSequence())) + { + throw new IOException("JPredConcise: " + +AppletFormatAdapter.INVALID_CHARACTERS +" : " + +ids.elementAt(i).toString() + ")"); + } + + if (maxLength != seq_entries.elementAt(i).toString().length()) + { + throw new IOException("JPredConcise: Entry (" + + ids.elementAt(i).toString() + + ") has an unexpected number of columns"); + } + + if (newSeq.getName().startsWith("QUERY") && + (QuerySeqPosition == -1)) + { + QuerySeqPosition = seqs.size(); + } + + seqs.addElement(newSeq); + } + } + + /** + * print + * + * @return String + */ + public String print() + { + return "Not Supported"; + } + + /** + * DOCUMENT ME! + * + * @param args DOCUMENT ME! + */ + public static void main(String[] args) + { + try + { + JPredFile blc = new JPredFile(args[0], "File"); + + for (int i = 0; i < blc.seqs.size(); i++) + { + System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() + + "\n" + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString() + + "\n"); + } + } + catch (java.io.IOException e) + { + System.err.println("Exception " + e); + e.printStackTrace(); + } + } + Vector annotSeqs=null; + /** + * removeNonSequences + */ + public void removeNonSequences() + { + if (annotSeqs!=null) + return; + annotSeqs = new Vector(); + Vector newseqs = new Vector(); + int i=0; + int j=seqs.size(); + for (; i sw) { // pad at end - alseqs[i].setSequence(t_alseqs[i].getSequence() + + alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() + insbuff.substring(0, sw - nw)); } } -- 1.7.10.2