+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
package jalview.datamodel;\r
\r
import java.util.Enumeration;\r
public class AlignedCodonFrame\r
{\r
/**\r
- * array of nucleotide positions for aligned codons at column of aligned proteins.\r
+ * array of nucleotide positions for aligned codons at column of aligned\r
+ * proteins.\r
*/\r
public int[][] codons = null;\r
+\r
/**\r
- * width of protein sequence alignement\r
- * implicit assertion that codons.length >= aaWidth\r
+ * width of protein sequence alignement implicit assertion that codons.length\r
+ * >= aaWidth\r
*/\r
- public int aaWidth=0;\r
+ public int aaWidth = 0;\r
+\r
/**\r
* initialise codon frame with a nominal alignment width\r
+ * \r
* @param aWidth\r
*/\r
public AlignedCodonFrame(int aWidth)\r
{\r
- if (aWidth<=0)\r
- {\r
- codons=null;\r
+ if (aWidth <= 0)\r
+ {\r
+ codons = null;\r
return;\r
- }\r
+ }\r
codons = new int[aWidth][];\r
for (int res = 0; res < aWidth; res++)\r
codons[res] = null;\r
\r
/**\r
* ensure that codons array is at least as wide as aslen residues\r
+ * \r
* @param aslen\r
* @return (possibly newly expanded) codon array\r
*/\r
}\r
return codons;\r
}\r
+\r
/**\r
- * @return width of aligned translated amino acid residues \r
+ * @return width of aligned translated amino acid residues\r
*/\r
public int getaaWidth()\r
{\r
return aaWidth;\r
}\r
+\r
/**\r
- * TODO: not an ideal solution - we reference the aligned amino acid sequences in order to make insertions on them\r
- * Better would be dnaAlignment and aaAlignment reference....\r
+ * TODO: not an ideal solution - we reference the aligned amino acid sequences\r
+ * in order to make insertions on them Better would be dnaAlignment and\r
+ * aaAlignment reference....\r
*/\r
- Vector a_aaSeqs=new Vector();\r
+ Vector a_aaSeqs = new Vector();\r
+\r
/**\r
- * increase aaWidth by one and insert a new aligned codon position space at aspos.\r
+ * increase aaWidth by one and insert a new aligned codon position space at\r
+ * aspos.\r
+ * \r
* @param aspos\r
*/\r
public void insertAAGap(int aspos, char gapCharacter)\r
- { \r
- // this aa appears before the aligned codons at aspos - so shift them in each pair of mapped sequences\r
+ {\r
+ // this aa appears before the aligned codons at aspos - so shift them in\r
+ // each pair of mapped sequences\r
aaWidth++;\r
- if (a_aaSeqs!=null)\r
+ if (a_aaSeqs != null)\r
{\r
- // we actually have to modify the aligned sequences here, so use the a_aaSeqs vector\r
+ // we actually have to modify the aligned sequences here, so use the\r
+ // a_aaSeqs vector\r
Enumeration sq = a_aaSeqs.elements();\r
while (sq.hasMoreElements())\r
{\r
}\r
}\r
checkCodonFrameWidth(aspos);\r
- if (aspos<aaWidth)\r
+ if (aspos < aaWidth)\r
{\r
aaWidth++;\r
- System.arraycopy(codons, aspos, codons, aspos+1, aaWidth-aspos);\r
- codons[aspos]=null; // clear so new codon position can be marked.\r
+ System.arraycopy(codons, aspos, codons, aspos + 1, aaWidth - aspos);\r
+ codons[aspos] = null; // clear so new codon position can be marked.\r
}\r
}\r
\r
{\r
aaWidth = aapos;\r
}\r
+\r
/**\r
* tied array of na Sequence objects.\r
*/\r
- SequenceI[] dnaSeqs=null;\r
+ SequenceI[] dnaSeqs = null;\r
+\r
/**\r
- * tied array of Mappings to protein sequence Objects and \r
