-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.analysis;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.NewickFile;\r
-\r
-import jalview.schemes.ResidueProperties;\r
-\r
-import jalview.util.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class NJTree\r
-{\r
- Vector cluster;\r
- SequenceI[] sequence;\r
-\r
- //SequenceData is a string representation of what the user\r
- //sees. The display may contain hidden columns.\r
- public AlignmentView seqData=null;\r
-\r
- int[] done;\r
- int noseqs;\r
- int noClus;\r
- float[][] distance;\r
- int mini;\r
- int minj;\r
- float ri;\r
- float rj;\r
- Vector groups = new Vector();\r
- SequenceNode maxdist;\r
- SequenceNode top;\r
- float maxDistValue;\r
- float maxheight;\r
- int ycount;\r
- Vector node;\r
- String type;\r
- String pwtype;\r
- Object found = null;\r
- Object leaves = null;\r
-\r
- boolean hasDistances = true; // normal case for jalview trees\r
- boolean hasBootstrap = false; // normal case for jalview trees\r
-\r
- private boolean hasRootDistance = true;\r
-\r
- /**\r
- * Create a new NJTree object with leaves associated with sequences in seqs,\r
- * and original alignment data represented by Cigar strings.\r
- * @param seqs SequenceI[]\r
- * @param odata Cigar[]\r
- * @param treefile NewickFile\r
- */\r
- public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile) {\r
- this(seqs, treefile);\r
- if (odata!=null)\r
- seqData = odata;\r
- /*\r
- sequenceString = new String[odata.length];\r
- char gapChar = jalview.util.Comparison.GapChars.charAt(0);\r
- for (int i = 0; i < odata.length; i++)\r
- {\r
- SequenceI oseq_aligned = odata[i].getSeq(gapChar);\r
- sequenceString[i] = oseq_aligned.getSequence();\r
- } */\r
- }\r
-\r
- /**\r
- * Creates a new NJTree object from a tree from an external source\r
- *\r
- * @param seqs SequenceI which should be associated with leafs of treefile\r
- * @param treefile A parsed tree\r
- */\r
- public NJTree(SequenceI[] seqs, NewickFile treefile)\r
- {\r
- this.sequence = seqs;\r
- top = treefile.getTree();\r
-\r
- /**\r
- * There is no dependent alignment to be recovered from an\r
- * imported tree.\r
- *\r
- if (sequenceString == null)\r
- {\r
- sequenceString = new String[seqs.length];\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- sequenceString[i] = seqs[i].getSequence();\r
- }\r
- }\r
- */\r
-\r
- hasDistances = treefile.HasDistances();\r
- hasBootstrap = treefile.HasBootstrap();\r
- hasRootDistance = treefile.HasRootDistance();\r
-\r
- maxheight = findHeight(top);\r
-\r
- SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);\r
-\r
- Vector leaves = new Vector();\r
- findLeaves(top, leaves);\r
-\r
- int i = 0;\r
- int namesleft = seqs.length;\r
-\r
- SequenceNode j;\r
- SequenceI nam;\r
- String realnam;\r
-\r
- while (i < leaves.size())\r
- {\r
- j = (SequenceNode) leaves.elementAt(i++);\r
- realnam = j.getName();\r
- nam = null;\r
-\r
- if (namesleft > -1)\r
- {\r
- nam = algnIds.findIdMatch(realnam);\r
- }\r
-\r
- if (nam != null)\r
- {\r
- j.setElement(nam);\r
- namesleft--;\r
- }\r
- else\r
- {\r
- j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));\r
- j.setPlaceholder(true);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * Creates a new NJTree object.\r
- *\r
- * @param sequence DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- */\r
- public NJTree(SequenceI[] sequence,\r
- AlignmentView seqData,\r
- String type,\r
- String pwtype,\r
- int start, int end)\r
- {\r
- this.sequence = sequence;\r
- this.node = new Vector();\r
- this.type = type;\r
- this.pwtype = pwtype;\r
- if (seqData!=null) {\r
- this.seqData = seqData;\r
- } else {\r
- SeqCigar[] seqs = new SeqCigar[sequence.length];\r
- for(int i=0; i<sequence.length; i++)\r
- {\r
- seqs[i] = new SeqCigar(sequence[i], start, end);\r
- }\r
- CigarArray sdata = new CigarArray(seqs);\r
- sdata.addOperation(CigarArray.M, end-start+1);\r
- this.seqData = new AlignmentView(sdata);\r
- }\r
-\r
- if (!(type.equals("NJ")))\r
- {\r
- type = "AV";\r
- }\r
-\r
- if (!(pwtype.equals("PID")))\r
- {\r
- type = "BL";\r
- }\r
-\r
- int i = 0;\r
-\r
- done = new int[sequence.length];\r
-\r
- while ((i < sequence.length) && (sequence[i] != null))\r
- {\r
- done[i] = 0;\r
- i++;\r
- }\r
-\r
- noseqs = i++;\r
-\r
- distance = findDistances(this.seqData.getSequenceStrings(Comparison.GapChars.charAt(0)));\r
-\r
- makeLeaves();\r
-\r
- noClus = cluster.size();\r
-\r
- cluster();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String toString()\r
- {\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());\r
-\r
- return fout.print(false, true); // distances only\r
- }\r
-\r
- /**\r
- *\r
- * used when the alignment associated to a tree has changed.\r
- *\r
- * @param alignment Vector\r
- */\r
- public void UpdatePlaceHolders(Vector alignment)\r
- {\r
- Vector leaves = new Vector();\r
- findLeaves(top, leaves);\r
-\r
- int sz = leaves.size();\r
- SequenceIdMatcher seqmatcher = null;\r
- int i = 0;\r
-\r
- while (i < sz)\r
- {\r
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
-\r
- if (alignment.contains(leaf.element()))\r
- {\r
- leaf.setPlaceholder(false);\r
- }\r
- else\r
- {\r
- if (seqmatcher == null)\r
- {\r
- // Only create this the first time we need it\r
- SequenceI[] seqs = new SequenceI[alignment.size()];\r
-\r
- for (int j = 0; j < seqs.length; j++)\r
- seqs[j] = (SequenceI) alignment.elementAt(j);\r
-\r
- seqmatcher = new SequenceIdMatcher(seqs);\r
- }\r
-\r
- SequenceI nam = seqmatcher.findIdMatch(leaf.getName());\r
-\r
- if (nam != null)\r
- {\r
- leaf.setPlaceholder(false);\r
- leaf.setElement(nam);\r
- }\r
- else\r
- {\r
- leaf.setPlaceholder(true);\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void cluster()\r
- {\r
- while (noClus > 2)\r
- {\r
- if (type.equals("NJ"))\r
- {\r
- findMinNJDistance();\r
- }\r
- else\r
- {\r
- findMinDistance();\r
- }\r
-\r
- Cluster c = joinClusters(mini, minj);\r
-\r
- done[minj] = 1;\r
-\r
- cluster.setElementAt(null, minj);\r
- cluster.setElementAt(c, mini);\r
-\r
- noClus--;\r
- }\r
-\r
- boolean onefound = false;\r
-\r
- int one = -1;\r
- int two = -1;\r
-\r
- for (int i = 0; i < noseqs; i++)\r
- {\r
- if (done[i] != 1)\r
- {\r
- if (onefound == false)\r
- {\r
- two = i;\r
- onefound = true;\r
- }\r
- else\r
- {\r
- one = i;\r
- }\r
- }\r
- }\r
-\r
- joinClusters(one, two);\r
- top = (SequenceNode) (node.elementAt(one));\r
-\r
- reCount(top);\r
- findHeight(top);\r
- findMaxDist(top);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Cluster joinClusters(int i, int j)\r
- {\r
- float dist = distance[i][j];\r
-\r
- int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
- int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
-\r
- int[] value = new int[noi + noj];\r
-\r
- for (int ii = 0; ii < noi; ii++)\r
- {\r
- value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];\r
- }\r
-\r
- for (int ii = noi; ii < (noi + noj); ii++)\r
- {\r
- value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];\r
- }\r
-\r
- Cluster c = new Cluster(value);\r
-\r
- ri = findr(i, j);\r
- rj = findr(j, i);\r
-\r
- if (type.equals("NJ"))\r
- {\r
- findClusterNJDistance(i, j);\r
- }\r
- else\r
- {\r
- findClusterDistance(i, j);\r
- }\r
-\r
- SequenceNode sn = new SequenceNode();\r
-\r
- sn.setLeft((SequenceNode) (node.elementAt(i)));\r
- sn.setRight((SequenceNode) (node.elementAt(j)));\r
-\r
- SequenceNode tmpi = (SequenceNode) (node.elementAt(i));\r
- SequenceNode tmpj = (SequenceNode) (node.elementAt(j));\r
-\r
- if (type.equals("NJ"))\r
- {\r
- findNewNJDistances(tmpi, tmpj, dist);\r
- }\r
- else\r
- {\r
- findNewDistances(tmpi, tmpj, dist);\r
- }\r
-\r
- tmpi.setParent(sn);\r
- tmpj.setParent(sn);\r
-\r
- node.setElementAt(sn, i);\r
-\r
- return c;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param tmpi DOCUMENT ME!\r
- * @param tmpj DOCUMENT ME!\r
- * @param dist DOCUMENT ME!\r
- */\r
- public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,\r
- float dist)\r
- {\r
-\r
- tmpi.dist = ((dist + ri) - rj) / 2;\r
- tmpj.dist = (dist - tmpi.dist);\r
-\r
- if (tmpi.dist < 0)\r
- {\r
- tmpi.dist = 0;\r
- }\r
-\r
- if (tmpj.dist < 0)\r
- {\r
- tmpj.dist = 0;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param tmpi DOCUMENT ME!\r
- * @param tmpj DOCUMENT ME!\r
- * @param dist DOCUMENT ME!\r
- */\r
- public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,\r
- float dist)\r
- {\r
- float ih = 0;\r
- float jh = 0;\r
-\r
- SequenceNode sni = tmpi;\r
- SequenceNode snj = tmpj;\r
-\r
- while (sni != null)\r
- {\r
- ih = ih + sni.dist;\r
- sni = (SequenceNode) sni.left();\r
- }\r
-\r
- while (snj != null)\r
- {\r
- jh = jh + snj.dist;\r
- snj = (SequenceNode) snj.left();\r
- }\r
-\r
- tmpi.dist = ((dist / 2) - ih);\r
- tmpj.dist = ((dist / 2) - jh);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- */\r
- public void findClusterDistance(int i, int j)\r
- {\r
- int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
- int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
-\r
- // New distances from cluster to others\r
- float[] newdist = new float[noseqs];\r
-\r
- for (int l = 0; l < noseqs; l++)\r
- {\r
- if ((l != i) && (l != j))\r
- {\r
- newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +\r
- noj);\r
- }\r
- else\r
- {\r
- newdist[l] = 0;\r
- }\r
- }\r
-\r
- for (int ii = 0; ii < noseqs; ii++)\r
- {\r
- distance[i][ii] = newdist[ii];\r
- distance[ii][i] = newdist[ii];\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- */\r
- public void findClusterNJDistance(int i, int j)\r
- {\r
-\r
- // New distances from cluster to others\r
- float[] newdist = new float[noseqs];\r
-\r
- for (int l = 0; l < noseqs; l++)\r
- {\r
- if ((l != i) && (l != j))\r
- {\r
- newdist[l] = ((distance[i][l] + distance[j][l]) -\r
- distance[i][j]) / 2;\r
- }\r
- else\r
- {\r
- newdist[l] = 0;\r
- }\r
- }\r
-\r
- for (int ii = 0; ii < noseqs; ii++)\r
- {\r
- distance[i][ii] = newdist[ii];\r
- distance[ii][i] = newdist[ii];\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float findr(int i, int j)\r
- {\r
- float tmp = 1;\r
-\r
- for (int k = 0; k < noseqs; k++)\r
- {\r
- if ((k != i) && (k != j) && (done[k] != 1))\r
- {\r
- tmp = tmp + distance[i][k];\r
- }\r
- }\r
-\r
- if (noClus > 2)\r
- {\r
- tmp = tmp / (noClus - 2);\r
- }\r
-\r
- return tmp;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float findMinNJDistance()\r
- {\r
- float min = 100000;\r
-\r
- for (int i = 0; i < (noseqs - 1); i++)\r
- {\r
- for (int j = i + 1; j < noseqs; j++)\r
- {\r
- if ((done[i] != 1) && (done[j] != 1))\r
- {\r
- float tmp = distance[i][j] - (findr(i, j) + findr(j, i));\r
-\r
- if (tmp < min)\r
- {\r
- mini = i;\r
- minj = j;\r
-\r
- min = tmp;\r
- }\r
- }\r
- }\r
- }\r
-\r
- return min;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float findMinDistance()\r
- {\r
- float min = 100000;\r
-\r
- for (int i = 0; i < (noseqs - 1); i++)\r
- {\r
- for (int j = i + 1; j < noseqs; j++)\r
- {\r
- if ((done[i] != 1) && (done[j] != 1))\r
- {\r
- if (distance[i][j] < min)\r
- {\r
- mini = i;\r
- minj = j;\r
-\r
- min = distance[i][j];\r
- }\r
- }\r
- }\r
- }\r
-\r
- return min;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float[][] findDistances(String[] sequenceString)\r
- {\r
- float[][] distance = new float[noseqs][noseqs];\r
-\r
- if (pwtype.equals("PID"))\r
- {\r
- for (int i = 0; i < (noseqs - 1); i++)\r
- {\r
- for (int j = i; j < noseqs; j++)\r
- {\r
- if (j == i)\r
- {\r
- distance[i][i] = 0;\r
- }\r
- else\r
- {\r
- distance[i][j] = 100 -\r
- Comparison.PID(sequenceString[i], sequenceString[j]);\r
-\r
- distance[j][i] = distance[i][j];\r
- }\r
- }\r
- }\r
- }\r
- else if (pwtype.equals("BL"))\r
- {\r
- int maxscore = 0;\r
- int end = sequenceString[0].length();\r
- for (int i = 0; i < (noseqs - 1); i++)\r
- {\r
- for (int j = i; j < noseqs; j++)\r
- {\r
- int score = 0;\r
-\r
- for (int k = 0; k < end; k++)\r
- {\r
- try\r
- {\r
- score += ResidueProperties.getBLOSUM62(\r
- sequenceString[i].substring(k, k + 1),\r
- sequenceString[j].substring(k, k + 1));\r
- }\r
- catch (Exception ex)\r
- {\r
- System.err.println("err creating BLOSUM62 tree");\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- distance[i][j] = (float) score;\r
-\r
- if (score > maxscore)\r
- {\r
- maxscore = score;\r
- }\r
- }\r
- }\r
-\r
- for (int i = 0; i < (noseqs - 1); i++)\r
- {\r
- for (int j = i; j < noseqs; j++)\r
- {\r
- distance[i][j] = (float) maxscore - distance[i][j];\r
- distance[j][i] = distance[i][j];\r
- }\r
- }\r
- }\r
- /* else if (pwtype.equals("SW"))\r
- {\r
- float max = -1;\r
-\r
- for (int i = 0; i < (noseqs - 1); i++)\r
- {\r
- for (int j = i; j < noseqs; j++)\r
- {\r
- AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment(System.out);\r
- distance[i][j] = (float) as.maxscore;\r
-\r
- if (max < distance[i][j])\r
- {\r
- max = distance[i][j];\r
- }\r
- }\r
- }\r
-\r
- for (int i = 0; i < (noseqs - 1); i++)\r
- {\r
- for (int j = i; j < noseqs; j++)\r
- {\r
- distance[i][j] = max - distance[i][j];\r
- distance[j][i] = distance[i][j];\r
- }\r
- }\r
- }/*/\r
-\r
- return distance;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void makeLeaves()\r
- {\r
- cluster = new Vector();\r
-\r
- for (int i = 0; i < noseqs; i++)\r
- {\r
- SequenceNode sn = new SequenceNode();\r
-\r
- sn.setElement(sequence[i]);\r
- sn.setName(sequence[i].getName());\r
- node.addElement(sn);\r
-\r
- int[] value = new int[1];\r
- value[0] = i;\r
-\r
- Cluster c = new Cluster(value);\r
- cluster.addElement(c);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- * @param leaves DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector findLeaves(SequenceNode node, Vector leaves)\r
- {\r
- if (node == null)\r
- {\r
- return leaves;\r
- }\r
-\r
- if ((node.left() == null) && (node.right() == null))\r
- {\r
- leaves.addElement(node);\r
-\r
- return leaves;\r
- }\r
- else\r
- {\r
- findLeaves((SequenceNode) node.left(), leaves);\r
- findLeaves((SequenceNode) node.right(), leaves);\r
- }\r
-\r
- return leaves;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- * @param count DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Object findLeaf(SequenceNode node, int count)\r
- {\r
- found = _findLeaf(node, count);\r
-\r
- return found;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- * @param count DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Object _findLeaf(SequenceNode node, int count)\r
- {\r
- if (node == null)\r
- {\r
- return null;\r
- }\r
-\r
- if (node.ycount == count)\r
- {\r
- found = node.element();\r
-\r
- return found;\r
- }\r
- else\r
- {\r
- _findLeaf((SequenceNode) node.left(), count);\r
- _findLeaf((SequenceNode) node.right(), count);\r
- }\r
-\r
- return found;\r
- }\r
-\r
- /**\r
- * printNode is mainly for debugging purposes.\r
- *\r
- * @param node SequenceNode\r
- */\r
- public void printNode(SequenceNode node)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if ((node.left() == null) && (node.right() == null))\r
- {\r
- System.out.println("Leaf = " +\r
- ((SequenceI) node.element()).getName());\r
- System.out.println("Dist " + ((SequenceNode) node).dist);\r
- System.out.println("Boot " + node.getBootstrap());\r
- }\r
- else\r
- {\r
- System.out.println("Dist " + ((SequenceNode) node).dist);\r
- printNode((SequenceNode) node.left());\r
- printNode((SequenceNode) node.right());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- */\r
- public void findMaxDist(SequenceNode node)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if ((node.left() == null) && (node.right() == null))\r
- {\r
- float dist = ((SequenceNode) node).dist;\r
-\r
- if (dist > maxDistValue)\r
- {\r
- maxdist = (SequenceNode) node;\r
- maxDistValue = dist;\r
- }\r
- }\r
- else\r
- {\r
- findMaxDist((SequenceNode) node.left());\r
- findMaxDist((SequenceNode) node.right());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getGroups()\r
- {\r
- return groups;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float getMaxHeight()\r
- {\r
- return maxheight;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- * @param threshold DOCUMENT ME!\r
- */\r
- public void groupNodes(SequenceNode node, float threshold)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if ((node.height / maxheight) > threshold)\r
- {\r
- groups.addElement(node);\r
- }\r
- else\r
- {\r
- groupNodes((SequenceNode) node.left(), threshold);\r
- groupNodes((SequenceNode) node.right(), threshold);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float findHeight(SequenceNode node)\r
- {\r
- if (node == null)\r
- {\r
- return maxheight;\r
- }\r
-\r
- if ((node.left() == null) && (node.right() == null))\r
- {\r
- node.height = ((SequenceNode) node.parent()).height + node.dist;\r
-\r
- if (node.height > maxheight)\r
- {\r
- return node.height;\r
- }\r
- else\r
- {\r
- return maxheight;\r
- }\r
- }\r
- else\r
- {\r
- if (node.parent() != null)\r
- {\r
- node.height = ((SequenceNode) node.parent()).height +\r
- node.dist;\r
- }\r
- else\r
- {\r
- maxheight = 0;\r
- node.height = (float) 0.0;\r
- }\r
-\r
- maxheight = findHeight((SequenceNode) (node.left()));\r
- maxheight = findHeight((SequenceNode) (node.right()));\r
- }\r
-\r
- return maxheight;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceNode reRoot()\r
- {\r
- if (maxdist != null)\r
- {\r
- ycount = 0;\r
-\r
- float tmpdist = maxdist.dist;\r
-\r
- // New top\r
- SequenceNode sn = new SequenceNode();\r
- sn.setParent(null);\r
-\r
- // New right hand of top\r
- SequenceNode snr = (SequenceNode) maxdist.parent();\r
- changeDirection(snr, maxdist);\r
- System.out.println("Printing reversed tree");\r
- printN(snr);\r
- snr.dist = tmpdist / 2;\r
- maxdist.dist = tmpdist / 2;\r
-\r
- snr.setParent(sn);\r
- maxdist.setParent(sn);\r
-\r
- sn.setRight(snr);\r
- sn.setLeft(maxdist);\r
-\r
- top = sn;\r
-\r
- ycount = 0;\r
- reCount(top);\r
- findHeight(top);\r
- }\r
-\r
- return top;\r
- }\r
- /**\r
- *\r
- * @return true if original sequence data can be recovered\r
- */\r
- public boolean hasOriginalSequenceData() {\r
- return seqData!=null;\r
- }\r
- /**\r
- * Returns original alignment data used for calculation - or null where\r
- * not available.\r
- *\r
- * @return null or cut'n'pasteable alignment\r
- */\r
- public String printOriginalSequenceData(char gapChar)\r
- {\r
- if (seqData==null)\r
- return null;\r
-\r
- StringBuffer sb = new StringBuffer();\r
- String[] seqdatas = seqData.getSequenceStrings(gapChar);\r
- for(int i=0; i<seqdatas.length; i++)\r
- {\r
- sb.append(new jalview.util.Format("%-" + 15 + "s").form(\r
- sequence[i].getName()));\r
- sb.append(" "+seqdatas[i]+"\n");\r
- }\r
- return sb.toString();\r
- }\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- */\r
- public void printN(SequenceNode node)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if ((node.left() != null) && (node.right() != null))\r
- {\r
- printN((SequenceNode) node.left());\r
- printN((SequenceNode) node.right());\r
- }\r
- else\r
- {\r
- System.out.println(" name = " +\r
- ((SequenceI) node.element()).getName());\r
- }\r
-\r
- System.out.println(" dist = " + ((SequenceNode) node).dist + " " +\r
- ((SequenceNode) node).count + " " + ((SequenceNode) node).height);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- */\r
- public void reCount(SequenceNode node)\r
- {\r
- ycount = 0;\r
- _reCount(node);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- */\r
- public void _reCount(SequenceNode node)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if ((node.left() != null) && (node.right() != null))\r
- {\r
- _reCount((SequenceNode) node.left());\r
- _reCount((SequenceNode) node.right());\r
-\r
- SequenceNode l = (SequenceNode) node.left();\r
- SequenceNode r = (SequenceNode) node.right();\r
-\r
- ((SequenceNode) node).count = l.count + r.count;\r
- ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;\r
- }\r
- else\r
- {\r
- ((SequenceNode) node).count = 1;\r
- ((SequenceNode) node).ycount = ycount++;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- */\r
- public void swapNodes(SequenceNode node)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- SequenceNode tmp = (SequenceNode) node.left();\r
-\r
- node.setLeft(node.right());\r
- node.setRight(tmp);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- * @param dir DOCUMENT ME!\r
- */\r
- public void changeDirection(SequenceNode node, SequenceNode dir)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if (node.parent() != top)\r
- {\r
- changeDirection((SequenceNode) node.parent(), node);\r
-\r
- SequenceNode tmp = (SequenceNode) node.parent();\r
-\r
- if (dir == node.left())\r
- {\r
- node.setParent(dir);\r
- node.setLeft(tmp);\r
- }\r
- else if (dir == node.right())\r
- {\r
- node.setParent(dir);\r
- node.setRight(tmp);\r
- }\r
- }\r
- else\r
- {\r
- if (dir == node.left())\r
- {\r
- node.setParent(node.left());\r
-\r
- if (top.left() == node)\r
- {\r
- node.setRight(top.right());\r
- }\r
- else\r
- {\r
- node.setRight(top.left());\r
- }\r
- }\r
- else\r
- {\r
- node.setParent(node.right());\r
-\r
- if (top.left() == node)\r
- {\r
- node.setLeft(top.right());\r
- }\r
- else\r
- {\r
- node.setLeft(top.left());\r
- }\r
- }\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceNode getMaxDist()\r
- {\r
- return maxdist;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceNode getTopNode()\r
- {\r
- return top;\r
- }\r
- /**\r
- *\r
- * @return true if tree has real distances\r
- */\r
- public boolean isHasDistances() {\r
- return hasDistances;\r
- }\r
-\r
- /**\r
- *\r
- * @return true if tree has real bootstrap values\r
- */\r
- public boolean isHasBootstrap() {\r
- return hasBootstrap;\r
- }\r
-\r
- public boolean isHasRootDistance()\r
- {\r
- return hasRootDistance;\r
- }\r
-\r
-}\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-class Cluster\r
-{\r
- int[] value;\r
-\r
- /**\r
- * Creates a new Cluster object.\r
- *\r
- * @param value DOCUMENT ME!\r
- */\r
- public Cluster(int[] value)\r
- {\r
- this.value = value;\r
- }\r
-}\r
-\r
+/*
+* 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
+*/
+package jalview.analysis;
+
+import jalview.datamodel.*;
+
+import jalview.io.NewickFile;
+
+import jalview.schemes.ResidueProperties;
+
+import jalview.util.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NJTree
+{
+ Vector cluster;
+ SequenceI[] sequence;
+
+ //SequenceData is a string representation of what the user
+ //sees. The display may contain hidden columns.
