X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=a43dc42ad400bddad9197261b064d74a5762268f;hb=e75315ad5faf541f6943e9395c81a078369f2f63;hp=ec5d267bc70fde34932b668ed2faeed91ae69893;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index ec5d267..a43dc42 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -26,19 +26,21 @@ // TODO: Extended SequenceNodeI to hold parsed NHX strings package jalview.io; -import java.util.Locale; - -import jalview.datamodel.SequenceNode; -import jalview.util.MessageManager; - import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; +import java.util.Locale; import java.util.StringTokenizer; import com.stevesoft.pat.Regex; +import jalview.bin.Jalview; +import jalview.bin.Jalview.ExitCode; +import jalview.datamodel.BinaryNode; +import jalview.datamodel.SequenceNode; +import jalview.util.MessageManager; + /** * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the * tree distances and topology are unreliable when they are parsed. TODO: on @@ -78,7 +80,7 @@ import com.stevesoft.pat.Regex; */ public class NewickFile extends FileParse { - SequenceNode root; + BinaryNode root; private boolean HasBootstrap = false; @@ -145,7 +147,7 @@ public class NewickFile extends FileParse * @param newtree * DOCUMENT ME! */ - public NewickFile(SequenceNode newtree) + public NewickFile(BinaryNode newtree) { root = newtree; } @@ -174,7 +176,7 @@ public class NewickFile extends FileParse * @param distances * DOCUMENT ME! */ - public NewickFile(SequenceNode newtree, boolean bootstrap, + public NewickFile(BinaryNode newtree, boolean bootstrap, boolean distances) { root = newtree; @@ -194,7 +196,7 @@ public class NewickFile extends FileParse * @param rootdistance * DOCUMENT ME! */ - public NewickFile(SequenceNode newtree, boolean bootstrap, + public NewickFile(BinaryNode newtree, boolean bootstrap, boolean distances, boolean rootdistance) { root = newtree; @@ -275,8 +277,8 @@ public class NewickFile extends FileParse root = new SequenceNode(); - SequenceNode realroot = null; - SequenceNode c = root; + BinaryNode realroot = null; + BinaryNode c = root; int d = -1; int cp = 0; @@ -286,18 +288,17 @@ public class NewickFile extends FileParse String nodename = null; String commentString2 = null; // comments after simple node props - float DefDistance = (float) 0.001; // @param Default distance for a node - + double DefDistance = (float) 0.001; // @param Default distance for a node - // very very small int DefBootstrap = -1; // @param Default bootstrap for a node - float distance = DefDistance; + double distance = DefDistance; int bootstrap = DefBootstrap; boolean ascending = false; // flag indicating that we are leaving the // current node - Regex majorsyms = new Regex( - "[(\\['),;]"); + Regex majorsyms = new Regex("[(\\['),;]"); int nextcp = 0; int ncp = cp; @@ -324,21 +325,21 @@ public class NewickFile extends FileParse { c.setRight(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false)); - c = (SequenceNode) c.right(); + c = c.right(); } else { if (c.left() != null) { // Dummy node for polytomy - keeps c.left free for new node - SequenceNode tmpn = new SequenceNode(null, c, null, 0, 0, true); + BinaryNode tmpn = new SequenceNode(null, c, null, 0, 0, true); tmpn.SetChildren(c.left(), c.right()); c.setRight(tmpn); } c.setLeft(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false)); - c = (SequenceNode) c.left(); + c = c.left(); } if (realroot == null) @@ -356,8 +357,7 @@ public class NewickFile extends FileParse // Deal with quoted fields case '\'': - Regex qnodename = new Regex( - "'([^']|'')+'"); + Regex qnodename = new Regex("'([^']|'')+'"); if (qnodename.searchFrom(nf, fcp)) { @@ -365,8 +365,7 @@ public class NewickFile extends FileParse nodename = new String( qnodename.stringMatched().substring(1, nl - 1)); // unpack any escaped colons - Regex xpandquotes = Regex - .perlCode("s/''/'/"); + Regex xpandquotes = Regex.perlCode("s/''/'/"); String widernodename = xpandquotes.replaceAll(nodename); nodename = widernodename; // jump to after end of quoted nodename @@ -396,12 +395,11 @@ public class NewickFile extends FileParse // node string contains Comment or structured/extended NH format info /* * if ((fcp-cp>1 && nf.substring(cp,fcp).trim().length()>1)) { // will - * process in remains System.err.println("skipped text: + * process in remains jalview.bin.Console.errPrintln("skipped text: * '"+nf.substring(cp,fcp)+"'"); } */ // verify termination. - Regex comment = new Regex( - "]"); + Regex comment = new Regex("]"); if (comment.searchFrom(nf, fcp)) { // Skip the comment field @@ -432,12 +430,9 @@ public class NewickFile extends FileParse + fstring.substring(cend + 1); } - Regex uqnodename = new Regex( - "\\b([^' :;\\](),]+)"); - Regex nbootstrap = new Regex( - "\\s*([0-9+]+)\\s*:"); - Regex ndist = new Regex( - ":([-0-9Ee.+]+)"); + Regex uqnodename = new Regex("\\b([^' :;\\](),]+)"); + Regex nbootstrap = new Regex("\\s*([0-9+]+)\\s*:"); + Regex ndist = new Regex(":([-0-9Ee.+]+)"); if (!parsednodename && uqnodename.search(fstring) && ((uqnodename.matchedFrom(1) == 0) || (fstring @@ -494,7 +489,8 @@ public class NewickFile extends FileParse { try { - distance = (Float.valueOf(ndist.stringMatched(1))).floatValue(); + distance = (Double.valueOf(ndist.stringMatched(1))) + .floatValue(); HasDistances = true; nodehasdistance = true; } catch (Exception e) @@ -525,7 +521,7 @@ public class NewickFile extends FileParse else { // Find a place to put the leaf - SequenceNode newnode = new SequenceNode(null, c, nodename, + BinaryNode newnode = new SequenceNode(null, c, nodename, (HasDistances) ? distance : DefDistance, (HasBootstrap) ? bootstrap : DefBootstrap, false); parseNHXNodeProps(c, commentString2); @@ -545,7 +541,7 @@ public class NewickFile extends FileParse { // Insert a dummy node for polytomy // dummy nodes have distances - SequenceNode newdummy = new SequenceNode(null, c, null, + BinaryNode newdummy = new SequenceNode(null, c, null, (HasDistances ? 0 : DefDistance), 0, true); newdummy.SetChildren(c.left(), newnode); c.setLeft(newdummy); @@ -584,7 +580,7 @@ public class NewickFile extends FileParse // Just advance focus, if we need to if ((c.left() != null) && (!c.left().isLeaf())) { - c = (SequenceNode) c.left(); + c = c.left(); } } } @@ -622,7 +618,7 @@ public class NewickFile extends FileParse } // THe next line is failing for topali trees - not sure why yet. if // (root.right()!=null && root.isDummy()) - root = (SequenceNode) root.right().detach(); // remove the imaginary root. + root = root.right().detach(); // remove the imaginary root. if (!RootHasDistance) { @@ -638,7 +634,7 @@ public class NewickFile extends FileParse * @param commentString * @param commentString2 */ - private void parseNHXNodeProps(SequenceNode c, String commentString) + private void parseNHXNodeProps(BinaryNode c, String commentString) { // TODO: store raw comment on the sequenceNode so it can be recovered when // tree is output @@ -670,7 +666,7 @@ public class NewickFile extends FileParse // more codes here. } catch (Exception e) { - System.err.println( + jalview.bin.Console.errPrintln( "Couldn't parse code '" + code + "' = '" + value + "'"); e.printStackTrace(System.err); } @@ -685,7 +681,7 @@ public class NewickFile extends FileParse * * @return DOCUMENT ME! */ - public SequenceNode getTree() + public BinaryNode getTree() { return root; } @@ -839,7 +835,7 @@ public class NewickFile extends FileParse * * @return DOCUMENT ME! */ - private String printNodeField(SequenceNode c) + private String printNodeField(BinaryNode c) { return ((c.getName() == null) ? "" : nodeName(c.getName())) + ((HasBootstrap) ? ((c.getBootstrap() > -1) @@ -856,7 +852,7 @@ public class NewickFile extends FileParse * * @return DOCUMENT ME! */ - private String printRootField(SequenceNode root) + private String printRootField(BinaryNode root) { return (printRootInfo) ? (((root.getName() == null) ? "" : nodeName(root.getName())) @@ -871,7 +867,7 @@ public class NewickFile extends FileParse } // Non recursive call deals with root node properties - public void print(StringBuffer tf, SequenceNode root) + public void print(StringBuffer tf, BinaryNode root) { if (root != null) { @@ -883,20 +879,20 @@ public class NewickFile extends FileParse { if (root.isDummy()) { - _print(tf, (SequenceNode) root.right()); - _print(tf, (SequenceNode) root.left()); + _print(tf, root.right()); + _print(tf, root.left()); } else { tf.append("("); - _print(tf, (SequenceNode) root.right()); + _print(tf, root.right()); if (root.left() != null) { tf.append(","); } - _print(tf, (SequenceNode) root.left()); + _print(tf, root.left()); tf.append(")" + printRootField(root)); } } @@ -904,7 +900,7 @@ public class NewickFile extends FileParse } // Recursive call for non-root nodes - public void _print(StringBuffer tf, SequenceNode c) + public void _print(StringBuffer tf, BinaryNode c) { if (c != null) { @@ -916,24 +912,24 @@ public class NewickFile extends FileParse { if (c.isDummy()) { - _print(tf, (SequenceNode) c.left()); + _print(tf, c.left()); if (c.left() != null) { tf.append(","); } - _print(tf, (SequenceNode) c.right()); + _print(tf, c.right()); } else { tf.append("("); - _print(tf, (SequenceNode) c.right()); + _print(tf, c.right()); if (c.left() != null) { tf.append(","); } - _print(tf, (SequenceNode) c.left()); + _print(tf, c.left()); tf.append(")" + printNodeField(c)); } } @@ -951,9 +947,9 @@ public class NewickFile extends FileParse { if (args == null || args.length != 1) { - System.err.println( - "Takes one argument - file name of a newick tree file."); - System.exit(0); + Jalview.exit( + "Takes one argument - file name of a newick tree file.", + ExitCode.INVALID_ARGUMENT); } File fn = new File(args[0]); @@ -968,31 +964,35 @@ public class NewickFile extends FileParse } treefile.close(); - System.out.println("Read file :\n"); + jalview.bin.Console.outPrintln("Read file :\n"); NewickFile trf = new NewickFile(args[0], DataSourceType.FILE); trf.parse(); - System.out.println("Original file :\n"); + jalview.bin.Console.outPrintln("Original file :\n"); Regex nonl = new Regex("\n+", ""); - System.out.println(nonl.replaceAll(newickfile.toString()) + "\n"); - - System.out.println("Parsed file.\n"); - System.out.println("Default output type for original input.\n"); - System.out.println(trf.print()); - System.out.println("Without bootstraps.\n"); - System.out.println(trf.print(false)); - System.out.println("Without distances.\n"); - System.out.println(trf.print(true, false)); - System.out.println("Without bootstraps but with distanecs.\n"); - System.out.println(trf.print(false, true)); - System.out.println("Without bootstraps or distanecs.\n"); - System.out.println(trf.print(false, false)); - System.out.println("With bootstraps and with distances.\n"); - System.out.println(trf.print(true, true)); + jalview.bin.Console + .outPrintln(nonl.replaceAll(newickfile.toString()) + "\n"); + + jalview.bin.Console.outPrintln("Parsed file.\n"); + jalview.bin.Console + .outPrintln("Default output type for original input.\n"); + jalview.bin.Console.outPrintln(trf.print()); + jalview.bin.Console.outPrintln("Without bootstraps.\n"); + jalview.bin.Console.outPrintln(trf.print(false)); + jalview.bin.Console.outPrintln("Without distances.\n"); + jalview.bin.Console.outPrintln(trf.print(true, false)); + jalview.bin.Console + .outPrintln("Without bootstraps but with distanecs.\n"); + jalview.bin.Console.outPrintln(trf.print(false, true)); + jalview.bin.Console.outPrintln("Without bootstraps or distanecs.\n"); + jalview.bin.Console.outPrintln(trf.print(false, false)); + jalview.bin.Console + .outPrintln("With bootstraps and with distances.\n"); + jalview.bin.Console.outPrintln(trf.print(true, true)); } catch (java.io.IOException e) { - System.err.println("Exception\n" + e); + jalview.bin.Console.errPrintln("Exception\n" + e); e.printStackTrace(); } }