- SequenceI[] aaSeqs=null;\r
- * MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element \r
+ * tied array of Mappings to protein sequence Objects and SequenceI[]\r
+ * aaSeqs=null; MapLists where eac maps from the corresponding dnaSeqs element\r
+ * to corresponding aaSeqs element\r
*/\r
- Mapping[] dnaToProt=null;\r
+ Mapping[] dnaToProt = null;\r
+\r
/**\r
- * add a mapping between the dataset sequences for the associated dna and protein sequence objects\r
+ * add a mapping between the dataset sequences for the associated dna and\r
+ * protein sequence objects\r
+ * \r
* @param dnaseq\r
* @param aaseq\r
* @param map\r
*/\r
public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)\r
- { \r
- int nlen=1;\r
- if (dnaSeqs!=null)\r
+ {\r
+ int nlen = 1;\r
+ if (dnaSeqs != null)\r
{\r
- nlen = dnaSeqs.length+1;\r
+ nlen = dnaSeqs.length + 1;\r
}\r
SequenceI[] ndna = new SequenceI[nlen];\r
Mapping[] ndtp = new Mapping[nlen];\r
- if (dnaSeqs!=null)\r
+ if (dnaSeqs != null)\r
{\r
- System.arraycopy(dnaSeqs,0,ndna, 0, dnaSeqs.length);\r
- System.arraycopy(dnaToProt,0,ndtp, 0, dnaSeqs.length);\r
+ System.arraycopy(dnaSeqs, 0, ndna, 0, dnaSeqs.length);\r
+ System.arraycopy(dnaToProt, 0, ndtp, 0, dnaSeqs.length);\r
}\r
dnaSeqs = ndna;\r
dnaToProt = ndtp;\r
nlen--;\r
- dnaSeqs[nlen] = (dnaseq.getDatasetSequence()==null) ? dnaseq : dnaseq.getDatasetSequence();\r
+ dnaSeqs[nlen] = (dnaseq.getDatasetSequence() == null) ? dnaseq : dnaseq\r
+ .getDatasetSequence();\r
Mapping mp = new Mapping(map);\r
// JBPNote DEBUG! THIS !\r
- //dnaseq.transferAnnotation(aaseq, mp);\r
- //aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));\r
- mp.to = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();\r
+ // dnaseq.transferAnnotation(aaseq, mp);\r
+ // aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));\r
+ mp.to = (aaseq.getDatasetSequence() == null) ? aaseq : aaseq\r
+ .getDatasetSequence();\r
a_aaSeqs.addElement(aaseq);\r
dnaToProt[nlen] = mp;\r
}\r
\r
-\r
public SequenceI[] getdnaSeqs()\r
{\r
return dnaSeqs;\r
}\r
+\r
public SequenceI[] getAaSeqs()\r
{\r
- if (dnaToProt==null)\r
+ if (dnaToProt == null)\r
return null;\r
SequenceI[] sqs = new SequenceI[dnaToProt.length];\r
- for (int sz=0; sz<dnaToProt.length; sz++)\r
+ for (int sz = 0; sz < dnaToProt.length; sz++)\r
{\r
- sqs[sz] = dnaToProt[sz].to;\r
+ sqs[sz] = dnaToProt[sz].to;\r
}\r
return sqs;\r
}\r
+\r
public MapList[] getdnaToProt()\r
{\r
- if (dnaToProt==null)\r
+ if (dnaToProt == null)\r
return null;\r
MapList[] sqs = new MapList[dnaToProt.length];\r
- for (int sz=0; sz<dnaToProt.length; sz++)\r
+ for (int sz = 0; sz < dnaToProt.length; sz++)\r
{\r
- sqs[sz] = dnaToProt[sz].map;\r
+ sqs[sz] = dnaToProt[sz].map;\r
}\r
return sqs;\r
}\r
+\r
public Mapping[] getProtMappings()\r
{\r
return dnaToProt;\r
}\r
+\r
/**\r
* \r
* @param sequenceRef\r
*/\r
public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)\r
{\r
- if (dnaSeqs==null)\r
+ if (dnaSeqs == null)\r
{\r
return null;\r
}\r
SequenceI dnads = dnaSeqRef.getDatasetSequence();\r
- for (int ds=0;ds<dnaSeqs.length; ds++)\r
+ for (int ds = 0; ds < dnaSeqs.length; ds++)\r
{\r
- if (dnaSeqs[ds]==dnaSeqRef || dnaSeqs[ds]==dnads)\r
+ if (dnaSeqs[ds] == dnaSeqRef || dnaSeqs[ds] == dnads)\r