+ public AlignmentView seqData=null;
+
+ int[] done;
+ int noseqs;
+ int noClus;
+ float[][] distance;
+ int mini;
+ int minj;
+ float ri;
+ float rj;
+ Vector groups = new Vector();
+ SequenceNode maxdist;
+ SequenceNode top;
+ float maxDistValue;
+ float maxheight;
+ int ycount;
+ Vector node;
+ String type;
+ String pwtype;
+ Object found = null;
+ Object leaves = null;
+
+ boolean hasDistances = true; // normal case for jalview trees
+ boolean hasBootstrap = false; // normal case for jalview trees
+
+ private boolean hasRootDistance = true;
+
+ /**
+ * Create a new NJTree object with leaves associated with sequences in seqs,
+ * and original alignment data represented by Cigar strings.
+ * @param seqs SequenceI[]
+ * @param odata Cigar[]
+ * @param treefile NewickFile
+ */
+ public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile) {
+ this(seqs, treefile);
+ if (odata!=null)
+ seqData = odata;
+ /*
+ sequenceString = new String[odata.length];
+ char gapChar = jalview.util.Comparison.GapChars.charAt(0);
+ for (int i = 0; i < odata.length; i++)
+ {
+ SequenceI oseq_aligned = odata[i].getSeq(gapChar);
+ sequenceString[i] = oseq_aligned.getSequence();
+ } */
+ }
+
+ /**
+ * Creates a new NJTree object from a tree from an external source
+ *
+ * @param seqs SequenceI which should be associated with leafs of treefile
+ * @param treefile A parsed tree
+ */
+ public NJTree(SequenceI[] seqs, NewickFile treefile)
+ {
+ this.sequence = seqs;
+ top = treefile.getTree();
+
+ /**
+ * There is no dependent alignment to be recovered from an
+ * imported tree.
+ *
+ if (sequenceString == null)
+ {
+ sequenceString = new String[seqs.length];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ sequenceString[i] = seqs[i].getSequence();
+ }
+ }
+ */
+
+ hasDistances = treefile.HasDistances();
+ hasBootstrap = treefile.HasBootstrap();
+ hasRootDistance = treefile.HasRootDistance();
+
+ maxheight = findHeight(top);
+
+ SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
+
+ Vector leaves = new Vector();
+ findLeaves(top, leaves);
+
+ int i = 0;
+ int namesleft = seqs.length;
+
+ SequenceNode j;
+ SequenceI nam;
+ String realnam;
+
+ while (i < leaves.size())
+ {
+ j = (SequenceNode) leaves.elementAt(i++);
+ realnam = j.getName();
+ nam = null;
+
+ if (namesleft > -1)
+ {
+ nam = algnIds.findIdMatch(realnam);
+ }
+
+ if (nam != null)
+ {
+ j.setElement(nam);
+ namesleft--;
+ }
+ else
+ {
+ j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
+ j.setPlaceholder(true);
+ }
+ }
+ }
+
+ /**
+ * Creates a new NJTree object.
+ *
+ * @param sequence DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param pwtype DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ */
+ public NJTree(SequenceI[] sequence,
+ AlignmentView seqData,
+ String type,
+ String pwtype,
+ int start, int end)
+ {
+ this.sequence = sequence;
+ this.node = new Vector();
+ this.type = type;
+ this.pwtype = pwtype;
+ if (seqData!=null) {
+ this.seqData = seqData;
+ } else {
+ SeqCigar[] seqs = new SeqCigar[sequence.length];
+ for(int i=0; i<sequence.length; i++)
+ {
+ seqs[i] = new SeqCigar(sequence[i], start, end);
+ }
+ CigarArray sdata = new CigarArray(seqs);
+ sdata.addOperation(CigarArray.M, end-start+1);
+ this.seqData = new AlignmentView(sdata, start);
+ }
+
+ if (!(type.equals("NJ")))
+ {
+ type = "AV";
+ }
+
+ if (!(pwtype.equals("PID")))
+ {
+ type = "BL";
+ }
+
+ int i = 0;
+
+ done = new int[sequence.length];
+
+ while ((i < sequence.length) && (sequence[i] != null))
+ {
+ done[i] = 0;
+ i++;
+ }
+
+ noseqs = i++;
+
+ distance = findDistances(this.seqData.getSequenceStrings(Comparison.GapChars.charAt(0)));
+
+ makeLeaves();
+
+ noClus = cluster.size();
+
+ cluster();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString()
+ {
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
+
+ return fout.print(false, true); // distances only
+ }
+
+ /**
+ *
+ * used when the alignment associated to a tree has changed.
+ *
+ * @param alignment Vector
+ */
+ public void UpdatePlaceHolders(Vector alignment)
+ {
+ Vector leaves = new Vector();
+ findLeaves(top, leaves);
+
+ int sz = leaves.size();
+ SequenceIdMatcher seqmatcher = null;
+ int i = 0;
+
+ while (i < sz)
+ {
+ SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+
+ if (alignment.contains(leaf.element()))
+ {
+ leaf.setPlaceholder(false);
+ }
+ else
+ {
+ if (seqmatcher == null)
+ {
+ // Only create this the first time we need it
+ SequenceI[] seqs = new SequenceI[alignment.size()];
+
+ for (int j = 0; j < seqs.length; j++)
+ seqs[j] = (SequenceI) alignment.elementAt(j);
+
+ seqmatcher = new SequenceIdMatcher(seqs);
+ }
+
+ SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
+
+ if (nam != null)
+ {
+ leaf.setPlaceholder(false);
+ leaf.setElement(nam);
+ }
+ else
+ {
+ leaf.setPlaceholder(true);
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void cluster()
+ {
+ while (noClus > 2)
+ {
+ if (type.equals("NJ"))
+ {
+ findMinNJDistance();
+ }
+ else
+ {
+ findMinDistance();
+ }
+
+ Cluster c = joinClusters(mini, minj);
+
+ done[minj] = 1;
+
+ cluster.setElementAt(null, minj);
+ cluster.setElementAt(c, mini);
+
+ noClus--;
+ }
+
+ boolean onefound = false;
+
+ int one = -1;
+ int two = -1;
+
+ for (int i = 0; i < noseqs; i++)
+ {
+ if (done[i] != 1)
+ {
+ if (onefound == false)
+ {
+ two = i;
+ onefound = true;
+ }
+ else
+ {
+ one = i;
+ }
+ }
+ }
+
+ joinClusters(one, two);
+ top = (SequenceNode) (node.elementAt(one));
+
+ reCount(top);
+ findHeight(top);
+ findMaxDist(top);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param j DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Cluster joinClusters(int i, int j)
+ {
+ float dist = distance[i][j];
+
+ int noi = ((Cluster) cluster.elementAt(i)).value.length;
+ int noj = ((Cluster) cluster.elementAt(j)).value.length;
+
+ int[] value = new int[noi + noj];
+
+ for (int ii = 0; ii < noi; ii++)
+ {
+ value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
+ }
+
+ for (int ii = noi; ii < (noi + noj); ii++)
+ {
+ value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
+ }
+
+ Cluster c = new Cluster(value);
+
+ ri = findr(i, j);
+ rj = findr(j, i);
+
+ if (type.equals("NJ"))
+ {
+ findClusterNJDistance(i, j);
+ }
+ else
+ {
+ findClusterDistance(i, j);
+ }
+
+ SequenceNode sn = new SequenceNode();
+
+ sn.setLeft((SequenceNode) (node.elementAt(i)));
+ sn.setRight((SequenceNode) (node.elementAt(j)));
+
+ SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
+ SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
+
+ if (type.equals("NJ"))
+ {
+ findNewNJDistances(tmpi, tmpj, dist);
+ }
+ else
+ {
+ findNewDistances(tmpi, tmpj, dist);
+ }
+
+ tmpi.setParent(sn);
+ tmpj.setParent(sn);
+
+ node.setElementAt(sn, i);
+
+ return c;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tmpi DOCUMENT ME!
+ * @param tmpj DOCUMENT ME!
+ * @param dist DOCUMENT ME!
+ */
+ public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
+ float dist)
+ {
+
+ tmpi.dist = ((dist + ri) - rj) / 2;
+ tmpj.dist = (dist - tmpi.dist);
+
+ if (tmpi.dist < 0)
+ {
+ tmpi.dist = 0;
+ }
+
+ if (tmpj.dist < 0)
+ {
+ tmpj.dist = 0;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tmpi DOCUMENT ME!
+ * @param tmpj DOCUMENT ME!
+ * @param dist DOCUMENT ME!
+ */
+ public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+ float dist)
+ {
+ float ih = 0;
+ float jh = 0;
+
+ SequenceNode sni = tmpi;
+ SequenceNode snj = tmpj;
+
+ while (sni != null)
+ {
+ ih = ih + sni.dist;
+ sni = (SequenceNode) sni.left();
+ }
+
+ while (snj != null)
+ {
+ jh = jh + snj.dist;
+ snj = (SequenceNode) snj.left();
+ }
+
+ tmpi.dist = ((dist / 2) - ih);
+ tmpj.dist = ((dist / 2) - jh);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param j DOCUMENT ME!
+ */
+ public void findClusterDistance(int i, int j)
+ {
+ int noi = ((Cluster) cluster.elementAt(i)).value.length;
+ int noj = ((Cluster) cluster.elementAt(j)).value.length;
+
+ // New distances from cluster to others
+ float[] newdist = new float[noseqs];
+
+ for (int l = 0; l < noseqs; l++)
+ {
+ if ((l != i) && (l != j))
+ {
+ newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
+ noj);
+ }
+ else
+ {
+ newdist[l] = 0;
+ }
+ }
+
+ for (int ii = 0; ii < noseqs; ii++)
+ {
+ distance[i][ii] = newdist[ii];
+ distance[ii][i] = newdist[ii];
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param j DOCUMENT ME!
+ */
+ public void findClusterNJDistance(int i, int j)
+ {
+
+ // New distances from cluster to others
+ float[] newdist = new float[noseqs];
+
+ for (int l = 0; l < noseqs; l++)
+ {
+ if ((l != i) && (l != j))
+ {
+ newdist[l] = ((distance[i][l] + distance[j][l]) -
+ distance[i][j]) / 2;
+ }
+ else
+ {
+ newdist[l] = 0;
+ }
+ }
+
+ for (int ii = 0; ii < noseqs; ii++)
+ {
+ distance[i][ii] = newdist[ii];
+ distance[ii][i] = newdist[ii];
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param j DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float findr(int i, int j)
+ {
+ float tmp = 1;
+
+ for (int k = 0; k < noseqs; k++)
+ {
+ if ((k != i) && (k != j) && (done[k] != 1))
+ {
+ tmp = tmp + distance[i][k];
+ }
+ }
+
+ if (noClus > 2)
+ {
+ tmp = tmp / (noClus - 2);
+ }
+
+ return tmp;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float findMinNJDistance()
+ {
+ float min = 100000;
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i + 1; j < noseqs; j++)
+ {
+ if ((done[i] != 1) && (done[j] != 1))
+ {
+ float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
+
+ if (tmp < min)
+ {
+ mini = i;
+ minj = j;
+
+ min = tmp;
+ }
+ }
+ }
+ }
+
+ return min;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float findMinDistance()
+ {
+ float min = 100000;
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i + 1; j < noseqs; j++)
+ {
+ if ((done[i] != 1) && (done[j] != 1))
+ {
+ if (distance[i][j] < min)
+ {
+ mini = i;
+ minj = j;
+
+ min = distance[i][j];
+ }
+ }
+ }
+ }
+
+ return min;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float[][] findDistances(String[] sequenceString)
+ {
+ float[][] distance = new float[noseqs][noseqs];
+
+ if (pwtype.equals("PID"))
+ {
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i; j < noseqs; j++)
+ {
+ if (j == i)
+ {
+ distance[i][i] = 0;
+ }
+ else
+ {
+ distance[i][j] = 100 -
+ Comparison.PID(sequenceString[i], sequenceString[j]);
+
+ distance[j][i] = distance[i][j];
+ }
+ }
+ }
+ }
+ else if (pwtype.equals("BL"))
+ {
+ int maxscore = 0;
+ int end = sequenceString[0].length();
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i; j < noseqs; j++)
+ {
+ int score = 0;
+
+ for (int k = 0; k < end; k++)
+ {
+ try
+ {
+ score += ResidueProperties.getBLOSUM62(
+ sequenceString[i].substring(k, k + 1),
+ sequenceString[j].substring(k, k + 1));
+ }
+ catch (Exception ex)
+ {
+ System.err.println("err creating BLOSUM62 tree");
+ ex.printStackTrace();
+ }
+ }
+
+ distance[i][j] = (float) score;
+
+ if (score > maxscore)
+ {
+ maxscore = score;
+ }
+ }
+ }
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i; j < noseqs; j++)
+ {
+ distance[i][j] = (float) maxscore - distance[i][j];
+ distance[j][i] = distance[i][j];
+ }
+ }
+ }
+ /* else if (pwtype.equals("SW"))
+ {
+ float max = -1;
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i; j < noseqs; j++)
+ {
+ AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
+ as.calcScoreMatrix();
+ as.traceAlignment();
+ as.printAlignment(System.out);
+ distance[i][j] = (float) as.maxscore;
+
+ if (max < distance[i][j])
+ {
+ max = distance[i][j];
+ }
+ }
+ }
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i; j < noseqs; j++)
+ {
+ distance[i][j] = max - distance[i][j];
+ distance[j][i] = distance[i][j];
+ }
+ }
+ }/*/
+
+ return distance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeLeaves()
+ {
+ cluster = new Vector();
+
+ for (int i = 0; i < noseqs; i++)
+ {
+ SequenceNode sn = new SequenceNode();
+
+ sn.setElement(sequence[i]);
+ sn.setName(sequence[i].getName());
+ node.addElement(sn);
+
+ int[] value = new int[1];
+ value[0] = i;
+
+ Cluster c = new Cluster(value);
+ cluster.addElement(c);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param leaves DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector findLeaves(SequenceNode node, Vector leaves)
+ {
+ if (node == null)
+ {
+ return leaves;
+ }
+
+ if ((node.left() == null) && (node.right() == null))
+ {
+ leaves.addElement(node);
+
+ return leaves;
+ }
+ else
+ {
+ findLeaves((SequenceNode) node.left(), leaves);
+ findLeaves((SequenceNode) node.right(), leaves);
+ }
+
+ return leaves;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param count DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object findLeaf(SequenceNode node, int count)
+ {
+ found = _findLeaf(node, count);
+
+ return found;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param count DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object _findLeaf(SequenceNode node, int count)
+ {
+ if (node == null)
+ {
+ return null;
+ }
+
+ if (node.ycount == count)
+ {
+ found = node.element();
+
+ return found;
+ }
+ else
+ {
+ _findLeaf((SequenceNode) node.left(), count);
+ _findLeaf((SequenceNode) node.right(), count);
+ }
+
+ return found;
+ }
+
+ /**
+ * printNode is mainly for debugging purposes.
+ *
+ * @param node SequenceNode
+ */
+ public void printNode(SequenceNode node)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if ((node.left() == null) && (node.right() == null))
+ {
+ System.out.println("Leaf = " +
+ ((SequenceI) node.element()).getName());
+ System.out.println("Dist " + ((SequenceNode) node).dist);
+ System.out.println("Boot " + node.getBootstrap());
+ }
+ else
+ {
+ System.out.println("Dist " + ((SequenceNode) node).dist);
+ printNode((SequenceNode) node.left());
+ printNode((SequenceNode) node.right());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ */
+ public void findMaxDist(SequenceNode node)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if ((node.left() == null) && (node.right() == null))
+ {
+ float dist = ((SequenceNode) node).dist;
+
+ if (dist > maxDistValue)
+ {
+ maxdist = (SequenceNode) node;
+ maxDistValue = dist;
+ }
+ }
+ else
+ {
+ findMaxDist((SequenceNode) node.left());
+ findMaxDist((SequenceNode) node.right());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getGroups()
+ {
+ return groups;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float getMaxHeight()
+ {
+ return maxheight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param threshold DOCUMENT ME!
+ */
+ public void groupNodes(SequenceNode node, float threshold)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if ((node.height / maxheight) > threshold)
+ {
+ groups.addElement(node);
+ }
+ else
+ {
+ groupNodes((SequenceNode) node.left(), threshold);
+ groupNodes((SequenceNode) node.right(), threshold);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float findHeight(SequenceNode node)
+ {
+ if (node == null)
+ {
+ return maxheight;
+ }
+
+ if ((node.left() == null) && (node.right() == null))
+ {
+ node.height = ((SequenceNode) node.parent()).height + node.dist;
+
+ if (node.height > maxheight)
+ {
+ return node.height;
+ }
+ else
+ {
+ return maxheight;
+ }
+ }
+ else
+ {
+ if (node.parent() != null)
+ {
+ node.height = ((SequenceNode) node.parent()).height +
+ node.dist;
+ }
+ else
+ {
+ maxheight = 0;
+ node.height = (float) 0.0;
+ }
+
+ maxheight = findHeight((SequenceNode) (node.left()));
+ maxheight = findHeight((SequenceNode) (node.right()));
+ }
+
+ return maxheight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceNode reRoot()
+ {
+ if (maxdist != null)
+ {
+ ycount = 0;
+
+ float tmpdist = maxdist.dist;
+
+ // New top
+ SequenceNode sn = new SequenceNode();
+ sn.setParent(null);
+
+ // New right hand of top
+ SequenceNode snr = (SequenceNode) maxdist.parent();
+ changeDirection(snr, maxdist);
+ System.out.println("Printing reversed tree");
+ printN(snr);
+ snr.dist = tmpdist / 2;
+ maxdist.dist = tmpdist / 2;
+
+ snr.setParent(sn);
+ maxdist.setParent(sn);
+
+ sn.setRight(snr);
+ sn.setLeft(maxdist);
+
+ top = sn;
+
+ ycount = 0;
+ reCount(top);
+ findHeight(top);
+ }
+
+ return top;
+ }
+ /**
+ *
+ * @return true if original sequence data can be recovered
+ */
+ public boolean hasOriginalSequenceData() {
+ return seqData!=null;
+ }
+ /**
+ * Returns original alignment data used for calculation - or null where
+ * not available.
+ *
+ * @return null or cut'n'pasteable alignment
+ */
+ public String printOriginalSequenceData(char gapChar)
+ {
+ if (seqData==null)
+ return null;
+
+ StringBuffer sb = new StringBuffer();
+ String[] seqdatas = seqData.getSequenceStrings(gapChar);
+ for(int i=0; i<seqdatas.length; i++)
+ {
+ sb.append(new jalview.util.Format("%-" + 15 + "s").form(
+ sequence[i].getName()));
+ sb.append(" "+seqdatas[i]+"\n");
+ }
+ return sb.toString();
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ */
+ public void printN(SequenceNode node)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if ((node.left() != null) && (node.right() != null))
+ {
+ printN((SequenceNode) node.left());
+ printN((SequenceNode) node.right());
+ }
+ else
+ {
+ System.out.println(" name = " +
+ ((SequenceI) node.element()).getName());
+ }
+
+ System.out.println(" dist = " + ((SequenceNode) node).dist + " " +
+ ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ */
+ public void reCount(SequenceNode node)
+ {
+ ycount = 0;
+ _reCount(node);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ */
+ public void _reCount(SequenceNode node)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if ((node.left() != null) && (node.right() != null))
+ {
+ _reCount((SequenceNode) node.left());
+ _reCount((SequenceNode) node.right());
+
+ SequenceNode l = (SequenceNode) node.left();
+ SequenceNode r = (SequenceNode) node.right();
+
+ ((SequenceNode) node).count = l.count + r.count;
+ ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+ }
+ else
+ {
+ ((SequenceNode) node).count = 1;
+ ((SequenceNode) node).ycount = ycount++;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ */
+ public void swapNodes(SequenceNode node)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ SequenceNode tmp = (SequenceNode) node.left();
+
+ node.setLeft(node.right());
+ node.setRight(tmp);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param dir DOCUMENT ME!
