X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=b3c0011b52ea2d1ad4284cb7faf4fbc1566d6189;hb=9fd03d86789221ae4f6cf720cadf3d99cc68ac33;hp=1e9c5ed812736ef6f289dc06129439317a8e8ab5;hpb=0424fec4a6d71684f56978f61eadd4ceb0652a60;p=jalview.git diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index 1e9c5ed..b3c0011 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -26,17 +26,20 @@ // TODO: Extended SequenceNodeI to hold parsed NHX strings package jalview.io; -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.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 @@ -76,7 +79,7 @@ import com.stevesoft.pat.Regex; */ public class NewickFile extends FileParse { - SequenceNode root; + BinaryNode root; private boolean HasBootstrap = false; @@ -143,7 +146,7 @@ public class NewickFile extends FileParse * @param newtree * DOCUMENT ME! */ - public NewickFile(SequenceNode newtree) + public NewickFile(BinaryNode newtree) { root = newtree; } @@ -172,7 +175,7 @@ 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; @@ -192,7 +195,7 @@ 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; @@ -273,8 +276,8 @@ 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; @@ -284,18 +287,17 @@ 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; @@ -322,21 +324,21 @@ public class NewickFile extends FileParse { c.setRight(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false)); - c = (SequenceNode) c.right(); + c = (BinaryNode) 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 = (BinaryNode) c.left(); } if (realroot == null) @@ -354,8 +356,7 @@ public class NewickFile extends FileParse // Deal with quoted fields case '\'': - Regex qnodename = new Regex( - "'([^']|'')+'"); + Regex qnodename = new Regex("'([^']|'')+'"); if (qnodename.searchFrom(nf, fcp)) { @@ -363,8 +364,7 @@ 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 @@ -398,8 +398,7 @@ public class NewickFile extends FileParse * '"+nf.substring(cp,fcp)+"'"); } */ // verify termination. - Regex comment = new Regex( - "]"); + Regex comment = new Regex("]"); if (comment.searchFrom(nf, fcp)) { // Skip the comment field @@ -430,12 +429,9 @@ 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 @@ -475,7 +471,7 @@ public class NewickFile extends FileParse { try { - bootstrap = (new Integer(nbootstrap.stringMatched(1))) + bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1))) .intValue(); HasBootstrap = true; } catch (Exception e) @@ -492,7 +488,8 @@ public class NewickFile extends FileParse { try { - distance = (new Float(ndist.stringMatched(1))).floatValue(); + distance = (Double.valueOf(ndist.stringMatched(1))) + .floatValue(); HasDistances = true; nodehasdistance = true; } catch (Exception e) @@ -523,7 +520,7 @@ 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); @@ -543,7 +540,7 @@ 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); @@ -582,7 +579,7 @@ public class NewickFile extends FileParse // Just advance focus, if we need to if ((c.left() != null) && (!c.left().isLeaf())) { - c = (SequenceNode) c.left(); + c = (BinaryNode) c.left(); } } } @@ -636,7 +633,7 @@ 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 @@ -656,10 +653,10 @@ public class NewickFile extends FileParse try { // parse out code/value pairs - if (code.toLowerCase().equals("b")) + if (code.toLowerCase(Locale.ROOT).equals("b")) { int v = -1; - Float iv = new Float(value); + Float iv = Float.valueOf(value); v = iv.intValue(); // jalview only does integer bootstraps // currently c.setBootstrap(v); @@ -683,7 +680,7 @@ public class NewickFile extends FileParse * * @return DOCUMENT ME! */ - public SequenceNode getTree() + public BinaryNode getTree() { return root; } @@ -837,7 +834,7 @@ 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) @@ -854,7 +851,7 @@ 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())) @@ -869,7 +866,7 @@ 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) { @@ -881,20 +878,20 @@ 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)); } } @@ -902,7 +899,7 @@ 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) { @@ -914,24 +911,24 @@ 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)); } } @@ -949,9 +946,8 @@ 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.", 0); } File fn = new File(args[0]);