return dnaToProt[ds].to;\r
}\r
return null;\r
}\r
+\r
/**\r
* \r
* @param sequenceRef\r
*/\r
public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)\r
{\r
- if (dnaToProt==null)\r
+ if (dnaToProt == null)\r
{\r
return null;\r
}\r
SequenceI aads = aaSeqRef.getDatasetSequence();\r
- for (int as=0;as<dnaToProt.length; as++)\r
+ for (int as = 0; as < dnaToProt.length; as++)\r
{\r
- if (dnaToProt[as].to==aaSeqRef || dnaToProt[as].to==aads)\r
+ if (dnaToProt[as].to == aaSeqRef || dnaToProt[as].to == aads)\r
return dnaSeqs[as];\r
}\r
return null;\r
}\r
+\r
/**\r
* test to see if codon frame involves seq in any way\r
- * @param seq a nucleotide or protein sequence\r
- * @return true if a mapping exists to or from this sequence to any translated sequence\r
+ * \r
+ * @param seq\r
+ * a nucleotide or protein sequence\r
+ * @return true if a mapping exists to or from this sequence to any translated\r
+ * sequence\r
*/\r
public boolean involvesSequence(SequenceI seq)\r
{\r
- return getAaForDnaSeq(seq)!=null || getDnaForAaSeq(seq)!=null;\r
+ return getAaForDnaSeq(seq) != null || getDnaForAaSeq(seq) != null;\r
}\r
+\r
/**\r
- * Add search results for regions in other sequences that translate or are translated from a particular position in seq \r
+ * Add search results for regions in other sequences that translate or are\r
+ * translated from a particular position in seq\r
+ * \r
* @param seq\r
- * @param index position in seq\r
- * @param results where highlighted regions go\r
+ * @param index\r
+ * position in seq\r
+ * @param results\r
+ * where highlighted regions go\r
*/\r
- public void markMappedRegion(SequenceI seq, int index, SearchResults results)\r
+ public void markMappedRegion(SequenceI seq, int index,\r
+ SearchResults results)\r
{\r
- if (dnaToProt==null)\r
+ if (dnaToProt == null)\r
{\r
return;\r
}\r
int[] codon;\r
SequenceI ds = seq.getDatasetSequence();\r
- for (int mi = 0; mi<dnaToProt.length; mi++)\r
+ for (int mi = 0; mi < dnaToProt.length; mi++)\r
{\r
- if (dnaSeqs[mi]==seq || dnaSeqs[mi]==ds)\r
+ if (dnaSeqs[mi] == seq || dnaSeqs[mi] == ds)\r
{\r
// DEBUG System.err.println("dna pos "+index);\r
- codon = dnaToProt[mi].map.locateInTo(index,index);\r
- if (codon!=null)\r
+ codon = dnaToProt[mi].map.locateInTo(index, index);\r
+ if (codon != null)\r
{\r
- for (int i=0; i<codon.length; i+=2)\r
- {\r
- results.addResult(dnaToProt[mi].to, codon[i], codon[i+1]);\r
- }\r
+ for (int i = 0; i < codon.length; i += 2)\r
+ {\r
+ results.addResult(dnaToProt[mi].to, codon[i], codon[i + 1]);\r
+ }\r
}\r
- } else\r
- if (dnaToProt[mi].to==seq || dnaToProt[mi].to==ds)\r
+ }\r
+ else if (dnaToProt[mi].to == seq || dnaToProt[mi].to == ds)\r
+ {\r
+ // DEBUG System.err.println("aa pos "+index);\r
{\r
- // DEBUG System.err.println("aa pos "+index);\r
+ codon = dnaToProt[mi].map.locateInFrom(index, index);\r
+ if (codon != null)\r
{\r
- codon = dnaToProt[mi].map.locateInFrom(index, index);\r
- if (codon!=null)\r
+ for (int i = 0; i < codon.length; i += 2)\r
{\r
- for (int i=0; i<codon.length; i+=2)\r
- {\r
- results.addResult(dnaSeqs[mi], codon[i], codon[i+1]);\r
- }\r
+ results.addResult(dnaSeqs[mi], codon[i], codon[i + 1]);\r
+ }\r
}\r
}\r
- }\r
+ }\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff