<classpathentry kind="lib" path="lib/VARNAv3-91.jar"/>
<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
+ <classpathentry kind="lib" path="lib/jersey-client-1.19.jar"/>
+ <classpathentry kind="lib" path="lib/jersey-core-1.19.jar"/>
+ <classpathentry kind="lib" path="lib/jersey-json-1.19.jar"/>
+ <classpathentry kind="lib" path="lib/jsr311-api-1.1.1.jar"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
secondary structure annotation</td>
</tr>
</table>
+ <p>
+ <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
+ , "file":"estrogenReceptorCdna.fa"
+ , "file2":"estrogenReceptorProtein.fa"
+ , "defaultColour":"Purine/Pyrimidine"
+ , "showAnnotation":"false"
+ , "windowHeight":"300"
+ , "windowWidth":"800"
+ , "showFullId":"false"} prots=true /></td>
+ <td valign="center">Displays a split window view of protein and its related cDNA</td>
+ </tr>
+ </table>
</div>
secondary structure annotation</td>
</tr>
</table>
+ <p>
+ <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="estrogenReceptorCdna.fa"/>
+<param name="file2" value="estrogenReceptorProtein.fa"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="300"/>
+<param name="windowWidth" value="800"/>
+<param name="showAnnotation" value="false"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Displays a split window view of protein and its related cDNA</td>
+ </tr>
+ </table>
</div>
<!-- content template end -->
--- /dev/null
+>EMBLCDS|ADZ17331/1-1593 Homo sapiens (human) estrogen nuclear receptor beta variant a
+atggatataaaaaactcaccatctagccttaattctccttcctcctacaactgcagtcaatccatcttaccc
+ctggagcacggctccatatacataccttcctcctatgtagacagccaccatgaatatccagccatgacattc
+tatagccctgctgtgatgaattacagcattcccagcaatgtcactaacttggaaggtgggcctggtcggcag
+accacaagcccaaatgtgttgtggccaacacctgggcacctttctcctttagtggtccatcgccagttatca
+catctgtatgcggaacctcaaaagagtccctggtgtgaagcaagatcgctagaacacaccttacctgtaaac
+agagagacactgaaaaggaaggttagtgggaaccgttgcgccagccctgttactggtccaggttcaaagagg
+gatgctcacttctgcgctgtctgcagcgattacgcatcgggatatcactatggagtctggtcgtgtgaagga
+tgtaaggccttttttaaaagaagcattcaaggacataatgattatatttgtccagctacaaatcagtgtaca
+atcgataaaaaccggcgcaagagctgccaggcctgccgacttcggaagtgttacgaagtgggaatggtgaag
+tgtggctcccggagagagagatgtgggtaccgccttgtgcggagacagagaagtgccgacgagcagctgcac
+tgtgccggcaaggccaagagaagtggcggccacgcgccccgagtgcgggagctgctgctggacgccctgagc
+cccgagcagctagtgctcaccctcctggaggctgagccgccccatgtgctgatcagccgccccagtgcgccc
+ttcaccgaggcctccatgatgatgtccctgaccaagttggccgacaaggagttggtacacatgatcagctgg
+gccaagaagattcccggctttgtggagctcagcctgttcgaccaagtgcggctcttggagagctgttggatg
+gaggtgttaatgatggggctgatgtggcgctcaattgaccaccccggcaagctcatctttgctccagatctt
+gttctggacagggatgaggggaaatgcgtagaaggaattctggaaatctttgacatgctcctggcaactact
+tcaaggtttcgagagttaaaactccaacacaaagaatatctctgtgtcaaggccatgatcctgctcaattcc
+agtatgtaccctctggtcacagcgacccaggatgctgacagcagccggaagctggctcacttgctgaacgcc
+gtgaccgatgctttggtttgggtgattgccaagagcggcatctcctcccagcagcaatccatgcgcctggct
+aacctcctgatgctcctgtcccacgtcaggcatgcgagtaacaagggcatggaacatctgctcaacatgaag
+tgcaaaaatgtggtcccagtgtatgacctgctgctggagatgctgaatgcccacgtgcttcgcgggtgcaag
+tcctccatcacggggtccgagtgcagcccggcagaggacagtaaaagcaaagagggctcccagaacccacag
+tctcagtga
+>EMBLCDS|AAK93056/1-1455 Drosophila melanogaster (fruit fly) GH28308p
+atgtccgacggcgtcagcatcttgcacatcaaacaggaggtggacactccatcggcgtcctgctttagtccc
+agctccaagtcaacggccacgcagagtggcacaaacggcctgaaatcctcgccctcggtttcgccggaaagg
+cagctctgcagctcgacgacctctctatcctgcgatttgcacaatgtatccttaagcaatgatggcgatagt
+ctgaaaggaagtggtacaagtggcggcaatggcggaggaggaggtggtggtacgagtggtggaaatgcgacc
+aatgcgagtgccggagctggatcgggatccgtcagggacgagctccgccgattgtgtttggtttgtggcgat
+gtggccagtggattccactatggtgtggcgagttgtgaggcttgcaaagcgttctttaaacgcaccatccaa
+ggcaacatcgagtacacgtgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgccaa
+gcgtgtcgcttccagaaatgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgtgga
+ggacggcagaagtaccgaaggaatcctgtatcaaactcttaccagactatgcagctgctataccaatccaac
+accacctcgctgtgcgatgtcaagatactggaggtgctcaattcatatgagccggatgccttgagcgtccaa
+acgccgccgccgcaagtccacacgactagcataactaatgatgaggcctcatcctcctcgggcagcataaaa
+ctggagtccagcgttgttacgcccaatgggacttgcattttccaaaacaacaacaacaatgatcccaatgag
+atactaagcgtccttagtgatatttacgacaaggaattggtcagcgtcattggctgggccaagcagatacct
+ggctttatagatctgccacttaacgaccagatgaagcttctccaggtgtcgtgggcagagatcctgacgctc
+cagctgaccttccggtccctaccgttcaatggcaagttatgcttcgccacggatgtctggatggatgaacat
+ttggccaaggagtgcggttacacggagttctactaccactgcgtccagatcgcacagcgcatggaaagaata
+tcgccacgaagggaggagtactacttgctaaaggcgctcctgctggccaactgcgacattctgctggatgat
+cagagttccctgcgcgcatttcgtgatacgattcttaattctctaaacgatgtggtctacttgctgcgtcat
+tcgtcggccgtgtcgcatcagcaacaattgctgcttttgctgccttcgctgcggcaggcggatgatatcctg
+cgaagattttggcgtggaattgcacgcgatgaagtcattaccatgaagaaactgttcctcgagatgctcgag
+ccgctggccaggtga
+>EMBLCDS|BAA89539/1-2133 Anguilla japonica (Japanese eel) progesterone receptor
+atggacaacaatcaccaagacaagatggaaagtctatacacgccagccagagcatcaccaactcctgatgca
+gaatcgattaaaagagccaggaatttgattaaaacatactcggagtcttttgggagttatgtggaggagata
+gttcgagacgactcgaataacatacaatctttgagcagcgtccctctcttgatgcgtaattttggaaacatg
+gacaccctaacctgcgcacctggctcgggtagtgacagtgagatttggaaagactttgttgttcccgggaac
+tctgtggtaagcaaagacacctgtggtcatgttgaaatatccactaaagccgaaaatttgtcttgggctgcc
+gcgcccttaagtagagaagaaaccctcgcgaaaggaactgttacggtcccagcgactgtgcctaaagaaagt