+ */
+ public void changeDirection(SequenceNode node, SequenceNode dir)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if (node.parent() != top)
+ {
+ changeDirection((SequenceNode) node.parent(), node);
+
+ SequenceNode tmp = (SequenceNode) node.parent();
+
+ if (dir == node.left())
+ {
+ node.setParent(dir);
+ node.setLeft(tmp);
+ }
+ else if (dir == node.right())
+ {
+ node.setParent(dir);
+ node.setRight(tmp);
+ }
+ }
+ else
+ {
+ if (dir == node.left())
+ {
+ node.setParent(node.left());
+
+ if (top.left() == node)
+ {
+ node.setRight(top.right());
+ }
+ else
+ {
+ node.setRight(top.left());
+ }
+ }
+ else
+ {
+ node.setParent(node.right());
+
+ if (top.left() == node)
+ {
+ node.setLeft(top.right());
+ }
+ else
+ {
+ node.setLeft(top.left());
+ }
+ }
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceNode getMaxDist()
+ {
+ return maxdist;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceNode getTopNode()
+ {
+ return top;
+ }
+ /**
+ *
+ * @return true if tree has real distances
+ */
+ public boolean isHasDistances() {
+ return hasDistances;
+ }
+
+ /**
+ *
+ * @return true if tree has real bootstrap values
+ */
+ public boolean isHasBootstrap() {
+ return hasBootstrap;
+ }
+
+ public boolean isHasRootDistance()
+ {
+ return hasRootDistance;
+ }
+
+}
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+class Cluster
+{
+ int[] value;
+
+ /**
+ * Creates a new Cluster object.
+ *
+ * @param value DOCUMENT ME!
+ */
+ public Cluster(int[] value)
+ {
+ this.value = value;
+ }
+}
+
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.bin;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.apache.log4j.SimpleLayout;\r
-import org.apache.log4j.Level;\r
-import org.apache.log4j.ConsoleAppender;\r
-\r
-\r
-/**\r
- * Stores and retrieves Jalview Application Properties\r
- * <br><br>Current properties include:\r
- * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)\r
- * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)\r
- * <br>logs.Jalview.Level - Cache.log stringified level.\r
- * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup\r
- * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.\r
- * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN\r
- * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR\r
- * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,\r
- * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE\r
-\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Cache\r
-{\r
- /**\r
- * Initialises the Apache Axis logger\r
- */\r
- public static Logger log;\r
-\r
- /** Jalview Properties */\r
- public static Properties applicationProperties = new Properties();\r
-\r
- /** Default file is ~/.jalview_properties */\r
- static String propertiesFile;\r
-\r
- public static void initLogger()\r
- {\r
- try\r
- {\r
- Logger laxis = Logger.getLogger("org.apache.axis");\r
- Logger lcastor = Logger.getLogger("org.exolab.castor");\r
- jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");\r
-\r
- laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",\r
- Level.INFO.toString())));\r
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",\r
- Level.INFO.toString())));\r
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(\r
- "logs.Jalview.level",\r
- Level.INFO.toString())));\r
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),\r
- "System.err");\r
- ap.setName("JalviewLogger");\r
-\r
- laxis.addAppender(ap);\r
- lcastor.addAppender(ap);\r
- jalview.bin.Cache.log.addAppender(ap);\r
- // Tell the user that debug is enabled\r
- jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");\r
- }\r
- catch (Exception ex)\r
- {\r
- System.err.println("Problems initializing the log4j system\n");\r
- }\r
- }\r
-\r
-\r
- /** Called when Jalview is started */\r
- public static void loadProperties(String propsFile)\r
- {\r
- propertiesFile = propsFile;\r
- if (propsFile == null)\r
- {\r
- propertiesFile = System.getProperty("user.home") + "/.jalview_properties";\r
- }\r
-\r
- try\r
- {\r
- FileInputStream fis = new FileInputStream(propertiesFile);\r
- applicationProperties.load(fis);\r
- applicationProperties.remove("LATEST_VERSION");\r
- applicationProperties.remove("VERSION");\r
- fis.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error reading properties file: "+ex);\r
- }\r
-\r
- if(getDefault("USE_PROXY", false))\r
- {\r
- System.out.println("Using proxyServer: "+getDefault("PROXY_SERVER", null)+\r
- " proxyPort: "+getDefault("PROXY_PORT", null));\r
- System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));\r
- System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));\r
- }\r
-\r
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar\r
- // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE\r
- // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW\r
- try\r
- {\r
- String buildDetails = "jar:"\r
- .concat(\r
- Cache.class.getProtectionDomain().getCodeSource().getLocation().toString()\r
- .concat("!/.build_properties")\r
- );\r
-\r
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);\r
-\r
- InputStream in = localJarFileURL.openStream();\r
- applicationProperties.load(in);\r
- in.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error reading build details: "+ex);\r
- applicationProperties.remove("VERSION");\r
- }\r
-\r
- String jnlpVersion = System.getProperty("jalview.version");\r
- String codeVersion = getProperty("VERSION");\r
-\r
-\r
- if(codeVersion==null)\r
- {\r
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!\r
- codeVersion = "Test";\r
- jnlpVersion = "Test";\r
- }\r
-\r
-\r
- System.out.println("Jalview Version: "+codeVersion);\r
-\r
-\r
- // jnlpVersion will be null if we're using InstallAnywhere\r
- // Dont do this check if running in headless mode\r
- if(jnlpVersion==null && (\r
- System.getProperty("java.awt.headless")==null\r
- || System.getProperty("java.awt.headless").equals("false")))\r
- {\r
-\r
- class VersionChecker\r
- extends Thread\r
- {\r
- public void run()\r
- {\r
- String jnlpVersion = null;\r
- try\r
- {\r
- java.net.URL url = new java.net.URL(\r
- "http://www.jalview.org/webstart/jalview.jnlp");\r
- BufferedReader in = new BufferedReader(new InputStreamReader(url.\r
- openStream()));\r
- String line = null;\r
- while ( (line = in.readLine()) != null)\r
- {\r
- if (line.indexOf("jalview.version") == -1)\r
- continue;\r
-\r
- line = line.substring(line.indexOf("value=") + 7);\r
- line = line.substring(0, line.lastIndexOf("\""));\r
- jnlpVersion = line;\r
- break;\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println(ex);\r
- jnlpVersion = getProperty("VERSION");\r
- }\r
-\r
- setProperty("LATEST_VERSION", jnlpVersion);\r
- }\r
- }\r
-\r
- VersionChecker vc = new VersionChecker();\r
- vc.start();\r
- }\r
- else\r
- {\r
- if(jnlpVersion!=null)\r
- setProperty("LATEST_VERSION", jnlpVersion);\r
- else\r
- applicationProperties.remove("LATEST_VERSION");\r
- }\r
-\r
- setProperty("VERSION", codeVersion);\r
-\r
- //LOAD USERDEFINED COLOURS\r
- jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));\r
- jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);\r
- }\r
-\r
-\r
-\r
- /**\r
- * Gets Jalview application property of given key. Returns null\r
- * if key not found\r
- *\r
- * @param key Name of property\r
- *\r
- * @return Property value\r
- */\r
- public static String getProperty(String key)\r
- {\r
- return applicationProperties.getProperty(key);\r
- }\r
-\r
-\r
- /** These methods are used when checking if the saved preference\r
- * is different to the default setting\r
- */\r
-\r
- public static boolean getDefault(String property, boolean def)\r
- {\r
- String string = getProperty(property);\r
- if (string != null)\r
- {\r
- def = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- return def;\r
- }\r
-\r
- /** These methods are used when checking if the saved preference\r
- * is different to the default setting\r
- */\r
- public static String getDefault(String property, String def)\r
- {\r
- String string = getProperty(property);\r
- if (string != null)\r
- {\r
- return string;\r
- }\r
-\r
- return def;\r
- }\r
-\r
-\r
- /**\r
- * Stores property in the file "HOME_DIR/.jalview_properties"\r
- *\r
- * @param key Name of object\r
- * @param obj String value of property\r
- *\r
- * @return String value of property\r
- */\r
- public static String setProperty(String key, String obj)\r
- {\r
- try\r
- {\r
- FileOutputStream out = new FileOutputStream(propertiesFile);\r
- applicationProperties.setProperty(key, obj);\r
- applicationProperties.store(out, "---JalviewX Properties File---");\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- { System.out.println("Error setting property: "+key+" "+obj+"\n"+ex); }\r
- return obj;\r
- }\r
-\r
- public static void saveProperties()\r
- {\r
- try\r
- {\r
- FileOutputStream out = new FileOutputStream(propertiesFile);\r
- applicationProperties.store(out, "---JalviewX Properties File---");\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- { System.out.println("Error saving properties: "+ex); }\r
- }\r
-}\r
+/*
+ * 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
+ */
+package jalview.bin;
+
+import java.io.*;
+
+import java.util.*;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.apache.log4j.Level;
+import org.apache.log4j.ConsoleAppender;
+
+
+/**
+ * Stores and retrieves Jalview Application Properties
+ * <br><br>Current properties include:
+ * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
+ * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
+ * <br>logs.Jalview.Level - Cache.log stringified level.
+ * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
+ * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
+ * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN
+ * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
+ * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
+ * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE
+
+ * @author $author$
+ * @version $Revision$
+ */
+public class Cache
+{
+ /**
+ * Initialises the Apache Axis logger
+ */
+ public static Logger log;
+
+ /** Jalview Properties */
+ public static Properties applicationProperties = new Properties();
+
+ /** Default file is ~/.jalview_properties */
+ static String propertiesFile;
+
+ public static void initLogger()
+ {
+ try
+ {
+ Logger laxis = Logger.getLogger("org.apache.axis");
+ Logger lcastor = Logger.getLogger("org.exolab.castor");
+ jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
+
+ laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
+ Level.INFO.toString())));
+ lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ Level.INFO.toString())));
+ jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Jalview.level",
+ Level.INFO.toString())));
+ ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+ "System.err");
+ ap.setName("JalviewLogger");
+
+ laxis.addAppender(ap);
+ lcastor.addAppender(ap);
+ jalview.bin.Cache.log.addAppender(ap);
+ // Tell the user that debug is enabled
+ jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
+ }
+ catch (Exception ex)
+ {
+ System.err.println("Problems initializing the log4j system\n");
+ }
+ }
+
+
+ /** Called when Jalview is started */
+ public static void loadProperties(String propsFile)
+ {
+ propertiesFile = propsFile;
+ if (propsFile == null)
+ {
+ propertiesFile = System.getProperty("user.home") + "/.jalview_properties";
+ }
+
+ try
+ {
+ FileInputStream fis = new FileInputStream(propertiesFile);
+ applicationProperties.load(fis);
+ applicationProperties.remove("LATEST_VERSION");
+ applicationProperties.remove("VERSION");
+ fis.close();
+ }
+ catch (Exception ex)
+ {
+ System.out.println("Error reading properties file: "+ex);
+ }
+
+ if(getDefault("USE_PROXY", false))
+ {
+ System.out.println("Using proxyServer: "+getDefault("PROXY_SERVER", null)+
+ " proxyPort: "+getDefault("PROXY_PORT", null));
+ System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
+ System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
+ }
+
+ // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+ // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
+ // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
+ try
+ {
+ String buildDetails = "jar:"
+ .concat(
+ Cache.class.getProtectionDomain().getCodeSource().getLocation().toString()
+ .concat("!/.build_properties")
+ );
+
+ java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ }
+ catch (Exception ex)
+ {
+ System.out.println("Error reading build details: "+ex);
+ applicationProperties.remove("VERSION");
+ }
+
+ String jnlpVersion = System.getProperty("jalview.version");
+ String codeVersion = getProperty("VERSION");
+
+
+ if(codeVersion==null)
+ {
+ // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+ codeVersion = "Test";
+ jnlpVersion = "Test";
+ }
+
+
+ System.out.println("Jalview Version: "+codeVersion);
+
+
+ // jnlpVersion will be null if we're using InstallAnywhere
+ // Dont do this check if running in headless mode
+ if(jnlpVersion==null && (
+ System.getProperty("java.awt.headless")==null
+ || System.getProperty("java.awt.headless").equals("false")))
+ {
+
+ class VersionChecker
+ extends Thread
+ {
+ public void run()
+ {
+ String jnlpVersion = null;
+ try
+ {
+ java.net.URL url = new java.net.URL(
+ "http://www.jalview.org/webstart/jalview.jnlp");
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.
+ openStream()));
+ String line = null;
+ while ( (line = in.readLine()) != null)
+ {
+ if (line.indexOf("jalview.version") == -1)
+ continue;
+
+ line = line.substring(line.indexOf("value=") + 7);
+ line = line.substring(0, line.lastIndexOf("\""));
+ jnlpVersion = line;
+ break;
+ }
+ }
+ catch (Exception ex)
+ {
+ System.out.println(ex);
+ jnlpVersion = getProperty("VERSION");
+ }
+
+ setProperty("LATEST_VERSION", jnlpVersion);
+ }
+ }
+
+ VersionChecker vc = new VersionChecker();
+ vc.start();
+ }
+ else
+ {
+ if(jnlpVersion!=null)
+ setProperty("LATEST_VERSION", jnlpVersion);
+ else
+ applicationProperties.remove("LATEST_VERSION");
+ }
+
+ setProperty("VERSION", codeVersion);
+
+ //LOAD USERDEFINED COLOURS
+ jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
+ jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+ }
+
+
+
+ /**
+ * Gets Jalview application property of given key. Returns null
+ * if key not found
+ *
+ * @param key Name of property
+ *
+ * @return Property value
+ */
+ public static String getProperty(String key)
+ {
+ return applicationProperties.getProperty(key);
+ }
+
+
+ /** These methods are used when checking if the saved preference
+ * is different to the default setting
+ */
+
+ public static boolean getDefault(String property, boolean def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ def = Boolean.valueOf(string).booleanValue();
+ }
+
+ return def;
+ }
+
+ /** These methods are used when checking if the saved preference
+ * is different to the default setting
+ */
+ public static String getDefault(String property, String def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ return string;
+ }
+
+ return def;
+ }
+
+
+ /**
+ * Stores property in the file "HOME_DIR/.jalview_properties"
+ *
+ * @param key Name of object
+ * @param obj String value of property
+ *
+ * @return String value of property
+ */
+ public static String setProperty(String key, String obj)
+ {
+ try
+ {
+ FileOutputStream out = new FileOutputStream(propertiesFile);
+ applicationProperties.setProperty(key, obj);
+ applicationProperties.store(out, "---JalviewX Properties File---");
+ out.close();
+ }
+ catch (Exception ex)
+ { System.out.println("Error setting property: "+key+" "+obj+"\n"+ex); }
+ return obj;
+ }
+
+ public static void saveProperties()
+ {
+ try
+ {
+ FileOutputStream out = new FileOutputStream(propertiesFile);
+ applicationProperties.store(out, "---JalviewX Properties File---");
+ out.close();
+ }
+ catch (Exception ex)
+ { System.out.println("Error saving properties: "+ex); }
+ }
+ /**
+ * internal vamsas class discovery state
+ */
+ private static int vamsasJarsArePresent=-1;
+ /**
+ * Searches for vamsas client classes on class path.
+ * @return true if vamsas client is present on classpath
+ */
+ public static boolean vamsasJarsPresent() {
+ if (vamsasJarsArePresent==-1) {
+ try {
+ if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass("org.vamsas.client.VorbaId")!=null) {
+ jalview.bin.Cache.log.debug("Found Vamsas Classes (org.vamsas.client.VorbaId can be loaded)");
+ vamsasJarsArePresent=1;
+ }
+ } catch (Exception e) {
+ vamsasJarsArePresent=0;
+ jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ }
+ }
+ return (vamsasJarsArePresent>0);
+ }
+
+}
{
return ShowNewickTree(nf,title,600,500,4,5);
}
+ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
+ {
+ return ShowNewickTree(nf,title, input, 600,500,4,5);
+ }
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
+ return ShowNewickTree(nf, title, null, w, h, x, y);
+ }
/**
- * DOCUMENT ME!
+ * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
*
- * @param nf DOCUMENT ME!
- * @param title DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @param nf the tree
+ * @param title tree viewer title
+ * @param input Associated alignment input data (or null)
+ * @param w width
+ * @param h height
+ * @param x position
+ * @param y position
+ * @return TreePanel handle
*/
- public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
- {
+ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
TreePanel tp = null;
try
tp = new TreePanel(alignPanel,
"FromFile",
title,
- nf);
+ nf, input);
tp.setSize(w,h);
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.io.*;\r
-\r
-import java.awt.*;\r
-import java.awt.datatransfer.*;\r
-import java.awt.dnd.*;\r
-import java.awt.event.*;\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Desktop extends jalview.jbgui.GDesktop\r
- implements DropTargetListener, ClipboardOwner\r
-{\r
- /** DOCUMENT ME!! */\r
- public static Desktop instance;\r
- public static JDesktopPane desktop;\r
- static int openFrameCount = 0;\r
- static final int xOffset = 30;\r
- static final int yOffset = 30;\r
- public static jalview.ws.Discoverer discoverer;\r
-\r
- public static Object [] jalviewClipboard;\r
-\r
- static int fileLoadingCount= 0;\r
-\r
- /**\r
- * Creates a new Desktop object.\r
- */\r
- public Desktop()\r
- {\r
- instance = this;\r
-\r
- Image image = null;\r
-\r
- try\r
- {\r
- java.net.URL url = getClass().getResource("/images/logo.gif");\r
-\r
- if (url != null)\r
- {\r
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
-\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image, 0);\r
- mt.waitForID(0);\r
- setIconImage(image);\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));\r
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
- desktop = new JDesktopPane();\r
- desktop.setBackground(Color.white);\r
- getContentPane().setLayout(new BorderLayout());\r
- getContentPane().add(desktop, BorderLayout.CENTER);\r
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
-\r
- // This line prevents Windows Look&Feel resizing all new windows to maximum\r
- // if previous window was maximised\r
- desktop.setDesktopManager(new DefaultDesktopManager());\r
-\r
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
- String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
- String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
- String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
- String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
-\r
- if ((x != null) && (y != null) && (width != null) && (height != null))\r
- {\r
- setBounds(Integer.parseInt(x), Integer.parseInt(y),\r
- Integer.parseInt(width), Integer.parseInt(height));\r
- }\r
- else\r
- {\r
- setBounds((int) (screenSize.width - 900) / 2,\r
- (int) (screenSize.height - 650) / 2, 900, 650);\r
- }\r
-\r
- this.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent evt)\r
- {\r
- quit();\r
- }\r
- });\r
-\r
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
-\r
- /////////Add a splashscreen on startup\r
- /////////Add a splashscreen on startup\r
- JInternalFrame frame = new JInternalFrame();\r
-\r
- SplashScreen splash = new SplashScreen(frame, image);\r
- frame.setContentPane(splash);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- frame.setLocation((int) ((getWidth() - 750) / 2),\r
- (int) ((getHeight() - 160) / 2));\r
-\r
- addInternalFrame(frame, "", 750, 160, false);\r
-\r
- discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param frame DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- * @param w DOCUMENT ME!\r
- * @param h DOCUMENT ME!\r
- */\r
- public static synchronized void addInternalFrame(final JInternalFrame frame,\r
- String title, int w, int h)\r
- {\r
- addInternalFrame(frame, title, w, h, true);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param frame DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- * @param w DOCUMENT ME!\r
- * @param h DOCUMENT ME!\r
- * @param resizable DOCUMENT ME!\r
- */\r
- public static synchronized void addInternalFrame(final JInternalFrame frame,\r
- String title, int w, int h, boolean resizable)\r
- {\r
-\r
- frame.setTitle(title);\r
- if(frame.getWidth()<1 || frame.getHeight()<1)\r
- {\r
- frame.setSize(w, h);\r
- }\r
- // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN\r
- // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN\r
- // IF JALVIEW IS RUNNING HEADLESS\r
- /////////////////////////////////////////////////\r
- if (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true"))\r
- {\r
- return;\r
- }\r
-\r
-\r
- openFrameCount++;\r
-\r
- frame.setVisible(true);\r
- frame.setClosable(true);\r
- frame.setResizable(resizable);\r
- frame.setMaximizable(resizable);\r
- frame.setIconifiable(resizable);\r
- frame.setFrameIcon(null);\r
-\r
- if (frame.getX()<1 && frame.getY()<1)\r
- {\r
- frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);\r
- }\r
-\r
- final JMenuItem menuItem = new JMenuItem(title);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameActivated(javax.swing.event.\r
- InternalFrameEvent evt)\r
- {\r
- JInternalFrame itf = desktop.getSelectedFrame();\r
- if (itf != null)\r
- itf.requestFocus();\r
-\r
- }\r
-\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- openFrameCount--;\r
- windowMenu.remove(menuItem);\r
- JInternalFrame itf = desktop.getSelectedFrame();\r
- if (itf != null)\r
- itf.requestFocus();\r
- }\r
- ;\r
- });\r
-\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setSelected(true);\r
- frame.setIcon(false);\r
- }\r
- catch (java.beans.PropertyVetoException ex)\r
- {\r
-\r
- }\r
- }\r
- });\r
-\r
- windowMenu.add(menuItem);\r
-\r
- desktop.add(frame);\r
- frame.toFront();\r
- try{\r
- frame.setSelected(true);\r
- frame.requestFocus();\r
- }catch(java.beans.PropertyVetoException ve)\r
- {}\r
- }\r
-\r
- public void lostOwnership(Clipboard clipboard, Transferable contents)\r
- {\r
- Desktop.jalviewClipboard = null;\r
- }\r
-\r
- public void dragEnter(DropTargetDragEvent evt)\r
- {}\r
-\r
- public void dragExit(DropTargetEvent evt)\r
- {}\r
-\r
- public void dragOver(DropTargetDragEvent evt)\r
- {}\r
-\r
- public void dropActionChanged(DropTargetDragEvent evt)\r
- {}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void drop(DropTargetDropEvent evt)\r
- {\r
- Transferable t = evt.getTransferable();\r
- java.util.List files = null;\r
-\r
- try\r
- {\r
- DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");\r
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
- {\r
- //Works on Windows and MacOSX\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
- files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
- }\r
- else if (t.isDataFlavorSupported(uriListFlavor))\r
- {\r
- // This is used by Unix drag system\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
- String data = (String) t.getTransferData(uriListFlavor);\r
- files = new java.util.ArrayList(1);\r
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(\r
- data,\r
- "\r\n");\r
- st.hasMoreTokens(); )\r
- {\r
- String s = st.nextToken();\r
- if (s.startsWith("#"))\r
- {\r
- // the line is a comment (as per the RFC 2483)\r
- continue;\r
- }\r
-\r
- java.net.URI uri = new java.net.URI(s);\r
- java.io.File file = new java.io.File(uri);\r
- files.add(file);\r
- }\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- if (files != null)\r
- {\r
- try\r
- {\r
- for (int i = 0; i < files.size(); i++)\r
- {\r
- String file = files.get(i).toString();\r
- String protocol = FormatAdapter.FILE;\r
- String format = null;\r
-\r
- if (file.endsWith(".jar"))\r
- {\r
- format = "Jalview";\r
-\r
- }\r
- else\r
- {\r
- format = new IdentifyFile().Identify(file,\r
- protocol);\r
- }\r
-\r
-\r
- new FileLoader().LoadFile(file, protocol, format);\r
-\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]\r
- {\r
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
- "jar"\r
- },\r
- new String[]\r
- {\r
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- String format = null;\r
- if (chooser.getSelectedFormat().equals("Jalview"))\r
- {\r
- format = "Jalview";\r
- }\r
- else\r
- {\r
- format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);\r
- }\r
-\r
- if (viewport != null)\r
- new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);\r
- else\r
- new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);\r
- }\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputURLMenuItem_actionPerformed(AlignViewport viewport)\r
- {\r
- // This construct allows us to have a wider textfield\r
- // for viewing\r
- JLabel label = new JLabel("Enter URL of Input File");\r
- final JComboBox history = new JComboBox();\r
-\r
- JPanel panel = new JPanel(new GridLayout(2,1));\r
- panel.add(label);\r
- panel.add(history);\r
- history.setPreferredSize(new Dimension(400,20));\r
- history.setEditable(true);\r
- history.addItem("http://www.");\r
-\r
- String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");\r
-\r
- StringTokenizer st;\r
-\r
- if (historyItems != null)\r
- {\r
- st = new StringTokenizer(historyItems, "\t");\r
-\r
- while (st.hasMoreTokens())\r
- {\r
- history.addItem(st.nextElement());\r
- }\r
- }\r
-\r
- int reply = JOptionPane.showInternalConfirmDialog(desktop,\r
- panel, "Input Alignment From URL",\r
- JOptionPane.OK_CANCEL_OPTION );\r
-\r
-\r
- if (reply != JOptionPane.OK_OPTION )\r
- {\r
- return;\r
- }\r
-\r
- String url = history.getSelectedItem().toString();\r
-\r
- if (url.toLowerCase().endsWith(".jar"))\r
- {\r
- if (viewport != null)\r
- new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");\r
- else\r
- new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");\r
- }\r
- else\r
- {\r
- String format = new IdentifyFile().Identify(url, FormatAdapter.URL);\r
-\r
- if (format.equals("URL NOT FOUND"))\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
- if (viewport != null)\r
- new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);\r
- else\r
- new FileLoader().LoadFile(url, FormatAdapter.URL, format);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput(viewport);\r
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
- }\r
-\r
- /*\r
- * Exit the program\r
- */\r
- public void quit()\r
- {\r
- jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");\r
- jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");\r
- jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
- System.exit(0);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- StringBuffer message = new StringBuffer("JalView version " +\r
- jalview.bin.Cache.getProperty(\r
- "VERSION") +\r
- "; last updated: " +\r
- jalview.bin.\r
- Cache.getDefault("BUILD_DATE", "unknown"));\r
-\r
- if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(\r
- jalview.bin.Cache.getProperty("VERSION")))\r
- {\r
- message.append("\n\n!! Jalview version "\r
- + jalview.bin.Cache.getProperty("LATEST_VERSION")\r
- + " is available for download from http://www.jalview.org !!\n");\r
-\r
- }\r
-\r
- message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +\r
- "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +\r
- "\nFor all issues relating to Jalview, email help@jalview.org" +\r
- "\n\nIf you use JalView, please cite:" +\r
- "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +\r
- "\nBioinformatics, 2004 20;426-7.");\r
-\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-\r
- message.toString(), "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");\r
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);\r
-\r
- javax.help.HelpBroker hb = hs.createHelpBroker();\r
- hb.setCurrentID("home");\r
- hb.setDisplayed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
- new Preferences();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void saveState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "jar" },\r
- new String[] { "Jalview Project" }, "Jalview Project");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save State");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- java.io.File choice = chooser.getSelectedFile();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- new Jalview2XML().SaveState(choice);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void loadState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "jar" },\r
- new String[] { "Jalview Project" }, "Jalview Project");\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Restore state");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getAbsolutePath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
- new Jalview2XML().LoadJalviewAlign(choice);\r
- }\r
- }\r
-\r
- /* public void vamsasLoad_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty("LAST_DIRECTORY"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Load Vamsas file");\r
- chooser.setToolTipText("Import");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);\r
- vs.load(\r
- chooser.getSelectedFile().getAbsolutePath()\r
- );\r
- }\r
-\r
- }*/\r
-\r
-\r
- public void inputSequence_actionPerformed(ActionEvent e)\r
- {\r
- new SequenceFetcher(null);\r
- }\r
-\r
- JPanel progressPanel;\r
-\r
- public void startLoading(final String fileName)\r
- {\r
- if (fileLoadingCount == 0)\r
- {\r
- progressPanel = new JPanel(new BorderLayout());\r
- JProgressBar progressBar = new JProgressBar();\r
- progressBar.setIndeterminate(true);\r
-\r
- progressPanel.add(new JLabel("Loading File: " + fileName + " "),\r
- BorderLayout.WEST);\r
-\r
- progressPanel.add(progressBar, BorderLayout.CENTER);\r
-\r
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);\r
- }\r
- fileLoadingCount++;\r
- validate();\r
- }\r
-\r
- public void stopLoading()\r
- {\r
- fileLoadingCount--;\r
- if (fileLoadingCount < 1)\r
- {\r
- if(progressPanel!=null)\r
- {\r
- this.getContentPane().remove(progressPanel);\r
- progressPanel = null;\r
- }\r
- fileLoadingCount = 0;\r
- }\r
- validate();\r
- }\r
-\r
- public static int getViewCount(String viewId)\r
- {\r
- int count = 0;\r
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
- for (int t = 0; t < frames.length; t++)\r
- {\r
- if (frames[t] instanceof AlignFrame)\r
- {\r
- AlignFrame af = (AlignFrame) frames[t];\r
- for(int a=0; a<af.alignPanels.size(); a++)\r
- {\r
- if(viewId.equals(\r
- ((AlignmentPanel)af.alignPanels.elementAt(a)).av.getSequenceSetId() )\r
- )\r
- count ++;\r
- }\r
- }\r
- }\r
-\r
- return count;\r
- }\r
-\r
- public void explodeViews(AlignFrame af)\r
- {\r
- int size = af.alignPanels.size();\r
- if(size<2)\r
- return;\r
- af.closeMenuItem_actionPerformed(null);\r
-\r
- for(int i=0; i<size; i++)\r
- {\r
- AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);\r
- AlignFrame newaf = new AlignFrame(ap);\r
- if(ap.av.explodedPosition!=null)\r
- newaf.setBounds(ap.av.explodedPosition);\r
-\r
- ap.av.gatherViewsHere = false;\r
-\r
- PaintRefresher.Register(ap.seqPanel.seqCanvas, ap.av.getSequenceSetId());\r
- PaintRefresher.Register(ap.idPanel.idCanvas, ap.av.getSequenceSetId());\r
- PaintRefresher.Register(ap, ap.av.getSequenceSetId());\r
-\r
-\r
- newaf.viewport = ap.av;\r
- addInternalFrame(newaf, af.getTitle(),\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
-\r
- }\r
-\r
- public void gatherViews(AlignFrame source)\r
- {\r
- source.viewport.gatherViewsHere = true;\r
- source.viewport.explodedPosition = source.getBounds();\r
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
- String viewId = source.viewport.sequenceSetID;\r
-\r
- for (int t = 0; t < frames.length; t++)\r
- {\r
- if (frames[t] instanceof AlignFrame && frames[t] != source)\r
- {\r
- AlignFrame af = (AlignFrame) frames[t];\r
- boolean gatherThis = false;\r
- for (int a = 0; a < af.alignPanels.size(); a++)\r
- {\r
- AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);\r
- if (viewId.equals(ap.av.getSequenceSetId()))\r
- {\r
- gatherThis = true;\r
- ap.av.gatherViewsHere = false;\r
- ap.av.explodedPosition = af.getBounds();\r
- source.addAlignmentPanel(ap);\r
- }\r
- }\r
- if (gatherThis)\r
- af.closeMenuItem_actionPerformed(null);\r
- }\r
- }\r
-\r
- }\r
-\r
-\r
-}\r
-\r
+/*
+ * 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
+ */
+package jalview.gui;
+
+import jalview.io.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
+import java.awt.event.*;
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Desktop extends jalview.jbgui.GDesktop
+ implements DropTargetListener, ClipboardOwner
+{
+ /** DOCUMENT ME!! */
+ public static Desktop instance;
+ public static JDesktopPane desktop;
+ static int openFrameCount = 0;
+ static final int xOffset = 30;
+ static final int yOffset = 30;
+ public static jalview.ws.Discoverer discoverer;
+
+ public static Object [] jalviewClipboard;
+
+ static int fileLoadingCount= 0;
+
+ /**
+ * Creates a new Desktop object.
+ */
+ public Desktop()
+ {
+ instance = this;
+ doVamsasClientCheck();
+ Image image = null;
+
+ try
+ {
+ java.net.URL url = getClass().getResource("/images/logo.gif");
+
+ if (url != null)
+ {
+ image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+
+ MediaTracker mt = new MediaTracker(this);
+ mt.addImage(image, 0);
+ mt.waitForID(0);
+ setIconImage(image);
+ }
+ }
+ catch (Exception ex)
+ {
+ }
+
+ setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
+ setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ desktop = new JDesktopPane();
+ desktop.setBackground(Color.white);
+ getContentPane().setLayout(new BorderLayout());
+ getContentPane().add(desktop, BorderLayout.CENTER);
+ desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+
+ // This line prevents Windows Look&Feel resizing all new windows to maximum
+ // if previous window was maximised
+ desktop.setDesktopManager(new DefaultDesktopManager());
+
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ String x = jalview.bin.Cache.getProperty("SCREEN_X");
+ String y = jalview.bin.Cache.getProperty("SCREEN_Y");
+ String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
+ String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
+
+ if ((x != null) && (y != null) && (width != null) && (height != null))
+ {
+ setBounds(Integer.parseInt(x), Integer.parseInt(y),
+ Integer.parseInt(width), Integer.parseInt(height));
+ }
+ else
+ {
+ setBounds((int) (screenSize.width - 900) / 2,
+ (int) (screenSize.height - 650) / 2, 900, 650);
+ }
+
+ this.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ quit();
+ }
+ });
+
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+
+ /////////Add a splashscreen on startup
+ /////////Add a splashscreen on startup
+ JInternalFrame frame = new JInternalFrame();
+
+ SplashScreen splash = new SplashScreen(frame, image);
+ frame.setContentPane(splash);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.setLocation((int) ((getWidth() - 750) / 2),
+ (int) ((getHeight() - 160) / 2));
+
+ addInternalFrame(frame, "", 750, 160, false);
+
+ discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+ }
+
+ private void doVamsasClientCheck() {
+ if (jalview.bin.Cache.vamsasJarsPresent()) {
+ VamsasMenu.setVisible(true);
+ vamsasLoad.setVisible(true);
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frame DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame,
+ String title, int w, int h)
+ {
+ addInternalFrame(frame, title, w, h, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frame DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ * @param resizable DOCUMENT ME!
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame,
+ String title, int w, int h, boolean resizable)
+ {
+
+ frame.setTitle(title);
+ if(frame.getWidth()<1 || frame.getHeight()<1)
+ {
+ frame.setSize(w, h);
+ }
+ // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
+ // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
+ // IF JALVIEW IS RUNNING HEADLESS
+ /////////////////////////////////////////////////
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ return;
+ }
+
+
+ openFrameCount++;
+
+ frame.setVisible(true);
+ frame.setClosable(true);
+ frame.setResizable(resizable);
+ frame.setMaximizable(resizable);
+ frame.setIconifiable(resizable);
+ frame.setFrameIcon(null);
+
+ if (frame.getX()<1 && frame.getY()<1)
+ {
+ frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
+ }
+
+ final JMenuItem menuItem = new JMenuItem(title);
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameActivated(javax.swing.event.
+ InternalFrameEvent evt)
+ {
+ JInternalFrame itf = desktop.getSelectedFrame();
+ if (itf != null)
+ itf.requestFocus();
+
+ }
+
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ openFrameCount--;
+ windowMenu.remove(menuItem);
+ JInternalFrame itf = desktop.getSelectedFrame();
+ if (itf != null)
+ itf.requestFocus();
+ }
+ ;
+ });
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setSelected(true);
+ frame.setIcon(false);
+ }
+ catch (java.beans.PropertyVetoException ex)
+ {
+
+ }
+ }
+ });
+
+ windowMenu.add(menuItem);
+
+ desktop.add(frame);
+ frame.toFront();
+ try{
+ frame.setSelected(true);
+ frame.requestFocus();
+ }catch(java.beans.PropertyVetoException ve)
+ {}
+ }
+
+ public void lostOwnership(Clipboard clipboard, Transferable contents)
+ {
+ Desktop.jalviewClipboard = null;
+ }
+
+ public void dragEnter(DropTargetDragEvent evt)
+ {}
+
+ public void dragExit(DropTargetEvent evt)
+ {}
+
+ public void dragOver(DropTargetDragEvent evt)
+ {}
+
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {}
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void drop(DropTargetDropEvent evt)
+ {
+ Transferable t = evt.getTransferable();
+ java.util.List files = null;
+
+ try
+ {
+ DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ //Works on Windows and MacOSX
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+ }
+ else if (t.isDataFlavorSupported(uriListFlavor))
+ {
+ // This is used by Unix drag system
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ String data = (String) t.getTransferData(uriListFlavor);
+ files = new java.util.ArrayList(1);
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data,
+ "\r\n");
+ st.hasMoreTokens(); )
+ {
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+
+ java.net.URI uri = new java.net.URI(s);
+ java.io.File file = new java.io.File(uri);
+ files.add(file);
+ }
+ }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ if (files != null)
+ {
+ try
+ {
+ for (int i = 0; i < files.size(); i++)
+ {
+ String file = files.get(i).toString();
+ String protocol = FormatAdapter.FILE;
+ String format = null;
+
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
+
+ }
+ else
+ {
+ format = new IdentifyFile().Identify(file,
+ protocol);
+ }
+
+
+ new FileLoader().LoadFile(file, protocol, format);
+
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"),
+ new String[]
+ {
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+ "jar"
+ },
+ new String[]
+ {
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Open local file");
+ chooser.setToolTipText("Open");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+
+ String format = null;
+ if (chooser.getSelectedFormat().equals("Jalview"))
+ {
+ format = "Jalview";
+ }
+ else
+ {
+ format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
+ }
+
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
+ else
+ new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
+ }
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+ {
+ // This construct allows us to have a wider textfield
+ // for viewing
+ JLabel label = new JLabel("Enter URL of Input File");
+ final JComboBox history = new JComboBox();
+
+ JPanel panel = new JPanel(new GridLayout(2,1));
+ panel.add(label);
+ panel.add(history);
+ history.setPreferredSize(new Dimension(400,20));
+ history.setEditable(true);
+ history.addItem("http://www.");
+
+ String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+ StringTokenizer st;
+
+ if (historyItems != null)
+ {
+ st = new StringTokenizer(historyItems, "\t");
+
+ while (st.hasMoreTokens())
+ {
+ history.addItem(st.nextElement());
+ }
+ }
+
+ int reply = JOptionPane.showInternalConfirmDialog(desktop,
+ panel, "Input Alignment From URL",
+ JOptionPane.OK_CANCEL_OPTION );
+
+
+ if (reply != JOptionPane.OK_OPTION )
+ {
+ return;
+ }
+
+ String url = history.getSelectedItem().toString();
+
+ if (url.toLowerCase().endsWith(".jar"))
+ {
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
+ else
+ new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+ }
+ else
+ {
+ String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+
+ if (format.equals("URL NOT FOUND"))
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't locate " + url,
+ "URL not found",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+ else
+ new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(viewport);
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+ }
+
+ /*
+ * Exit the program
+ */
+ public void quit()
+ {
+ jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
+ jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+ System.exit(0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void aboutMenuItem_actionPerformed(ActionEvent e)
+ {
+ StringBuffer message = new StringBuffer("JalView version " +
+ jalview.bin.Cache.getProperty(
+ "VERSION") +
+ "; last updated: " +
+ jalview.bin.
+ Cache.getDefault("BUILD_DATE", "unknown"));
+
+ if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
+ jalview.bin.Cache.getProperty("VERSION")))
+ {
+ message.append("\n\n!! Jalview version "
+ + jalview.bin.Cache.getProperty("LATEST_VERSION")
+ + " is available for download from http://www.jalview.org !!\n");
+
+ }
+
+ message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
+ "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
+ "\nFor all issues relating to Jalview, email help@jalview.org" +
+ "\n\nIf you use JalView, please cite:" +
+ "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
+ "\nBioinformatics, 2004 20;426-7.");
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ message.toString(), "About Jalview",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void documentationMenuItem_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+ javax.help.HelpBroker hb = hs.createHelpBroker();
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void preferences_actionPerformed(ActionEvent e)
+ {
+ new Preferences();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveState_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "jar" },
+ new String[] { "Jalview Project" }, "Jalview Project");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save State");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ java.io.File choice = chooser.getSelectedFile();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ new Jalview2XML().SaveState(choice);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void loadState_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "jar" },
+ new String[] { "Jalview Project" }, "Jalview Project");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Restore state");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getAbsolutePath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+ new Jalview2XML().LoadJalviewAlign(choice);
+ }
+ }
+
+ /* public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Vamsas file");
+ chooser.setToolTipText("Import");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+ vs.load(
+ chooser.getSelectedFile().getAbsolutePath()
+ );
+ }
+
+ }*/
+
+
+ public void inputSequence_actionPerformed(ActionEvent e)
+ {
+ new SequenceFetcher(null);
+ }
+
+ JPanel progressPanel;
+
+ public void startLoading(final String fileName)
+ {
+ if (fileLoadingCount == 0)
+ {
+ progressPanel = new JPanel(new BorderLayout());
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel("Loading File: " + fileName + " "),
+ BorderLayout.WEST);
+
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ }
+ fileLoadingCount++;
+ validate();
+ }
+
+ public void stopLoading()
+ {
+ fileLoadingCount--;
+ if (fileLoadingCount < 1)
+ {
+ if(progressPanel!=null)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
+ fileLoadingCount = 0;
+ }
+ validate();
+ }
+
+ public static int getViewCount(String viewId)
+ {
+ int count = 0;
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[t];
+ for(int a=0; a<af.alignPanels.size(); a++)
+ {
+ if(viewId.equals(
+ ((AlignmentPanel)af.alignPanels.elementAt(a)).av.getSequenceSetId() )
+ )
+ count ++;
+ }
+ }
+ }
+
+ return count;
+ }
+
+ public void explodeViews(AlignFrame af)
+ {
+ int size = af.alignPanels.size();
+ if(size<2)
+ return;
+ af.closeMenuItem_actionPerformed(null);
+
+ for(int i=0; i<size; i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);
+ AlignFrame newaf = new AlignFrame(ap);
+ if(ap.av.explodedPosition!=null)
+ newaf.setBounds(ap.av.explodedPosition);
+
+ ap.av.gatherViewsHere = false;
+
+ PaintRefresher.Register(ap.seqPanel.seqCanvas, ap.av.getSequenceSetId());
+ PaintRefresher.Register(ap.idPanel.idCanvas, ap.av.getSequenceSetId());
+ PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
+
+ newaf.viewport = ap.av;
+ addInternalFrame(newaf, af.getTitle(),
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ }
+
+ public void gatherViews(AlignFrame source)
+ {
+ source.viewport.gatherViewsHere = true;
+ source.viewport.explodedPosition = source.getBounds();
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ String viewId = source.viewport.sequenceSetID;
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame && frames[t] != source)
+ {
+ AlignFrame af = (AlignFrame) frames[t];
+ boolean gatherThis = false;
+ for (int a = 0; a < af.alignPanels.size(); a++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+ if (viewId.equals(ap.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ ap.av.gatherViewsHere = false;
+ ap.av.explodedPosition = af.getBounds();
+ source.addAlignmentPanel(ap);
+ }
+ }
+ if (gatherThis)
+ af.closeMenuItem_actionPerformed(null);
+ }
+ }
+
+ }
+
+ jalview.gui.VamsasClient v_client=null;
+ public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+ if (v_client==null) {
+ // Start a session.
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Vamsas file");
+ chooser.setToolTipText("Import");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ v_client = new jalview.gui.VamsasClient(this,
+ chooser.getSelectedFile());
+ this.vamsasLoad.setText("Session Update");
+ this.vamsasStop.setVisible(true);
+ v_client.initial_update();
+ v_client.startWatcher();
+ }
+ } else {
+ // store current data in session.
+ v_client.push_update();
+ }
+ }
+ public void vamsasStop_actionPerformed(ActionEvent e) {
+ if (v_client!=null) {
+ v_client.end_session();
+ v_client=null;
+ this.vamsasStop.setVisible(false);
+ this.vamsasLoad.setText("Start Vamsas Session...");
+ }
+ }
+ /**
+ * hide vamsas user gui bits when a vamsas document event is being handled.
+ * @param b true to hide gui, false to reveal gui
+ */
+ public void setVamsasUpdate(boolean b) {
+ jalview.bin.Cache.log.debug("Setting gui for Vamsas update "+(b ? "in progress" : "finished"));
+ vamsasLoad.setVisible(!b);
+ vamsasStop.setVisible(!b);
+
+ }
+}
+
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import org.jibble.epsgraphics.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.image.*;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.imageio.*;\r
-\r
-import java.beans.PropertyChangeEvent;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class TreePanel extends GTreePanel\r
-{\r
- String type;\r
- String pwtype;\r
- TreeCanvas treeCanvas;\r
- NJTree tree;\r
- AlignViewport av;\r
-\r
- /**\r
- * Creates a new TreePanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param seqVector DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- * @param s DOCUMENT ME!\r
- * @param e DOCUMENT ME!\r
- */\r
- public TreePanel(AlignmentPanel ap, String type, String pwtype)\r
- {\r
- super();\r
- initTreePanel(ap, type, pwtype, null);\r
-\r
- // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- // showDistances(true);\r
- }\r
-\r
- /**\r
- * Creates a new TreePanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param seqVector DOCUMENT ME!\r
- * @param newtree DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- */\r
- public TreePanel(AlignmentPanel ap,\r
- String type,\r
- String pwtype,\r
- NewickFile newtree)\r
- {\r
- super();\r
- initTreePanel(ap, type, pwtype, newtree);\r
- }\r
-\r
- public AlignmentI getAlignment()\r
- {\r
- return treeCanvas.av.getAlignment();\r
- }\r
-\r
-\r
- void initTreePanel(AlignmentPanel ap, String type, String pwtype,\r
- NewickFile newTree)\r
- {\r
-\r
- av = ap.av;\r
- this.type = type;\r
- this.pwtype = pwtype;\r
-\r
- treeCanvas = new TreeCanvas(ap, scrollPane);\r
- scrollPane.setViewportView(treeCanvas);\r
-\r
- av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
- {\r
- public void propertyChange(PropertyChangeEvent evt)\r
- {\r
- if (evt.getPropertyName().equals("alignment"))\r
- {\r
- if(tree==null)\r
- System.out.println("tree is null");\r
- if(evt.getNewValue()==null)\r
- System.out.println("new value is null");\r
-\r
- tree.UpdatePlaceHolders( (Vector) evt.getNewValue());\r
-\r
- repaint();\r
- }\r
- }\r
- });\r
-\r
- this.av = av;\r
-\r
-\r
- TreeLoader tl = new TreeLoader(newTree);\r
- tl.start();\r
-\r
- }\r
-\r
- class TreeLoader extends Thread\r
- {\r
- NewickFile newtree;\r
- jalview.datamodel.AlignmentView odata=null;\r
- public TreeLoader(NewickFile newtree)\r
- {\r
- this.newtree = newtree;\r
- if (newtree != null)\r
- {\r
- // Must be outside run(), as Jalview2XML tries to\r
- // update distance/bootstrap visibility at the same time\r
- showBootstrap(newtree.HasBootstrap());\r
- showDistances(newtree.HasDistances());\r
- }\r
- }\r
-\r
- public void run()\r
- {\r
-\r
- if(newtree!=null)\r
- {\r
- if (odata==null) {\r
- tree = new NJTree(av.alignment.getSequencesArray(),\r
- newtree);\r
- } else {\r
- tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
- }\r
- if (!tree.hasOriginalSequenceData())\r
- allowOriginalSeqData(false);\r
- }\r
- else\r
- {\r
- int start, end;\r
- SequenceI [] seqs;\r
- AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
- if(av.getSelectionGroup()==null)\r
- {\r
- start = 0;\r
- end = av.alignment.getWidth();\r
- seqs = av.alignment.getSequencesArray();\r
- }\r
- else\r
- {\r
- start = av.getSelectionGroup().getStartRes();\r
- end = av.getSelectionGroup().getEndRes()+1;\r
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
- }\r
-\r
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
- showDistances(true);\r
- }\r
-\r
-\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- treeCanvas.setTree(tree);\r
- treeCanvas.repaint();\r
- av.setCurrentTree(tree);\r
-\r
- }\r
- }\r
-\r
- public void showDistances(boolean b)\r
- {\r
- treeCanvas.setShowDistances(b);\r
- distanceMenu.setSelected(b);\r
- }\r
-\r
- public void showBootstrap(boolean b)\r
- {\r
- treeCanvas.setShowBootstrap(b);\r
- bootstrapMenu.setSelected(b);\r
- }\r
-\r
- public void showPlaceholders(boolean b)\r
- {\r
- placeholdersMenu.setState(b);\r
- treeCanvas.setMarkPlaceholders(b);\r
- }\r
-\r
- private void allowOriginalSeqData(boolean b) {\r
- originalSeqData.setVisible(b);\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void textbox_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-\r
- StringBuffer buffer = new StringBuffer();\r
-\r
- if (type.equals("AV"))\r
- {\r
- buffer.append("Average distance tree using ");\r
- }\r
- else\r
- {\r
- buffer.append("Neighbour joining tree using ");\r
- }\r
-\r
- if (pwtype.equals("BL"))\r
- {\r
- buffer.append("BLOSUM62");\r
- }\r
- else\r
- {\r
- buffer.append("PID");\r
- }\r
-\r
- Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
-\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void saveAsNewick_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save tree as newick file");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(null);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- try\r
- {\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
- choice));\r
- out.println(output);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void printMenu_actionPerformed(ActionEvent e)\r
- {\r
- //Putting in a thread avoids Swing painting problems\r
- treeCanvas.startPrinting();\r
- }\r
-\r
-\r
- public void originalSeqData_actionPerformed(ActionEvent e)\r
- {\r
- if (!tree.hasOriginalSequenceData())\r
- {\r
- jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");\r
- return;\r
- }\r
- // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
- // or create a selection box around columns in alignment view\r
- // test Alignment(SeqCigar[])\r
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.\r
- getGapCharacter());\r
-\r
-\r
- if (alAndColsel != null && alAndColsel[0]!=null)\r
- {\r
- // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);\r
-\r
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);\r
- Alignment dataset = av.getAlignment().getDataset();\r
- if (dataset != null)\r
- {\r
- al.setDataset(dataset);\r
- }\r
-\r
- if (true)\r
- {\r
- // make a new frame!\r
- AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT\r
-);\r
-\r
- //>>>This is a fix for the moment, until a better solution is found!!<<<\r
- // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
-\r
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
- // msaorder);\r
-\r
- Desktop.addInternalFrame(af, "Original Data for " + this.title,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.fitToWindow = fitToWindow.isSelected();\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- if (treeCanvas == null)\r
- {\r
- return;\r
- }\r
-\r
- new FontChooser(this);\r
- }\r
-\r
- public Font getTreeFont()\r
- {\r
- return treeCanvas.font;\r
- }\r
-\r
- public void setTreeFont(Font font)\r
- {\r
- if(treeCanvas!=null)\r
- treeCanvas.setFont(font);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void distanceMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowDistances(distanceMenu.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void bootstrapMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void epsTree_actionPerformed(ActionEvent e)\r
- {\r
- boolean accurateText = true;\r
-\r
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
- "Prompt each time");\r
-\r
- // If we need to prompt, and if the GUI is visible then\r
- // Prompt for EPS rendering style\r
- if (renderStyle.equalsIgnoreCase("Prompt each time")\r
- && !\r
- (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true")))\r
- {\r
- EPSOptions eps = new EPSOptions();\r
- renderStyle = eps.getValue();\r
-\r
- if (renderStyle==null || eps.cancelled)\r
- return;\r
-\r
-\r
- }\r
-\r
- if (renderStyle.equalsIgnoreCase("text"))\r
- {\r
- accurateText = false;\r
- }\r
-\r
- int width = treeCanvas.getWidth();\r
- int height = treeCanvas.getHeight();\r
-\r
- try\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "eps" },\r
- new String[] { "Encapsulated Postscript" },\r
- "Encapsulated Postscript");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create EPS file from tree");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
- height);\r
-\r
- pg.setAccurateTextMode(accurateText);\r
-\r
- treeCanvas.draw(pg, width, height);\r
-\r
- pg.flush();\r
- pg.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void pngTree_actionPerformed(ActionEvent e)\r
- {\r
- int width = treeCanvas.getWidth();\r
- int height = treeCanvas.getHeight();\r
-\r
- try\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "png" },\r
- new String[] { "Portable network graphics" },\r
- "Portable network graphics");\r
-\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create PNG image from tree");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-\r
- BufferedImage bi = new BufferedImage(width, height,\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics png = bi.getGraphics();\r
-\r
- treeCanvas.draw(png, width, height);\r
-\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-}\r
+/*
+ * 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
+ */
+package jalview.gui;
+
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import org.jibble.epsgraphics.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+
+import java.io.*;
+
+import java.util.*;
+
+import javax.imageio.*;
+
+import java.beans.PropertyChangeEvent;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreePanel extends GTreePanel
+{
+ String type;
+ String pwtype;
+ TreeCanvas treeCanvas;
+ NJTree tree;
+ AlignViewport av;
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av DOCUMENT ME!
+ * @param seqVector DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param pwtype DOCUMENT ME!
+ * @param s DOCUMENT ME!
+ * @param e DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ {
+ super();
+ initTreePanel(ap, type, pwtype, null, null);
+
+ // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+ // showDistances(true);
+ }
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av DOCUMENT ME!
+ * @param seqVector DOCUMENT ME!
+ * @param newtree DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ * @param pwtype DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap,
+ String type,
+ String pwtype,
+ NewickFile newtree)
+ {
+ super();
+ initTreePanel(ap, type, pwtype, newtree, null);
+ }
+
+ public TreePanel(AlignmentPanel av,
+ String type,
+ String pwtype,
+ NewickFile newtree, AlignmentView inputData) {
+ super();
+ initTreePanel(av,type,pwtype,newtree,inputData);
+ }
+
+ public AlignmentI getAlignment()
+ {
+ return treeCanvas.av.getAlignment();
+ }
+ public AlignViewport getViewPort() {
+ return treeCanvas.av;
+ }
+
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newTree, AlignmentView inputData)
+ {
+
+ av = ap.av;
+ this.type = type;
+ this.pwtype = pwtype;
+
+ treeCanvas = new TreeCanvas(ap, scrollPane);
+ scrollPane.setViewportView(treeCanvas);
+
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ if(tree==null)
+ System.out.println("tree is null");
+ if(evt.getNewValue()==null)
+ System.out.println("new value is null");
+
+ tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
+
+ repaint();
+ }
+ }
+ });
+
+ this.av = av;
+
+
+ TreeLoader tl = new TreeLoader(newTree);
+ if (inputData!=null) {
+ tl.odata=inputData;
+ }
+ tl.start();
+
+ }
+
+ class TreeLoader extends Thread
+ {
+ NewickFile newtree;
+ jalview.datamodel.AlignmentView odata=null;
+ public TreeLoader(NewickFile newtree)
+ {
+ this.newtree = newtree;
+ if (newtree != null)
+ {
+ // Must be outside run(), as Jalview2XML tries to
+ // update distance/bootstrap visibility at the same time
+ showBootstrap(newtree.HasBootstrap());
+ showDistances(newtree.HasDistances());
+ }
+ }
+
+ public void run()
+ {
+
+ if(newtree!=null)
+ {
+ if (odata==null) {
+ tree = new NJTree(av.alignment.getSequencesArray(),
+ newtree);
+ } else {
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+ }
+ if (!tree.hasOriginalSequenceData())
+ allowOriginalSeqData(false);
+ }
+ else
+ {
+ int start, end;
+ SequenceI [] seqs;
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+ if(av.getSelectionGroup()==null)
+ {
+ start = 0;
+ end = av.alignment.getWidth();
+ seqs = av.alignment.getSequencesArray();
+ }
+ else
+ {
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes()+1;
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ }
+
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ showDistances(true);
+ }
+
+
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ treeCanvas.setTree(tree);
+ treeCanvas.repaint();
+ av.setCurrentTree(tree);
+
+ }
+ }
+
+ public void showDistances(boolean b)
+ {
+ treeCanvas.setShowDistances(b);
+ distanceMenu.setSelected(b);
+ }
+
+ public void showBootstrap(boolean b)
+ {
+ treeCanvas.setShowBootstrap(b);
+ bootstrapMenu.setSelected(b);
+ }
+
+ public void showPlaceholders(boolean b)
+ {
+ placeholdersMenu.setState(b);
+ treeCanvas.setMarkPlaceholders(b);
+ }
+
+ private void allowOriginalSeqData(boolean b) {
+ originalSeqData.setVisible(b);
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NJTree getTree()
+ {
+ return tree;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void textbox_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
+ StringBuffer buffer = new StringBuffer();
+
+ if (type.equals("AV"))
+ {
+ buffer.append("Average distance tree using ");
+ }
+ else
+ {
+ buffer.append("Neighbour joining tree using ");
+ }
+
+ if (pwtype.equals("BL"))
+ {
+ buffer.append("BLOSUM62");
+ }
+ else
+ {
+ buffer.append("PID");
+ }
+
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveAsNewick_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save tree as newick file");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+
+ try
+ {
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
+ java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+ choice));
+ out.println(output);
+ out.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void printMenu_actionPerformed(ActionEvent e)
+ {
+ //Putting in a thread avoids Swing painting problems
+ treeCanvas.startPrinting();
+ }
+
+
+ public void originalSeqData_actionPerformed(ActionEvent e)
+ {
+ if (!tree.hasOriginalSequenceData())
+ {
+ jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ return;
+ }
+ // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+ // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+ // or create a selection box around columns in alignment view
+ // test Alignment(SeqCigar[])
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+ getGapCharacter());
+
+
+ if (alAndColsel != null && alAndColsel[0]!=null)
+ {
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ Alignment dataset = av.getAlignment().getDataset();
+ if (dataset != null)
+ {
+ al.setDataset(dataset);
+ }
+
+ if (true)
+ {
+ // make a new frame!
+ AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT
+);
+
+ //>>>This is a fix for the moment, until a better solution is found!!<<<
+ // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+ // msaorder);
+
+ Desktop.addInternalFrame(af, "Original Data for " + this.title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void fitToWindow_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.fitToWindow = fitToWindow.isSelected();
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ if (treeCanvas == null)
+ {
+ return;
+ }
+
+ new FontChooser(this);
+ }
+
+ public Font getTreeFont()
+ {
+ return treeCanvas.font;
+ }
+
+ public void setTreeFont(Font font)
+ {
+ if(treeCanvas!=null)
+ treeCanvas.setFont(font);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void distanceMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowDistances(distanceMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void bootstrapMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void placeholdersMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void epsTree_actionPerformed(ActionEvent e)
+ {
+ boolean accurateText = true;
+
+ String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+ "Prompt each time");
+
+ // If we need to prompt, and if the GUI is visible then
+ // Prompt for EPS rendering style
+ if (renderStyle.equalsIgnoreCase("Prompt each time")
+ && !
+ (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true")))
+ {
+ EPSOptions eps = new EPSOptions();
+ renderStyle = eps.getValue();
+
+ if (renderStyle==null || eps.cancelled)
+ return;
+
+
+ }
+
+ if (renderStyle.equalsIgnoreCase("text"))
+ {
+ accurateText = false;
+ }
+
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ try
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "eps" },
+ new String[] { "Encapsulated Postscript" },
+ "Encapsulated Postscript");
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Create EPS file from tree");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
+
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
+
+ pg.setAccurateTextMode(accurateText);
+
+ treeCanvas.draw(pg, width, height);
+
+ pg.flush();
+ pg.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void pngTree_actionPerformed(ActionEvent e)
+ {
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ try
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "png" },
+ new String[] { "Portable network graphics" },
+ "Portable network graphics");
+
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Create PNG image from tree");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
+
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+
+ BufferedImage bi = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_RGB);
+ Graphics png = bi.getGraphics();
+
+ treeCanvas.draw(png, width, height);
+
+ ImageIO.write(bi, "png", out);
+ out.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+}
--- /dev/null
+/**
+ *
+ */
+package jalview.gui;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+
+import jalview.bin.Cache;
+import jalview.io.VamsasDatastore;
+
+import org.vamsas.client.UserHandle;
+import org.vamsas.client.simpleclient.FileWatcher;
+import org.vamsas.client.simpleclient.VamsasArchive;
+import org.vamsas.client.simpleclient.VamsasFile;
+import org.vamsas.objects.core.Entry;
+import org.vamsas.objects.core.VamsasDocument;
+import org.vamsas.test.simpleclient.ArchiveClient;
+import org.vamsas.test.simpleclient.ClientDoc;
+
+/**
+ * @author jimp
+ *
+ */
+public class VamsasClient extends ArchiveClient {
+ // Cache.preferences for vamsas client session arena
+ // preferences for check for default session at startup.
+ // user and organisation stuff.
+ public VamsasClient(Desktop jdesktop,
+ File sessionPath) {
+ super(System.getProperty("user.name"),System.getProperty("host.name"), "jalview","2.7",
+ sessionPath);
+ }
+ public void initial_update() {
+ Cache.log.info("Jalview loading the Vamsas Session.");
+ // load in the vamsas archive for the first time
+ ClientDoc cdoc = this.getUpdateable();
+ updateJalview(cdoc);
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return;
+ }
+
+ try
+ {
+ //REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
+ af.alignmentChanged();
+ }
+ }
+ } catch (Exception e) {
+ Cache.log.warn("Exception whilst refreshing jalview windows after a vamsas document update.", e);
+ }
+ doUpdate(cdoc);
+ cdoc.closeDoc();
+ }
+ /**
+ * this will close all windows currently in Jalview.
+ *
+
+ protected void closeWindows() {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return;
+ }
+
+ try
+ {
+ for (int i = frames.length - 1; i > -1; i--) {
+ frames[i].dispose();
+ }
+ } catch (Exception e) {
+ Cache.log.error("Whilst closing windows",e);
+ }
+
+ }
+
+ public void get_update(VamsasArchive doc) {
+ // Close windows - load update.
+ Cache.log.info("Jalview updating from Vamsas Session.");
+ }
+ */
+ VamsasClientWatcher watcher=null;
+ public void push_update() {
+ watchForChange=false;
+ try {
+ Thread.sleep(WATCH_SLEEP);
+ } catch (Exception e) {
+
+ };
+ ClientDoc cdoc = getUpdateable();
+ updateVamsasDocument(cdoc);
+ doUpdate(cdoc);
+ cdoc.closeDoc();
+ cdoc=null;
+ watchForChange=true;
+ if (watcher!=null) {
+ Thread wthread = new Thread() {
+ public void run() {
+ watcher.run();
+ }
+ };
+ wthread.start();
+
+ }
+ // collect all uncached alignments and put them into the vamsas dataset.
+ // store them.
+ Cache.log.info("Jalview updating the Vamsas Session.");
+ }
+ public void end_session() {
+ // stop any update/watcher thread.
+ watchForChange=false; // this makes any watch(long) loops return.
+ // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped.
+ try {
+ Thread.sleep(WATCH_SLEEP);
+ } catch (Exception e) {
+
+ };
+ Cache.log.info("Jalview disconnecting from the Vamsas Session.");
+ }
+ public void updateJalview(ClientDoc cdoc) {
+ ensureJvVamsas();
+ VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry());
+ vds.updateToJalview();
+ }
+ private void ensureJvVamsas() {
+ if (jv2vobj==null) {
+ jv2vobj = new IdentityHashMap();
+ vobj2jv = new Hashtable();
+ }
+ }
+ /**
+ * jalview object binding to VorbaIds
+ */
+ IdentityHashMap jv2vobj = null;
+ Hashtable vobj2jv = null;
+ public void updateVamsasDocument(ClientDoc doc) {
+ ensureJvVamsas();
+ VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj, baseProvEntry());
+ // wander through frames
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return;
+ }
+
+ try
+ {
+ //REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
+
+ // update alignment and root from frame.
+ vds.storeVAMSAS(af.getViewport(), af.getTitle());
+ }
+ }
+ }
+ catch (Exception e) {
+ Cache.log.error("Vamsas Document store exception",e);
+ }
+ }
+ private Entry baseProvEntry() {
+ org.vamsas.objects.core.Entry pentry = new org.vamsas.objects.core.Entry();
+ pentry.setUser(this.getProvenanceUser());
+ pentry.setApp(this.getClientHandle().getClientName());
+ pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
+ pentry.setAction("created");
+ return pentry;
+ }
+ protected class VamsasClientWatcher extends Thread implements Runnable {
+ /* (non-Javadoc)
+ * @see java.lang.Thread#run()
+ */
+ VamsasClient client=null;
+ VamsasClientWatcher(VamsasClient client) {
+ this.client = client;
+ }
+ boolean running=false;
+ public void run() {
+ running=true;
+ while (client.watchForChange) {
+ ClientDoc docio = client.watch(0);
+ if (docio!=null) {
+ client.disableGui(true);
+ Cache.log.debug("Updating jalview from changed vamsas document.");
+ client.updateJalview(docio);
+ Cache.log.debug("Finished updating from document change.");
+ docio.closeDoc();
+ docio=null;
+ client.disableGui(false);
+ }
+ }
+ running=false;
+
+ }
+
+ }
+ public void disableGui(boolean b) {
+ Desktop.instance.setVamsasUpdate(b);
+ }
+ public void startWatcher() {
+ if (watcher==null)
+ watcher=new VamsasClientWatcher(this);
+ Thread thr = new Thread() {
+ public void run() {
+ watcher.start();
+ }
+ };
+ thr.start();
+ }
+}
--- /dev/null
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+\r
+package jalview.io;\r
+\r
+import org.vamsas.client.Vobject;\r
+import org.vamsas.client.VorbaId;\r
+import org.vamsas.objects.core.*;\r
+import org.vamsas.objects.utils.DocumentStuff;\r
+import org.vamsas.test.simpleclient.ClientDoc;\r
+\r
+import jalview.bin.Cache;\r
+import jalview.datamodel.AlignmentAnnotation;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentView;\r
+import jalview.datamodel.DBRefEntry;\r
+import jalview.datamodel.SequenceFeature;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.gui.*;\r
+\r
+import java.io.*;\r
+import java.util.HashMap;\r
+import java.util.HashSet;\r
+import java.util.Hashtable;\r
+import java.util.IdentityHashMap;\r
+import java.util.Vector;\r
+import java.util.jar.*;\r
+import org.exolab.castor.xml.*;\r
+import org.exolab.castor.mapping.Mapping;\r
+\r
+/*\r
+ * \r
+ * static {\r
+ * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(\r
+ * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }\r
+ * \r
+ */\r
+\r
+public class VamsasDatastore {\r
+ Entry provEntry = null;\r
+\r
+ // AlignViewport av;\r
+\r
+ org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(\r
+ new java.util.Date());\r
+\r
+ ClientDoc cdoc;\r
+\r
+ Hashtable vobj2jv;\r
+\r
+ IdentityHashMap jv2vobj;\r
+\r
+ public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,\r
+ IdentityHashMap jv2vobj, Entry provEntry) {\r
+ this.cdoc = cdoc;\r
+ this.vobj2jv = vobj2jv;\r
+ this.jv2vobj = jv2vobj;\r
+ this.provEntry = provEntry;\r
+ }\r
+\r
+ /*\r
+ * public void storeJalview(String file, AlignFrame af) { try { // 1. Load the\r
+ * mapping information from the file Mapping map = new\r
+ * Mapping(getClass().getClassLoader()); java.net.URL url =\r
+ * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2.\r
+ * Unmarshal the data // Unmarshaller unmar = new Unmarshaller();\r
+ * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni =\r
+ * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data\r
+ * with the total price back and print the XML in the console Marshaller\r
+ * marshaller = new Marshaller( new FileWriter(file) );\r
+ * \r
+ * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {\r
+ * e.printStackTrace(); } }\r
+ * \r
+ * \r
+ */\r
+ /**\r
+ * @return the Vobject bound to Jalview datamodel object\r
+ */\r
+ protected Vobject getjv2vObj(Object jvobj) {\r
+ if (jv2vobj.containsKey(jvobj))\r
+ return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param vobj\r
+ * @return Jalview datamodel object bound to the vamsas document object\r
+ */\r
+ protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {\r
+ VorbaId id = vobj.getVorbaId();\r
+ if (id == null)\r
+ {\r
+ id = cdoc.registerObject(vobj);\r
+ Cache.log\r
+ .debug("Registering new object and returning null for getvObj2jv");\r
+ return null;\r
+ }\r
+ if (vobj2jv.containsKey(vobj.getVorbaId()))\r
+ return vobj2jv.get(vobj.getVorbaId());\r
+ return null;\r
+ }\r
+\r
+ protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {\r
+ VorbaId id = vobj.getVorbaId();\r
+ if (id == null)\r
+ {\r
+ id = cdoc.registerObject(vobj);\r
+ if (id==null || vobj.getVorbaId()==null)\r
+ Cache.log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);\r
+ }\r
+ \r
+ if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId)vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) {\r
+ Cache.log.debug("Warning? Overwriting existing vamsas id binding for "+vobj.getVorbaId(), new Exception("Overwriting vamsas id binding."));\r
+ }\r
+ else if (jv2vobj.containsKey(jvobj) && !((VorbaId)jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) \r
+ {\r
+ Cache.log.debug("Warning? Overwriting existing jalview object binding for "+jvobj, new Exception("Overwriting jalview object binding."));\r
+ }\r
+ /* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to bindjvvobj"));\r
+ }*/\r
+ // we just update the hash's regardless!\r
+ vobj2jv.put(vobj.getVorbaId(), jvobj);\r
+ // JBPNote - better implementing a hybrid invertible hash.\r
+ jv2vobj.put(jvobj, vobj.getVorbaId()); \r
+ }\r
+\r
+ /**\r
+ * put the alignment viewed by AlignViewport into cdoc.\r
+ * \r
+ * @param av alignViewport to be stored\r
+ * @param aFtitle title for alignment\r
+ */\r
+ public void storeVAMSAS(AlignViewport av, String aFtitle) {\r
+ try\r
+ {\r
+ jalview.datamodel.AlignmentI jal = av.getAlignment();\r
+ boolean nw = false;\r
+ VAMSAS root = null; // will be resolved based on Dataset Parent.\r
+ // /////////////////////////////////////////\r
+ // SAVE THE DATASET\r
+ if (jal.getDataset() == null)\r
+ {\r
+ Cache.log.warn("Creating new dataset for an alignment.");\r
+ jal.setDataset(null);\r
+ }\r
+ DataSet dataset = (DataSet) getjv2vObj(jal.getDataset());\r
+ if (dataset == null)\r
+ {\r
+ root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.\r
+ dataset = new DataSet();\r
+ root.addDataSet(dataset);\r
+ bindjvvobj(jal.getDataset(), dataset);\r
+ dataset.setProvenance(dummyProvenance());\r
+ dataset.getProvenance().addEntry(provEntry);\r
+ nw = true;\r
+ }\r
+ else\r
+ {\r
+ root = (VAMSAS) dataset.getV_parent();\r
+ }\r
+ // update dataset\r
+ Sequence sequence;\r
+ DbRef dbref;\r
+ // set new dataset and alignment sequences based on alignment Nucleotide\r
+ // flag.\r
+ // this *will* break when alignment contains both nucleotide and amino\r
+ // acid sequences.\r
+ String dict = jal.isNucleotide() ? org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA\r
+ : org.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;\r
+ for (int i = 0; i < jal.getHeight(); i++)\r
+ {\r
+ SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert\r
+ // referenced\r
+ // sequences\r
+ // to dataset.\r
+ sequence = (Sequence) getjv2vObj(sq);\r
+ if (sequence == null)\r
+ {\r
+ sequence = new Sequence();\r
+ bindjvvobj(sq, sequence);\r
+ sq.setVamsasId(sequence.getVorbaId().getId());\r
+ sequence.setSequence(sq.getSequence());\r
+ sequence.setDictionary(dict);\r
+ sequence.setName(jal.getDataset().getSequenceAt(i).getName());\r
+ sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());\r
+ sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd());\r
+ dataset.addSequence(sequence);\r
+ }\r
+ else\r
+ {\r
+ // verify principal attributes. and update any new\r
+ // features/references.\r
+ System.out.println("update dataset sequence object.");\r
+ }\r
+ if (sq.getSequenceFeatures() != null)\r
+ {\r
+ int sfSize = sq.getSequenceFeatures().length;\r
+\r
+ for (int sf = 0; sf < sfSize; sf++)\r
+ {\r
+ jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq\r
+ .getSequenceFeatures()[sf];\r
+\r
+ DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature);\r
+ if (dsa == null)\r
+ {\r
+ dsa = (DataSetAnnotations) getDSAnnotationFromJalview(\r
+ new DataSetAnnotations(), feature);\r
+ if (dsa.getProvenance() == null)\r
+ {\r
+ dsa.setProvenance(new Provenance());\r
+ }\r
+ addProvenance(dsa.getProvenance(), "created"); // JBPNote - need\r
+ // to update\r
+ dsa.setSeqRef(sequence);\r
+ bindjvvobj(feature, dsa);\r
+ dataset.addDataSetAnnotations(dsa);\r
+ }\r
+ else\r
+ {\r
+ // todo: verify and update dataset annotations for sequence\r
+ System.out.println("update dataset sequence annotations.");\r
+ }\r
+ }\r
+ }\r
+\r
+ if (sq.getDBRef() != null)\r
+ {\r
+ DBRefEntry[] entries = sq.getDBRef();\r
+ jalview.datamodel.DBRefEntry dbentry;\r
+ for (int db = 0; db < entries.length; db++)\r
+ {\r
+ dbentry = entries[db];\r
+ dbref = (DbRef) getjv2vObj(dbentry);\r
+ if (dbref == null)\r
+ {\r
+ dbref = new DbRef();\r
+ bindjvvobj(dbentry, dbref);\r
+ dbref.setAccessionId(dbentry.getAccessionId());\r
+ dbref.setSource(dbentry.getSource());\r
+ dbref.setVersion(dbentry.getVersion());\r
+ /*\r
+ * TODO: Maps are not yet supported by Jalview. Map vMap = new\r
+ * Map(); vMap.set dbref.addMap(vMap);\r
+ */\r
+ sequence.addDbRef(dbref);\r
+ }\r
+ else\r
+ {\r
+ // TODO: verify and update dbrefs in vamsas document\r
+ // there will be trouble when a dataset sequence is modified to\r
+ // contain more residues than were originally referenced - we must\r
+ // then make a number of dataset sequence entries\r
+ System.out\r
+ .println("update dataset sequence database references.");\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+ // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));\r
+ // ////////////////////////////////////////////\r
+\r
+ // ////////////////////////////////////////////\r
+ // Save the Alignments\r
+\r
+ Alignment alignment = (Alignment) getjv2vObj(av); // this is so we can get the alignviewport back \r
+ if (alignment == null)\r
+ {\r
+ alignment = new Alignment();\r
+ bindjvvobj(av, alignment);\r
+ if (alignment.getProvenance() == null)\r
+ alignment.setProvenance(new Provenance());\r
+ addProvenance(alignment.getProvenance(), "added"); // TODO: insert some\r
+ // sensible source\r
+ // here\r
+ dataset.addAlignment(alignment);\r
+ {\r
+ Property title = new Property();\r
+ title.setName("jalview:AlTitle");\r
+ title.setType("string");\r
+ title.setContent(aFtitle);\r
+ alignment.addProperty(title);\r
+ }\r
+ alignment.setGapChar(String.valueOf(av.getGapCharacter()));\r
+ AlignmentSequence alseq = null;\r
+ for (int i = 0; i < jal.getHeight(); i++)\r
+ {\r
+ alseq = new AlignmentSequence();\r
+ // TODO: VAMSAS: translate lowercase symbols to annotation ?\r
+ alseq.setSequence(jal.getSequenceAt(i).getSequence());\r
+ alseq.setName(jal.getSequenceAt(i).getName());\r
+ alseq.setStart(jal.getSequenceAt(i).getStart());\r
+ alseq.setEnd(jal.getSequenceAt(i).getEnd());\r
+ alseq.setRefid(getjv2vObj(jal.getSequenceAt(i).getDatasetSequence()));\r
+ alignment.addAlignmentSequence(alseq);\r
+ bindjvvobj(jal.getSequenceAt(i), alseq);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // todo: verify and update mutable alignment props.\r
+ if (alignment.getModifiable())\r
+ {\r
+ System.out.println("update alignment in document.");\r
+ }\r
+ else\r
+ {\r
+ System.out\r
+ .println("update edited alignment to new alignment in document.");\r
+ }\r
+ }\r
+ // ////////////////////////////////////////////\r
+ // SAVE Alignment Sequence Features\r
+ for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)\r
+ {\r
+ AlignmentSequence valseq;\r
+ SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment\r
+ .getAlignmentSequence(i));\r
+ if (alseq != null && alseq.getSequenceFeatures() != null)\r
+ {\r
+ jalview.datamodel.SequenceFeature[] features = alseq\r
+ .getSequenceFeatures();\r
+ for (int f = 0; f < features.length; f++)\r
+ {\r
+ if (features[f] != null)\r
+ {\r
+ AlignmentSequenceAnnotation valseqf = (AlignmentSequenceAnnotation) getjv2vObj(features[i]);\r
+ if (valseqf == null)\r
+ {\r
+\r
+ valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(\r
+ new AlignmentSequenceAnnotation(), features[i]);\r
+ if (valseqf.getProvenance() == null)\r
+ {\r
+ valseqf.setProvenance(new Provenance());\r
+ }\r
+ addProvenance(valseqf.getProvenance(), "created"); // JBPNote -\r
+ // need to\r
+ // update\r
+ bindjvvobj(features[i], valseqf);\r
+ valseq.addAlignmentSequenceAnnotation(valseqf);\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ // ////////////////////////////////////////////\r
+ // SAVE ANNOTATIONS\r
+ if (jal.getAlignmentAnnotation() != null)\r
+ {\r
+ jalview.datamodel.AlignmentAnnotation[] aa = jal\r
+ .getAlignmentAnnotation();\r
+ java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from\r
+ // alignment columns to\r
+ // sequence positions.\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (aa[i] == null || isJalviewOnly(aa[i]))\r
+ {\r
+ continue;\r
+ }\r
+ if (aa[i].sequenceRef != null)\r
+ {\r
+ org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);\r
+ org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[i]);\r
+ int[] gapMap = null;\r
+ if (AlSeqMaps.containsKey(aa[i].sequenceRef))\r
+ {\r
+ gapMap = (int[]) AlSeqMaps.get(aa[i].sequenceRef);\r
+ }\r
+ else\r
+ {\r
+ gapMap = new int[aa[i].sequenceRef.getLength()];\r
+ // map from alignment position to sequence position.\r
+ int[] sgapMap = aa[i].sequenceRef.gapMap();\r
+ for (int a = 0; a < sgapMap.length; a++)\r
+ gapMap[sgapMap[a]] = a;\r
+ }\r
+ if (an == null)\r
+ {\r
+ an = new org.vamsas.objects.core.AlignmentSequenceAnnotation();\r
+ Seg vSeg = new Seg();\r
+ vSeg.setStart(1);\r
+ vSeg.setInclusive(true);\r
+ vSeg.setEnd(gapMap.length);\r
+ an.addSeg(vSeg);\r
+ an.setType("jalview:SecondaryStructurePrediction");// TODO: better fix this rough guess ;)\r
+ alsref.addAlignmentSequenceAnnotation(an);\r
+ bindjvvobj(aa[i],an);\r
+ // LATER: much of this is verbatim from the alignmentAnnotation\r
+ // method below. suggests refactoring to make rangeAnnotation the\r
+ // base class\r
+ an.setDescription(aa[i].description);\r
+ if (aa[i].graph > 0)\r
+ an.setGraph(true); // aa[i].graph);\r
+ else\r
+ an.setGraph(false);\r
+ an.setLabel(aa[i].label);\r
+ an.setProvenance(dummyProvenance()); // get provenance as user\r
+ // created, or jnet, or\r
+ // something else.\r
+ an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -\r
+ // originally we\r
+ // were going to\r
+ // store\r
+ // graphGroup in\r
+ // the Jalview\r
+ // specific\r
+ // bits.\r
+ AnnotationElement ae;\r
+ for (int a = 0; a < aa[i].annotations.length; a++)\r
+ {\r
+ if (aa[i].annotations[a] == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ ae = new AnnotationElement();\r
+ ae.setDescription(aa[i].annotations[a].description);\r
+ ae.addGlyph(new Glyph());\r
+ ae.getGlyph(0)\r
+ .setContent(aa[i].annotations[a].displayCharacter); // assume\r
+ // jax-b\r
+ // takes\r
+ // care\r
+ // of\r
+ // utf8\r
+ // translation\r
+ if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH)\r
+ ae.addValue(aa[i].annotations[a].value);\r
+ ae.setPosition(gapMap[a]+1); // position w.r.t. AlignmentSequence\r
+ // symbols\r
+ if (aa[i].annotations[a].secondaryStructure != ' ')\r
+ {\r
+ // we only write an annotation where it really exists.\r
+ Glyph ss = new Glyph();\r
+ ss\r
+ .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);\r
+ ss.setContent(String\r
+ .valueOf(aa[i].annotations[a].secondaryStructure));\r
+ ae.addGlyph(ss);\r
+ }\r
+ an.addAnnotationElement(ae);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // update reference sequence Annotation\r
+ if (an.getModifiable())\r
+ {\r
+ // verify existing alignment sequence annotation is up to date\r
+ System.out.println("update alignment sequence annotation.");\r
+ }\r
+ else\r
+ {\r
+ // verify existing alignment sequence annotation is up to date\r
+ System.out\r
+ .println("make new alignment sequence annotation if modification has happened.");\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // add Alignment Annotation\r
+ org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);\r
+ if (an == null)\r
+ {\r
+ an = new org.vamsas.objects.core.AlignmentAnnotation();\r
+ an.setType("jalview:AnnotationRow");\r
+ an.setDescription(aa[i].description);\r
+ alignment.addAlignmentAnnotation(an);\r
+ Seg vSeg = new Seg();\r
+ vSeg.setStart(1);\r
+ vSeg.setInclusive(true);\r
+ vSeg.setEnd(jal.getWidth());\r
+ an.addSeg(vSeg);\r
+ if (aa[i].graph > 0)\r
+ an.setGraph(true); // aa[i].graph);\r
+ an.setLabel(aa[i].label);\r
+ an.setProvenance(dummyProvenance());\r
+ if (aa[i].graph!=aa[i].NO_GRAPH) {\r
+ an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -\r
+ // originally we\r
+ // were going to\r
+ // store\r
+ // graphGroup in\r
+ // the Jalview\r
+ // specific\r
+ // bits.\r
+ an.setGraph(true);\r
+ } else {\r
+ an.setGraph(false);\r
+ }\r
+ AnnotationElement ae;\r
+\r
+ for (int a = 0; a < aa[i].annotations.length; a++)\r
+ {\r
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ ae = new AnnotationElement();\r
+ ae.setDescription(aa[i].annotations[a].description);\r
+ ae.addGlyph(new Glyph());\r
+ ae.getGlyph(0)\r
+ .setContent(aa[i].annotations[a].displayCharacter); // assume\r
+ // jax-b\r
+ // takes\r
+ // care\r
+ // of\r
+ // utf8\r
+ // translation\r
+ ae.addValue(aa[i].annotations[a].value);\r
+ ae.setPosition(a+1);\r
+ if (aa[i].annotations[a].secondaryStructure != ' ')\r
+ {\r
+ Glyph ss = new Glyph();\r
+ ss\r
+ .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);\r
+ ss.setContent(String\r
+ .valueOf(aa[i].annotations[a].secondaryStructure));\r
+ ae.addGlyph(ss);\r
+ }\r
+ an.addAnnotationElement(ae);\r
+ }\r
+ if (aa[i].editable) {\r
+ //an.addProperty(newProperty("jalview:editable", null, "true"));\r
+ an.setModifiable(true);\r
+ }\r
+ if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH) {\r
+ an.setGraph(true);\r
+ an.setGroup(Integer.toString(aa[i].graphGroup));\r
+ an.addProperty(newProperty("jalview:graphType",null,\r
+ ((aa[i].graph==jalview.datamodel.AlignmentAnnotation.BAR_GRAPH) ? "BAR_GRAPH" : "LINE_GRAPH")));\r
+\r
+ /** and on and on.. \r
+ vProperty=new Property();\r
+ vProperty.setName("jalview:graphThreshhold");\r
+ vProperty.setContent(aa[i].threshold);\r
+ */\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (an.getModifiable())\r
+ {\r
+ // verify annotation - update (perhaps)\r
+ Cache.log.info("update alignment sequence annotation. not yet implemented.");\r
+ }\r
+ else\r
+ {\r
+ // verify annotation - update (perhaps)\r
+ Cache.log.info("updated alignment sequence annotation added.");\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ // /////////////////////////////////////////////////////\r
+\r
+ // //////////////////////////////////////////////\r
+ // /SAVE THE TREES\r
+ // /////////////////////////////////\r
+ // FIND ANY ASSOCIATED TREES\r
+ if (Desktop.desktop != null)\r
+ {\r
+ javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
+\r
+ for (int t = 0; t < frames.length; t++)\r
+ {\r
+ if (frames[t] instanceof TreePanel)\r
+ {\r
+ TreePanel tp = (TreePanel) frames[t];\r
+\r
+ if (tp.getAlignment() == jal)\r
+ {\r
+ Tree tree = (Tree) getjv2vObj(tp);\r
+ if (tree == null)\r
+ {\r
+ tree = new Tree();\r
+ bindjvvobj(tp, tree);\r
+ tree.setTitle(tp.getTitle());\r
+ Newick newick = new Newick();\r
+ // TODO: translate sequenceI to leaf mappings to vamsas\r
+ // references - see tree specification in schema.\r
+ newick.setContent(tp.getTree().toString());\r
+ newick.setTitle(tp.getTitle());\r
+ tree.addNewick(newick);\r
+ tree.setProvenance(makeTreeProvenance(jal, tp));\r
+ alignment.addTree(tree);\r
+ }\r
+ else\r
+ {\r
+ if (tree.getModifiable())\r
+ {\r
+ // verify any changes.\r
+ System.out.println("Update tree in document.");\r
+ }\r
+ else\r
+ {\r
+ System.out\r
+ .println("Add modified tree as new tree in document.");\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ // Store Jalview specific stuff in the Jalview appData\r
+ // not implemented in the SimpleDoc interface.\r
+ }\r
+\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ }\r
+\r
+ private Property newProperty(String name, String type, String content) {\r
+ Property vProperty=new Property();\r
+ vProperty.setName(name);\r
+ if (type!=null)\r
+ vProperty.setType(type);\r
+ else\r
+ vProperty.setType("String");\r
+ vProperty.setContent(content);\r
+ return vProperty;\r
+ }\r
+\r
+ /**\r
+ * correctly create a RangeAnnotation from a jalview sequence feature\r
+ * \r
+ * @param dsa\r
+ * (typically DataSetAnnotations or AlignmentSequenceAnnotation)\r
+ * @param feature\r
+ * (the feature to be mapped from)\r
+ * @return\r
+ */\r
+ private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,\r
+ SequenceFeature feature) {\r
+ dsa.setType(feature.getType());\r
+ Seg vSeg = new Seg();\r
+ vSeg.setStart(feature.getBegin());\r
+ vSeg.setEnd(feature.getEnd());\r
+ vSeg.setInclusive(true);\r
+ dsa.addSeg(vSeg);\r
+ dsa.setDescription(feature.getDescription());\r
+ dsa.setStatus(feature.getStatus());\r
+ if (feature.links != null && feature.links.size() > 0)\r
+ {\r
+ for (int i = 0, iSize = feature.links.size(); i < iSize; i++)\r
+ {\r
+ String link = (String) feature.links.elementAt(i);\r
+ int sep = link.indexOf('|');\r
+ if (sep > -1)\r
+ {\r
+ Link vLink = new Link();\r
+ if (sep > 0)\r
+ vLink.setContent(link.substring(0, sep - 1));\r
+ else\r
+ vLink.setContent("");\r
+ vLink.setHref(link.substring(sep + 1)); // TODO: validate href.\r
+ dsa.addLink(vLink);\r
+ }\r
+ }\r
+ }\r
+ dsa.setGroup(feature.getFeatureGroup());\r
+ return dsa;\r
+ }\r
+\r
+ /**\r
+ * correctly creates provenance for trees calculated on an alignment by\r
+ * jalview.\r
+ * \r
+ * @param jal\r
+ * @param tp\r
+ * @return\r
+ */\r
+ private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) {\r
+ Provenance prov = new Provenance();\r
+ prov.addEntry(new Entry());\r
+ prov.getEntry(0).setAction("imported "+tp.getTitle());\r
+ prov.getEntry(0).setUser(provEntry.getUser());\r
+ prov.getEntry(0).setApp(provEntry.getApp());\r
+ prov.getEntry(0).setDate(provEntry.getDate());\r
+ if (tp.getTree().hasOriginalSequenceData())\r
+ {\r
+ Input vInput = new Input();\r
+ // LATER: check to see if tree input data is contained in this alignment -\r
+ // or just correctly resolve the tree's seqData to the correct alignment in\r
+ // the document.\r
+ // vInput.setObjRef(getjv2vObj(jal));\r
+ vInput.setObjRef(getjv2vObj(tp.getViewPort()));\r
+ prov.getEntry(0).setAction("created "+tp.getTitle());\r
+ prov.getEntry(0).addInput(vInput);\r
+ vInput.setName("jalview:seqdist");\r
+ prov.getEntry(0).addParam(new Param());\r
+ prov.getEntry(0).getParam(0).setName("treeType");\r
+ prov.getEntry(0).getParam(0).setType("utf8");\r
+ prov.getEntry(0).getParam(0).setContent("NJ");\r
+ \r
+ int ranges[] = tp.getTree().seqData.getVisibleContigs();\r
+ // VisibleContigs are with respect to alignment coordinates. Still need offsets\r
+ int start= tp.getTree().seqData.getAlignmentOrigin();\r
+ for (int r = 0; r < ranges.length; r += 2)\r
+ {\r
+ Seg visSeg = new Seg();\r
+ visSeg.setStart(1+start+ranges[r]);\r
+ visSeg.setEnd(start+ranges[r + 1]);\r
+ visSeg.setInclusive(true);\r
+ vInput.addSeg(visSeg);\r
+ }\r
+ }\r
+ return prov;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param tp\r
+ * @return Object[] { AlignmentView, AlignmentI - reference alignment for\r
+ * input }\r
+ */\r
+ private Object[] recoverInputData(Provenance tp) {\r
+ for (int pe = 0; pe < tp.getEntryCount(); pe++)\r
+ {\r
+ if (tp.getEntry(pe).getInputCount() > 0)\r
+ {\r
+ if (tp.getEntry(pe).getInputCount() > 1)\r
+ Cache.log.warn("Ignoring additional input spec in provenance entry "\r
+ + tp.getEntry(pe).toString());\r
+ // LATER: deal sensibly with multiple inputs.\r
+ Input vInput = tp.getEntry(pe).getInput(0);\r
+ if (vInput.getObjRef() instanceof org.vamsas.objects.core.Alignment)\r
+ {\r
+ // recover an AlignmentView for the input data\r
+ AlignViewport javport = (AlignViewport) getvObj2jv((org.vamsas.client.Vobject) vInput\r
+ .getObjRef());\r
+ jalview.datamodel.AlignmentI jal = javport.getAlignment();\r
+ jalview.datamodel.CigarArray view = javport.getAlignment().getCompactAlignment();\r
+ int from = 1, to = jal.getWidth();\r
+ int offset=0; // deleteRange modifies its frame of reference\r
+ for (int r = 0, s = vInput.getSegCount(); r < s; r++)\r
+ {\r
+ Seg visSeg = vInput.getSeg(r);\r
+ int se[] = getSegRange(visSeg,true); // jalview doesn't do bidirection alignments yet.\r
+ if (to < se[1])\r
+ Cache.log.warn("Ignoring invalid segment in InputData spec.");\r
+ else\r
+ {\r
+ if (se[0] > from)\r
+ {\r
+ view.deleteRange(offset+from-1, offset+se[0] - 2);\r
+ offset-=se[0]-from;\r
+ }\r
+ from = se[1] + 1;\r
+ }\r
+ }\r
+ if (from < to)\r
+ {\r
+ view.deleteRange(offset+from-1, offset+to-1); // final deletion - TODO: check off by\r
+ // one for to\r
+ }\r
+ return new Object[] { new AlignmentView(view), jal };\r
+ }\r
+ }\r
+ }\r
+ Cache.log.debug("Returning null for input data recovery from provenance.");\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * get start<end range of segment, adjusting for inclusivity flag and\r
+ * polarity.\r
+ * \r
+ * @param visSeg\r
+ * @param ensureDirection when true - always ensure start is less than end.\r
+ * @return int[] { start, end, direction} where direction==1 for range running from end to start.\r
+ */\r
+ private int[] getSegRange(Seg visSeg, boolean ensureDirection) {\r
+ boolean incl = visSeg.getInclusive();\r
+ // adjust for inclusive flag.\r
+ int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of\r
+ // region.\r
+ int start = visSeg.getStart() + (incl ? 0 : pol);\r
+ int end = visSeg.getEnd() + (incl ? 0 : -pol);\r
+ if (ensureDirection && pol==-1)\r
+ {\r
+ // jalview doesn't deal with inverted ranges, yet.\r
+ int t = end;\r
+ end = start;\r
+ start = t;\r
+ }\r
+ return new int[] { start, end, pol<0 ? 1 : 0 };\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param annotation\r
+ * @return true if annotation is not to be stored in document\r
+ */\r
+ private boolean isJalviewOnly(AlignmentAnnotation annotation) {\r
+ return annotation.label.equals("Quality")\r
+ || annotation.label.equals("Conservation")\r
+ || annotation.label.equals("Consensus");\r
+ }\r
+ /**\r
+ * This will return the first AlignFrame viewing AlignViewport av.\r
+ * It will break if there are more than one AlignFrames viewing a particular av.\r
+ * This also shouldn't be in the io package.\r
+ * @param av\r
+ * @return alignFrame for av\r
+ */\r
+ public AlignFrame getAlignFrameFor(AlignViewport av) {\r
+ if (Desktop.desktop != null)\r
+ {\r
+ javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
+\r
+ for (int t = 0; t < frames.length; t++)\r
+ {\r
+ if (frames[t] instanceof AlignFrame) {\r
+ if (((AlignFrame) frames[t]).getViewport()==av)\r
+ return (AlignFrame) frames[t];\r
+ }\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+ public void updateToJalview() {\r
+ VAMSAS _roots[] = cdoc.getVamsasRoots();\r
+\r
+ for (int _root = 0; _root<_roots.length; _root++) {\r
+ VAMSAS root = _roots[_root];\r
+ boolean newds=false;\r
+ for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {\r
+ // ///////////////////////////////////\r
+ // ///LOAD DATASET\r
+ DataSet dataset = root.getDataSet(_ds);\r
+ int i, iSize = dataset.getSequenceCount();\r
+ Vector dsseqs;\r
+ jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);\r
+ int jremain=0;\r
+ if (jdataset==null) {\r
+ Cache.log.debug("Initialising new jalview dataset fields");\r
+ newds=true;\r
+ dsseqs=new Vector();\r
+ } else {\r
+ Cache.log.debug("Update jalview dataset from vamsas.");\r
+ jremain=jdataset.getHeight();\r
+ dsseqs=jdataset.getSequences();\r
+ }\r
+\r
+ // TODO: test sequence merging - we preserve existing non vamsas\r
+ // sequences but add in any new vamsas ones, and don't yet update any\r
+ // sequence attributes\r
+ for (i = 0; i < iSize ; i++)\r
+ {\r
+ Sequence vdseq = dataset.getSequence(i);\r
+ jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq);\r
+ if (dsseq!=null) {\r
+ if (!dsseq.getSequence().equals(vdseq.getSequence()))\r
+ throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");\r
+ jremain--;\r
+ } else {\r
+ dsseq = new jalview.datamodel.Sequence(\r
+ dataset.getSequence(i).getName(),\r
+ dataset.getSequence(i).getSequence(),\r
+ dataset.getSequence(i).getStart(),\r
+ dataset.getSequence(i).getEnd() );\r
+ bindjvvobj(dsseq, dataset.getSequence(i));\r
+ dsseq.setVamsasId(dataset.getSequence(i).getVorbaId().getId());\r
+ dsseqs.add(dsseq);\r
+ }\r
+ if (vdseq.getDbRefCount()>0) {\r
+ DbRef [] dbref = vdseq.getDbRef();\r
+ for(int db=0; db<dbref.length; db++)\r
+ {\r
+ jalview.datamodel.DBRefEntry dbr=(jalview.datamodel.DBRefEntry) getvObj2jv(dbref[db]);\r
+ if (dbr==null) {\r
+ // add new dbref\r
+ dsseq.addDBRef(dbr= new jalview.datamodel.DBRefEntry\r
+ (\r
+ dbref[db].getSource().toString(),\r
+ dbref[db].getVersion().toString(),\r
+ dbref[db].getAccessionId().toString()));\r
+ bindjvvobj(dbr, dbref[db]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (newds) {\r
+ SequenceI[] seqs = new SequenceI[dsseqs.size()];\r
+ for (i=0,iSize=dsseqs.size(); i<iSize; i++) {\r
+ seqs[i]=(SequenceI) dsseqs.elementAt(i);\r
+ dsseqs.setElementAt(null, i);\r
+ }\r
+ jdataset = new jalview.datamodel.Alignment(seqs);\r
+ Cache.log.debug("New vamsas dataset imported into jalview.");\r
+ bindjvvobj(jdataset, dataset);\r
+ }\r
+ // ////////\r
+ // add any new dataset sequence feature annotations\r
+ if (dataset.getDataSetAnnotations() != null) {\r
+ for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++) {\r
+ DataSetAnnotations dseta=dataset.getDataSetAnnotations(dsa);\r
+ SequenceI dsSeq=(SequenceI) getvObj2jv((Vobject) dseta.getSeqRef());\r
+ if (dsSeq==null) {\r
+ jalview.bin.Cache.log.warn("Couldn't resolve jalview sequenceI for dataset object reference "+((Vobject)dataset.getDataSetAnnotations(dsa).getSeqRef()).getVorbaId().getId());\r
+ } else {\r
+ if (dseta.getAnnotationElementCount()==0) {\r
+ jalview.datamodel.SequenceFeature sf=(jalview.datamodel.SequenceFeature) getvObj2jv(dseta);\r
+ if (sf==null) {\r
+ dsSeq.addSequenceFeature(sf=getJalviewSeqFeature(dseta));\r
+ bindjvvobj(sf, dseta);\r
+ }\r
+ } else {\r
+ // TODO: deal with alignmentAnnotation style annotation\r
+ // appearing on dataset sequences.\r
+ // JBPNote: we could just add them to all alignments but\r
+ // that may complicate cross references in the jalview\r
+ // datamodel\r
+ Cache.log.warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (dataset.getAlignmentCount()>0) {\r
+ // LOAD ALIGNMENTS from DATASET \r
+\r
+ for (int al=0,nal=dataset.getAlignmentCount(); al<nal; al++) {\r
+ org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(al);\r
+ AlignViewport av = (AlignViewport) getvObj2jv(alignment);\r
+ jalview.datamodel.AlignmentI jal=null;\r
+ if (av!=null)\r
+ jal = av.getAlignment(); \r
+ iSize = alignment.getAlignmentSequenceCount();\r
+ boolean newal=(jal==null) ? true : false;\r
+ Vector newasAnnots=new Vector();\r
+ char gapChar=' '; // default for new alignments read in from the document\r
+ if (jal!=null) {\r
+ dsseqs=jal.getSequences(); // for merge/update\r
+ gapChar=jal.getGapCharacter();\r
+ } else {\r
+ dsseqs=new Vector();\r
+ }\r
+ char valGapchar=alignment.getGapChar().charAt(0);\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ AlignmentSequence valseq = alignment.getAlignmentSequence(i);\r
+ jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);\r
+ if (alseq!=null) {\r
+ //TODO: upperCase/LowerCase situation here ? do we allow it ?\r
+ //if (!alseq.getSequence().equals(valseq.getSequence())) {\r
+ // throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");\r
+ if (Cache.log.isDebugEnabled())\r
+ Cache.log.debug("Updating apparently edited sequence "+alseq.getName());\r
+ // this might go *horribly* wrong\r
+ alseq.setSequence(new String(valseq.getSequence()).replace(valGapchar, gapChar));\r
+ jremain--;\r
+ } else {\r
+ alseq = new jalview.datamodel.Sequence(\r
+ valseq.getName(),\r
+ valseq.getSequence().replace(valGapchar, gapChar),\r
+ valseq.getStart(),\r
+ valseq.getEnd() );\r
+ \r
+ Vobject datsetseq = (Vobject)valseq.getRefid();\r
+ if (datsetseq!=null) {\r
+ alseq.setDatasetSequence((SequenceI)getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI\r
+ } else {\r
+ Cache.log.error("Invalid dataset sequence id (null) for alignment sequence "+valseq.getVorbaId());\r
+ }\r
+ bindjvvobj(alseq, valseq);\r
+ alseq.setVamsasId(valseq.getVorbaId().getId());\r
+ dsseqs.add(alseq);\r
+ }\r
+ if (valseq.getAlignmentSequenceAnnotationCount()>0) {\r
+ AlignmentSequenceAnnotation[] vasannot=valseq.getAlignmentSequenceAnnotation();\r
+ for (int a=0; a<vasannot.length; a++) {\r
+ jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations\r
+ if (asa==null) {\r
+ int se[] = getBounds(vasannot[a]);\r
+ asa = getjAlignmentAnnotation(jal, vasannot[a]);\r
+ asa.sequenceRef=alseq;\r
+ asa.createSequenceMapping(alseq, alseq.getStart()+se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.\r
+ bindjvvobj(asa, vasannot[a]);\r
+ newasAnnots.add(asa);\r
+ } else {\r
+ // update existing annotation - can do this in place\r
+ if (vasannot[a].getModifiable()) {\r
+ Cache.log.info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");\r
+ // TODO: should at least replace with new one - otherwise things will break\r
+ // basically do this:\r
+ // int se[] = getBounds(vasannot[a]);\r
+ // asa.update(getjAlignmentAnnotation(jal, vasannot[a])); // update from another annotation object in place.\r
+ // asa.createSequenceMapping(alseq, se[0], false); \r
+\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (jal==null) {\r
+ SequenceI[] seqs = new SequenceI[dsseqs.size()];\r
+ for (i=0,iSize=dsseqs.size(); i<iSize; i++) {\r
+ seqs[i]=(SequenceI) dsseqs.elementAt(i);\r
+ dsseqs.setElementAt(null, i);\r
+ }\r
+ jal = new jalview.datamodel.Alignment(seqs);\r
+ Cache.log.debug("New vamsas alignment imported into jalview "+alignment.getVorbaId().getId());\r
+ jal.setDataset(jdataset);\r
+ }\r
+ if (newasAnnots!=null && newasAnnots.size()>0) {\r
+ // Add the new sequence annotations in to the alignment.\r
+ for (int an=0,anSize=newasAnnots.size(); an<anSize; an++) {\r
+ jal.addAnnotation((AlignmentAnnotation) newasAnnots.elementAt(an));\r
+ // TODO: check if anything has to be done - like calling adjustForAlignment or something.\r
+ newasAnnots.setElementAt(null, an);\r
+ }\r
+ newasAnnots=null;\r
+ }\r
+ // //////////////////////////////////////////\r
+ // //LOAD ANNOTATIONS FOR THE ALIGNMENT\r
+ // ////////////////////////////////////\r
+ if (alignment.getAlignmentAnnotationCount()>0)\r
+ {\r
+ org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.getAlignmentAnnotation();\r
+\r
+ for (int j = 0; j < an.length; j++)\r
+ {\r
+ jalview.datamodel.AlignmentAnnotation jan=(jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);\r
+ if (jan!=null) {\r
+ // update or stay the same.\r
+ // TODO: should at least replace with a new one - otherwise things will break\r
+ // basically do this:\r
+ // jan.update(getjAlignmentAnnotation(jal, an[a])); // update from another annotation object in place.\r
+\r
+ Cache.log.debug("update from vamsas alignment annotation to existing jalview alignment annotation.");\r
+ if (an[j].getModifiable()) {\r
+ // TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited.\r
+ Cache.log.info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");\r
+ }\r
+ // TODO: compare annotation element rows\r
+ // TODO: compare props.\r
+ } else {\r
+ jan = getjAlignmentAnnotation(jal, an[j]);\r
+ jal.addAnnotation(jan);\r
+ bindjvvobj(jan, an[j]);\r
+ }\r
+ }\r
+ }\r
+ AlignFrame alignFrame;\r
+ if (av==null) {\r
+ Cache.log.debug("New alignframe for alignment "+alignment.getVorbaId());\r
+ // ///////////////////////////////\r
+ // construct alignment view\r
+ alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ av=alignFrame.getViewport();\r
+ String title = alignment.getProvenance().getEntry(alignment.getProvenance().getEntryCount()-1).getAction();\r
+ if (alignment.getPropertyCount()>0) {\r
+ for (int p=0,pe=alignment.getPropertyCount(); p<pe; p++) {\r
+ if (alignment.getProperty(p).getName().equals("jalview:AlTitle")) {\r
+ title = alignment.getProperty(p).getContent();\r
+ }\r
+ }\r
+ }\r
+ // TODO: automatically create meaningful title for a vamsas alignment using its provenance.\r
+ jalview.gui.Desktop.addInternalFrame(alignFrame, title + "("+alignment.getVorbaId()+")",\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+ bindjvvobj(av, alignment);\r
+ } else {\r
+ // find the alignFrame for jal.\r
+ // TODO: fix this so we retrieve the alignFrame handing av *directly*\r
+ alignFrame=getAlignFrameFor(av);\r
+ }\r
+ // LOAD TREES\r
+ // /////////////////////////////////////\r
+ if (alignment.getTreeCount() > 0)\r
+ {\r
+\r
+ for (int t = 0; t < alignment.getTreeCount(); t++)\r
+ {\r
+ Tree tree = alignment.getTree(t);\r
+ TreePanel tp=(TreePanel) getvObj2jv(tree);\r
+ if (tp!=null) {\r
+ Cache.log.info("Update from vamsas document to alignment associated tree not implemented yet.");\r
+ } else {\r
+ // make a new tree\r
+ Object[] idata = this.recoverInputData(tree.getProvenance());\r
+ try {\r
+ AlignmentView inputData=null;\r
+ if (idata!=null && idata[0]!=null)\r
+ inputData = (AlignmentView) idata[0];\r
+ tp = alignFrame.ShowNewickTree(\r
+ new jalview.io.NewickFile(tree.getNewick(0).getContent()),\r
+ tree.getNewick(0).getTitle()+" ("+tree.getVorbaId()+")",inputData,\r
+ 600, 500,\r
+ t * 20 + 50, t * 20 + 50);\r
+ bindjvvobj(tp, tree);\r
+ } catch (Exception e) {\r
+ Cache.log.warn("Problems parsing treefile '"+tree.getNewick(0).getContent()+"'",e);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ // bitfields - should be a template in j1.5\r
+ private static int HASSECSTR=0;\r
+ private static int HASVALS=1;\r
+ private static int HASHPHOB=2;\r
+ private static int HASDC=3;\r
+ private static int HASDESCSTR=4;\r
+ private static int HASTWOSTATE=5; // not used yet.\r
+ /**\r
+ * parses the AnnotationElements - if they exist - into jalview.datamodel.Annotation[] rows\r
+ * Two annotation rows are made if there are distinct annotation for both at 'pos' and 'after pos' at any particular site.\r
+ * @param annotation\r
+ * @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)}\r
+ */\r
+ private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation annotation) {\r
+ // set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made\r
+ // TODO: potentially we might make several annotation rows from one vamsas alignment annotation. the jv2Vobj binding mechanism\r
+ // may not quite cope with this (without binding an array of annotations to a vamsas alignment annotation)\r
+ // summary flags saying what we found over the set of annotation rows.\r
+ boolean[] AeContent = new boolean[] { false, false, false, false, false};\r
+ int[] rangeMap = getMapping(annotation);\r
+ jalview.datamodel.Annotation[][] anot=new jalview.datamodel.Annotation[][] { \r
+ new jalview.datamodel.Annotation[rangeMap.length],\r
+ new jalview.datamodel.Annotation[rangeMap.length]\r
+ };\r
+ boolean mergeable=true; //false if 'after positions cant be placed on same annotation row as positions. \r
+ \r
+ if (annotation.getAnnotationElementCount()>0) {\r
+ AnnotationElement ae[] = annotation.getAnnotationElement();\r
+ for (int aa = 0; aa < ae.length; aa++)\r
+ {\r
+ int pos = ae[aa].getPosition()-1;// pos counts from 1 to (|seg.start-seg.end|+1)\r
+ if (pos>=0 && pos<rangeMap.length) { \r
+ int row=ae[aa].getAfter()?1:0;\r
+ if (anot[row][pos]!=null) {\r
+ // only time this should happen is if the After flag is set.\r
+ Cache.log.debug("Ignoring duplicate annotation site at "+pos);\r
+ continue;\r
+ }\r
+ if (anot[1-row][pos]!=null)\r
+ mergeable=false;\r
+ String desc = "";\r
+ if (ae[aa].getDescription()!=null) {\r
+ desc = ae[aa].getDescription();\r
+ if (desc.length()>0) {\r
+ // have imported valid description string\r
+ AeContent[HASDESCSTR]=true;\r
+ }\r
+ }\r
+ String dc = null;//ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();\r
+ String ss = null;//ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();\r
+ java.awt.Color colour = null;\r
+ if (ae[aa].getGlyphCount()>0) {\r
+ Glyph[] glyphs = ae[aa].getGlyph();\r
+ for (int g=0; g<glyphs.length; g++) {\r
+ if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) {\r
+ ss=glyphs[g].getContent();\r
+ AeContent[HASSECSTR]=true;\r
+ } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) {\r
+ Cache.log.debug("ignoring hydrophobicity glyph marker.");\r
+ AeContent[HASHPHOB]=true;\r
+ char c=(dc=glyphs[g].getContent()).charAt(0);\r
+ // dc may get overwritten - but we still set the colour.\r
+ colour = new java.awt.Color(c=='+'?255:0,c=='.'?255:0,c=='-'?255:0);\r
+\r
+ } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.DEFAULT)) {\r
+ dc = glyphs[g].getContent();\r
+ AeContent[HASDC]=true;\r
+ } else {\r
+ Cache.log.debug("Ignoring unknown glyph type "+glyphs[g].getDict());\r
+ }\r
+ }\r
+ }\r
+ float val=0;\r
+ if (ae[aa].getValueCount()>0) {\r
+ AeContent[HASVALS]=true;\r
+ if (ae[aa].getValueCount()>1) {\r
+ Cache.log.warn("ignoring additional "+(ae[aa].getValueCount()-1)+"values in annotation element.");\r
+ }\r
+ val = ae[aa].getValue(0);\r
+ }\r
+ if (colour==null) {\r
+ anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val);\r
+ } else {\r
+ anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val, colour);\r
+ }\r
+ } else {\r
+ Cache.log.warn("Ignoring out of bound annotation element "+aa+" in "+annotation.getVorbaId().getId());\r
+ }\r
+ }\r
+ // decide on how many annotation rows are needed.\r
+ if (mergeable) {\r
+ for (int i=0; i<anot[0].length;i++) {\r
+ if (anot[1][i]!=null) {\r
+ anot[0][i] = anot[1][i];\r
+ anot[0][i].description = anot[0][i].description+" (after)";\r
+ AeContent[HASDESCSTR]=true; // we have valid description string data\r
+ anot[1][i] = null;\r
+ }\r
+ }\r
+ anot[1] = null;\r
+ } else {\r
+ for (int i=0; i<anot[0].length;i++) {\r
+ anot[1][i].description = anot[1][i].description+" (after)";\r
+ }\r
+ }\r
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };\r
+ } else {\r
+ // no annotations to parse. Just return an empty annotationElement[] array.\r
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };\r
+ }\r
+ // return null;\r
+ }\r
+ /**\r
+ * @param jal the jalview alignment to which the annotation will be attached (ideally - freshly updated from corresponding vamsas alignment)\r
+ * @param annotation\r
+ * @return unbound jalview alignment annotation object.\r
+ */\r
+ private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.datamodel.AlignmentI jal, org.vamsas.objects.core.RangeAnnotation annotation) {\r
+ jalview.datamodel.AlignmentAnnotation jan =null;\r
+ if (annotation==null)\r
+ return null;\r
+ // boolean hasSequenceRef=annotation.getClass().equals(org.vamsas.objects.core.AlignmentSequenceAnnotation.class);\r
+ //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class));\r
+ /*int se[] = getBounds(annotation);\r
+ if (se==null)\r
+ se=new int[] {0,jal.getWidth()-1};\r
+ */\r
+ Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);\r
+ String a_label=annotation.getLabel();\r
+ String a_descr=annotation.getDescription();\r
+ if (a_label==null || a_label.length()==0) {\r
+ a_label = annotation.getType();\r
+ if (a_label.length()==0)\r
+ a_label = "Unamed annotation";\r
+ }\r
+ if (a_descr==null || a_descr.length()==0) {\r
+ a_descr = "Annotation of type '"+annotation.getType()+"'";\r
+ }\r
+ if (parsedRangeAnnotation==null) {\r
+ Cache.log.debug("Inserting empty annotation row elements for a whole-alignment annotation.");\r
+ \r
+ \r
+ } else {\r
+ if (parsedRangeAnnotation[3]!=null) {\r
+ Cache.log.warn("Ignoring 'After' annotation row in "+annotation.getVorbaId());\r
+ }\r
+ jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];\r
+ boolean[] has=(boolean[])parsedRangeAnnotation[0];\r
+ // VAMSAS: getGraph is only on derived annotation for alignments - in this way its 'odd' - there is already an existing TODO about removing this flag as being redundant\r
+ /*if ((annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class) && ((org.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())\r
+ || (hasSequenceRef=true && ((org.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {\r
+ */\r
+ if (has[HASVALS]) {\r
+ // make bounds and automatic description strings for jalview user's benefit (these shouldn't be written back to vamsas document)\r
+ boolean first=true;\r
+ float min=0,max=1;\r
+ int lastval=0;\r
+ for (int i=0;i<arow.length; i++) {\r
+ if (arow[i]!=null) {\r
+ if (i-lastval>1) {\r
+ // do some interpolation *between* points\r
+ if (arow[lastval]!=null) {\r
+ float interval = arow[i].value-arow[lastval].value;\r
+ interval/=i-lastval;\r
+ float base = arow[lastval].value;\r
+ for (int ip=lastval+1,np=0; ip<i; np++,ip++) {\r
+ arow[ip] = new jalview.datamodel.Annotation("","",' ', interval*np+base);\r
+ // NB - Interpolated points don't get a tooltip and description.\r
+ }\r
+ }\r
+ }\r
+ lastval=i;\r
+ // check range - shouldn't we have a min and max property in the annotation object ?\r
+ if (first) { min=max=arow[i].value; first=false;}\r
+ else { if (arow[i].value<min) { min=arow[i].value; }\r
+ else if (arow[i].value>max) { max=arow[i].value; }\r
+ }\r
+ // make tooltip and display char value\r
+ if (!has[HASDESCSTR]) arow[i].description = arow[i].value + "";\r
+ if (!has[HASDC]) arow[i].displayCharacter=arow[i].value+"";\r
+ } \r
+ }\r
+ int type=jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;\r
+ if (has[HASHPHOB]) {\r
+ type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;\r
+ }\r
+ jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type);\r
+ } else {\r
+ jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow);\r
+ jan.setThreshold(null);\r
+ }\r
+ if (annotation.getLinkCount()>0) {\r
+ Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation.");\r
+ }\r
+ if (annotation.getModifiable()) {\r
+ jan.editable=true;\r
+ }\r
+\r
+ if (annotation.getPropertyCount()>0) {\r
+ // look for special jalview properties\r
+ org.vamsas.objects.core.Property[] props=annotation.getProperty();\r
+ for (int p=0;p<props.length; p++) {\r
+ if (props[p].getName().equalsIgnoreCase("jalview:graphType")) {\r
+ try { \r
+ // probably a jalview annotation graph so recover the visualization hints.\r
+ jan.graph = jalview.datamodel.AlignmentAnnotation.getGraphValueFromString(props[p].getContent());\r
+ } catch (Exception e) {\r
+ Cache.log.debug("Invalid graph type value in jalview:graphType property.");\r
+ }\r
+ try {\r
+ if (annotation.getGroup()!=null && annotation.getGroup().length()>0)\r
+ jan.graphGroup = Integer.parseInt(annotation.getGroup());\r
+ } catch (Exception e) {\r
+ Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ return jan;\r
+\r
+ } \r
+\r
+ return null;\r
+ }\r
+\r
+ private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta) {\r
+ int[] se = getBounds(dseta);\r
+ SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta.getType(),\r
+ dseta.getDescription(), dseta.getStatus(), se[0], se[1], dseta\r
+ .getGroup());\r
+ if (dseta.getLinkCount() > 0)\r
+ {\r
+ Link[] links = dseta.getLink();\r
+ for (int i = 0; i < links.length; i++)\r
+ {\r
+ sf.addLink(links[i].getContent() + "|" + links[i].getHref());\r
+ }\r
+ }\r
+ return sf;\r
+ }\r
+\r
+ /**\r
+ * get real bounds of a RangeType's specification. start and end are an\r
+ * inclusive range within which all segments and positions lie.\r
+ * TODO: refactor to vamsas utils\r
+ * @param dseta\r
+ * @return int[] { start, end}\r
+ */\r
+ private int[] getBounds(RangeType dseta) {\r
+ if (dseta != null)\r
+ {\r
+ int[] se = null;\r
+ if (dseta.getSegCount()>0 && dseta.getPosCount()>0)\r
+ throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+ if (dseta.getSegCount() > 0)\r
+ {\r
+ se = getSegRange(dseta.getSeg(0),true);\r
+ for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)\r
+ {\r
+ int nse[] = getSegRange(dseta.getSeg(s), true);\r
+ if (se[0] > nse[0])\r
+ se[0] = nse[0];\r
+ if (se[1] < nse[1])\r
+ se[1] = nse[1];\r
+ }\r
+ }\r
+ if (dseta.getPosCount() > 0)\r
+ {\r
+ // could do a polarity for pos range too. and pass back indication of discontinuities.\r
+ int pos = dseta.getPos(0).getI();\r
+ se = new int[] { pos, pos };\r
+ for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
+ {\r
+ pos = dseta.getPos(p).getI();\r
+ if (se[0] > pos)\r
+ se[0] = pos;\r
+ if (se[1] < pos)\r
+ se[1] = pos;\r
+ }\r
+ }\r
+ return se;\r
+ }\r
+ return null;\r
+ }\r
+ /**\r
+ * map from a rangeType's internal frame to the referenced object's coordinate frame.\r
+ * @param dseta\r
+ * @return int [] { ref(pos)...} for all pos in rangeType's frame.\r
+ */\r
+ private int[] getMapping(RangeType dseta) {\r
+ Vector posList=new Vector();\r
+ if (dseta != null)\r
+ {\r
+ int[] se = null;\r
+ if (dseta.getSegCount()>0 && dseta.getPosCount()>0)\r
+ throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+ if (dseta.getSegCount() > 0)\r
+ {\r
+ for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)\r
+ {\r
+ se = getSegRange(dseta.getSeg(s), false);\r
+ int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);\r
+ for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {\r
+ posList.add(new Integer(p));\r
+ }\r
+ }\r
+ } \r
+ else if (dseta.getPosCount() > 0)\r
+ {\r
+ int pos = dseta.getPos(0).getI();\r
+\r
+ for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
+ {\r
+ pos = dseta.getPos(p).getI();\r
+ posList.add(new Integer(pos));\r
+ }\r
+ }\r
+ }\r
+ if (posList!=null && posList.size()>0) {\r
+ int[] range=new int[posList.size()];\r
+ for (int i=0; i<range.length; i++)\r
+ range[i] = ((Integer)posList.elementAt(i)).intValue();\r
+ posList.clear();\r
+ return range;\r
+ }\r
+ return null;\r
+ }\r
+ /* not needed now. \r
+ * Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov) {\r
+ jalview.datamodel.ProvenanceEntry[] entries = null;\r
+ // TODO: fix App and Action here.\r
+ Provenance prov = new Provenance();\r
+ org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(\r
+ new java.util.Date());\r
+ Entry provEntry;\r
+\r
+ if (jprov != null)\r
+ {\r
+ entries = jprov.getEntries();\r
+ for (int i = 0; i < entries.length; i++)\r
+ {\r
+ provEntry = new Entry();\r
+ try\r
+ {\r
+ date = new org.exolab.castor.types.Date(entries[i].getDate());\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+\r
+ date = new org.exolab.castor.types.Date(entries[i].getDate());\r
+ }\r
+ provEntry.setDate(date);\r
+ provEntry.setUser(entries[i].getUser());\r
+ provEntry.setAction(entries[i].getAction());\r
+ prov.addEntry(provEntry);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ provEntry = new Entry();\r
+ provEntry.setDate(date);\r
+ provEntry.setUser(System.getProperty("user.name")); // TODO: ext string\r
+ provEntry.setApp("JVAPP"); // TODO: ext string\r
+ provEntry.setAction(action);\r
+ prov.addEntry(provEntry);\r
+ }\r
+\r
+ return prov;\r
+ }\r
+ */\r
+ jalview.datamodel.Provenance getJalviewProvenance(Provenance prov) {\r
+ // TODO: fix App and Action entries and check use of provenance in jalview.\r
+ jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();\r
+ for (int i = 0; i < prov.getEntryCount(); i++)\r
+ {\r
+ jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i).getAction(),\r
+ prov.getEntry(i).getDate().toDate(), prov.getEntry(i).getId());\r
+ }\r
+\r
+ return jprov;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return default initial provenance list for a Jalview created vamsas\r
+ * object.\r
+ */\r
+ Provenance dummyProvenance() {\r
+ return dummyProvenance(null);\r
+ }\r
+\r
+ Entry dummyPEntry(String action) {\r
+ Entry entry = new Entry();\r
+ entry.setApp(this.provEntry.getApp());\r
+ if (action != null)\r
+ entry.setAction(action);\r
+ else\r
+ entry.setAction("created.");\r
+ entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));\r
+ entry.setUser(this.provEntry.getUser());\r
+ return entry;\r
+ }\r
+\r
+ Provenance dummyProvenance(String action) {\r
+ Provenance prov = new Provenance();\r
+ prov.addEntry(dummyPEntry(action));\r
+ return prov;\r
+ }\r
+\r
+ void addProvenance(Provenance p, String action) {\r
+ p.addEntry(dummyPEntry(action));\r
+ }\r
+\r
+}\r
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.jbgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class GDesktop extends JFrame\r
-{\r
- protected static JMenu windowMenu = new JMenu();\r
- JMenuBar DesktopMenubar = new JMenuBar();\r
- JMenu FileMenu = new JMenu();\r
- JMenu HelpMenu = new JMenu();\r
- JMenuItem inputLocalFileMenuItem = new JMenuItem();\r
- JMenuItem inputURLMenuItem = new JMenuItem();\r
- JMenuItem inputTextboxMenuItem = new JMenuItem();\r
- JMenuItem quit = new JMenuItem();\r
- JMenuItem aboutMenuItem = new JMenuItem();\r
- JMenuItem documentationMenuItem = new JMenuItem();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- JMenu toolsMenu = new JMenu();\r
- JMenuItem preferences = new JMenuItem();\r
- JMenuItem saveState = new JMenuItem();\r
- JMenuItem loadState = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
- JMenuItem vamsasLoad = new JMenuItem();\r
- JMenuItem inputSequence = new JMenuItem();\r
-\r
- /**\r
- * Creates a new GDesktop object.\r
- */\r
- public GDesktop()\r
- {\r
- try\r
- {\r
- jbInit();\r
- this.setJMenuBar(DesktopMenubar);\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws Exception DOCUMENT ME!\r
- */\r
- private void jbInit() throws Exception\r
- {\r
- FileMenu.setMnemonic('F');\r
- FileMenu.setText("File");\r
- HelpMenu.setText("Help");\r
- inputLocalFileMenuItem.setMnemonic('L');\r
- inputLocalFileMenuItem.setText("from File");\r
- inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputLocalFileMenuItem_actionPerformed(null);\r
- }\r
- });\r
- inputURLMenuItem.setMnemonic('U');\r
- inputURLMenuItem.setText("from URL");\r
- inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputURLMenuItem_actionPerformed(null);\r
- }\r
- });\r
- inputTextboxMenuItem.setMnemonic('C');\r
- inputTextboxMenuItem.setText("from Textbox");\r
- inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputTextboxMenuItem_actionPerformed(null);\r
- }\r
- });\r
- quit.setMnemonic('Q');\r
- quit.setText("Quit");\r
- quit.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- quit();\r
- }\r
- });\r
- aboutMenuItem.setText("About");\r
- aboutMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- aboutMenuItem_actionPerformed(e);\r
- }\r
- });\r
- documentationMenuItem.setText("Documentation");\r
- documentationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- documentationMenuItem_actionPerformed(e);\r
- }\r
- });\r
- this.getContentPane().setLayout(flowLayout1);\r
- windowMenu.setText("Window");\r
- preferences.setText("Preferences...");\r
- preferences.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- preferences_actionPerformed(e);\r
- }\r
- });\r
- toolsMenu.setText("Tools");\r
- saveState.setMnemonic('S');\r
- saveState.setText("Save Project");\r
- saveState.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveState_actionPerformed(e);\r
- }\r
- });\r
- loadState.setMnemonic('L');\r
- loadState.setText("Load Project");\r
- loadState.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- loadState_actionPerformed(e);\r
- }\r
- });\r
- jMenu1.setMnemonic('I');\r
- jMenu1.setText("Input Alignment");\r
- vamsasLoad.setText("Vamsas");\r
- vamsasLoad.setVisible(false);\r
- vamsasLoad.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- vamsasLoad_actionPerformed(e);\r
- }\r
- });\r
- inputSequence.setText("Fetch Sequence(s)...");\r
- inputSequence.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputSequence_actionPerformed(e);\r
- }\r
- });\r
- DesktopMenubar.add(FileMenu);\r
- DesktopMenubar.add(toolsMenu);\r
- DesktopMenubar.add(HelpMenu);\r
- DesktopMenubar.add(windowMenu);\r
- FileMenu.add(jMenu1);\r
- FileMenu.add(inputSequence);\r
- FileMenu.addSeparator();\r
- FileMenu.add(saveState);\r
- FileMenu.add(loadState);\r
- FileMenu.addSeparator();\r
- FileMenu.add(quit);\r
- HelpMenu.add(aboutMenuItem);\r
- HelpMenu.add(documentationMenuItem);\r
- toolsMenu.add(preferences);\r
- jMenu1.add(inputLocalFileMenuItem);\r
- jMenu1.add(inputURLMenuItem);\r
- jMenu1.add(inputTextboxMenuItem);\r
- jMenu1.add(vamsasLoad);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- protected void quit()\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void SaveState_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void saveState_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void loadState_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void loadJalviewAlign_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- public void vamsasLoad_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void inputSequence_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-}\r
+/*
+* 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
+*/
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GDesktop extends JFrame
+{
+ protected static JMenu windowMenu = new JMenu();
+ JMenuBar DesktopMenubar = new JMenuBar();
+ JMenu FileMenu = new JMenu();
+ JMenu HelpMenu = new JMenu();
+ protected JMenu VamsasMenu = new JMenu();
+ JMenuItem inputLocalFileMenuItem = new JMenuItem();
+ JMenuItem inputURLMenuItem = new JMenuItem();
+ JMenuItem inputTextboxMenuItem = new JMenuItem();
+ JMenuItem quit = new JMenuItem();
+ JMenuItem aboutMenuItem = new JMenuItem();
+ JMenuItem documentationMenuItem = new JMenuItem();
+ FlowLayout flowLayout1 = new FlowLayout();
+ JMenu toolsMenu = new JMenu();
+ JMenuItem preferences = new JMenuItem();
+ JMenuItem saveState = new JMenuItem();
+ JMenuItem loadState = new JMenuItem();
+ JMenu jMenu1 = new JMenu();
+ protected JMenuItem vamsasLoad = new JMenuItem();
+ JMenuItem inputSequence = new JMenuItem();
+ protected JMenuItem vamsasStop = new JMenuItem();
+
+ /**
+ * Creates a new GDesktop object.
+ */
+ public GDesktop()
+ {
+ try
+ {
+ jbInit();
+ this.setJMenuBar(DesktopMenubar);
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ private void jbInit() throws Exception
+ {
+ FileMenu.setMnemonic('F');
+ FileMenu.setText("File");
+ HelpMenu.setText("Help");
+ VamsasMenu.setText("Vamsas");
+ VamsasMenu.setMnemonic('V');
+ VamsasMenu.setToolTipText("Share data with other vamsas applications.");
+ inputLocalFileMenuItem.setMnemonic('L');
+ inputLocalFileMenuItem.setText("from File");
+ inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ inputLocalFileMenuItem_actionPerformed(null);
+ }
+ });
+ inputURLMenuItem.setMnemonic('U');
+ inputURLMenuItem.setText("from URL");
+ inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ inputURLMenuItem_actionPerformed(null);
+ }
+ });
+ inputTextboxMenuItem.setMnemonic('C');
+ inputTextboxMenuItem.setText("from Textbox");
+ inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ inputTextboxMenuItem_actionPerformed(null);
+ }
+ });
+ quit.setMnemonic('Q');
+ quit.setText("Quit");
+ quit.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ quit();
+ }
+ });
+ aboutMenuItem.setText("About");
+ aboutMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ aboutMenuItem_actionPerformed(e);
+ }
+ });
+ documentationMenuItem.setText("Documentation");
+ documentationMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ documentationMenuItem_actionPerformed(e);
+ }
+ });
+ this.getContentPane().setLayout(flowLayout1);
+ windowMenu.setText("Window");
+ preferences.setText("Preferences...");
+ preferences.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ preferences_actionPerformed(e);
+ }
+ });
+ toolsMenu.setText("Tools");
+ saveState.setMnemonic('S');
+ saveState.setText("Save Project");
+ saveState.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(e);
+ }
+ });
+ loadState.setMnemonic('L');
+ loadState.setText("Load Project");
+ loadState.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ loadState_actionPerformed(e);
+ }
+ });
+ jMenu1.setMnemonic('I');
+ jMenu1.setText("Input Alignment");
+ vamsasLoad.setText("Start Vamsas Session...");
+ vamsasLoad.setVisible(false);
+ vamsasLoad.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasLoad_actionPerformed(e);
+ }
+ });
+ inputSequence.setText("Fetch Sequence(s)...");
+ inputSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ inputSequence_actionPerformed(e);
+ }
+ });
+ vamsasStop.setText("Stop Vamsas Session");
+ vamsasStop.setVisible(false);
+ vamsasStop.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasStop_actionPerformed(e);
+ }
+ }); DesktopMenubar.add(FileMenu);
+ DesktopMenubar.add(toolsMenu);
+ VamsasMenu.setVisible(false);
+ DesktopMenubar.add(VamsasMenu);
+ DesktopMenubar.add(HelpMenu);
+ DesktopMenubar.add(windowMenu);
+ FileMenu.addSeparator();
+ FileMenu.add(jMenu1);
+ FileMenu.add(inputSequence);
+ FileMenu.addSeparator();
+ FileMenu.add(saveState);
+ FileMenu.add(loadState);
+ FileMenu.addSeparator();
+ FileMenu.add(quit);
+ HelpMenu.add(aboutMenuItem);
+ HelpMenu.add(documentationMenuItem);
+ VamsasMenu.add(vamsasLoad);
+ VamsasMenu.add(vamsasStop);
+ toolsMenu.add(preferences);
+ jMenu1.add(inputLocalFileMenuItem);
+ jMenu1.add(inputURLMenuItem);
+ jMenu1.add(inputTextboxMenuItem);
+ // jMenu1.add(vamsasLoad);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.AlignViewport av)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport av)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ protected void quit()
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void aboutMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void documentationMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void SaveState_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void preferences_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveState_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void loadState_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void loadJalviewAlign_actionPerformed(ActionEvent e)
+ {
+ }
+
+ public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void inputSequence_actionPerformed(ActionEvent e)
+ {
+
+ }
+ public void vamsasStop_actionPerformed(ActionEvent e)
+ {
+
+ }
+}
git://source.jalview.org / jalview.git / commitdiff