+tttaccgcaacatcaaacacttcttcagccagtggaatctctattaaagatgaacaacaatctttgctcaaa
+atggaaccacagtcttctgacttttgtccttatacagcaaatataccgaaattgaatccatcttatctgacc
+aatactgcgagtacgaaacaacttggatatggcgaacagccggacacttcagcgcactcctctccacctgct
+cagaagattgttttagatactgctcgatactcggccgatttatgttcggataaccctttaccgcaagcgaca
+aatatcaaaacagatccttgtagtagtttctcttctttcgttggagaagggatccttactagggcatctatg
+ggctactcacagcaagcgattcagacattgccggtgcacaagagtgaaccgttcaggttgtctgcttcgagc
+gcgcccgcggattctccgttttggtgccaatccacgggtccttctgaggatcatcatctgcagattgactat
+ctatctcccgctggactccacagcacatgcaaatacagttccacgaacgcgtacagctcctatttaggtgtg
+ctgccccagagggtgtgcgtcatctgtggggatgaagcatcaggctgtcactatggtgtcctcacctgtggc
+agctgtaaggtgttctttaagagggcagtggaaggccatcataactacttgtgtgctggacggaatgactgc
+atcgtggacaagatccgtaggaaaaactgtcctgcttgtcgcctcagaaagtgctaccaggcgggaatgata
+ctgggaggtcggaagctgaagaagttgggggctctgaaggcagcagggctgacccaggccctggtggcccac
+tcactgactcctcggaggctctctggtgacagccaggccctgatgcccctgggctgccttccaggggtccgg
+gagctgcacctttccccacagatcatcagcgtgctggagagcattgagcctgaggtggtgtactctggttat
+gacaactcccagcctgacatgcccaatatgctgctcaacagcctcaaccgcttatgtgagaggcagctgctg
+aggattgtcaagtggtccaagtctttaccaggttttcgcagtttacacatcaatgaccaaatggctctgatc
+cagtactcctggatgagcttaatggtattttctttgggttggcggtctttccaaaatgtcaccagtgattac
+ctgtactttgcacctgacctcattctcaacgaagagtatatgaggaggtctccaatatttgacctgtgcatg
+gccatgcagttcatccctcaagagtttgccaatctccaggtgaccaaggaggagtttctgtgcatgaaggtc
+ttgctgttgctcaacacagtgcctctggaggggttgaagagccagccacagtttgatgagatgaggcagaat
+tacatccatgaactcaccaaggccattcacctgcgagagaatggtgtggtcgcctgctcccagcgtttctac
+cacctgaccaagctgatggaccacatgcatgacattgtgaagaagctccacctgtactgcctgagcactttc
+attcaggcagatgccatgcgggtagagttccccgagatgatgtcagaagtcatcgcctcccagctgcctcgg
+gtgctcgctggaatggtgaaaccccttctttttcacaccaaatga
+>EMBLCDS|AHW56473/1-1590 Homo sapiens (human) partial estrogen receptor 2 isoform A
+atggatataaaaaactcaccatctagccttaattctccttcctcctacaactgcagtcaatccatcttaccc
+ctggagcacggctccatatacataccttcctcctatgtagacagccaccatgaatatccagccatgacattc
+tatagccctgctgtgatgaattacagcattcccagcaatgtcactaacttggaaggtgggcctggtcggcag
+accacaagcccaaatgtgttgtggccaacacctgggcacctttctcctttagtggtccatcgccagttatca
+catctgtatgcggaacctcaaaagagtccctggtgtgaagcaagatcgctagaacacaccttacctgtaaac
+agagagacactgaaaaggaaggttagtgggaaccgttgcgccagccctgttactggtccaggttcaaagagg
+gatgctcacttctgcgctgtctgcagcgattacgcatcgggatatcactatggagtctggtcgtgtgaagga
+tgtaaggccttttttaaaagaagcattcaaggacataatgattatatttgtccagctacaaatcagtgtaca
+atcgataaaaaccggcgcaagagctgccaggcctgccgacttcggaagtgttacgaagtgggaatggtgaag
+tgtggctcccggagagagagatgtgggtaccgccttgtgcggagacagagaagtgccgacgagcagctgcac
+tgtgccggcaaggccaagagaagtggcggccacgcgccccgagtgcgggagctgctgctggacgccctgagc
+cccgagcagctagtgctcaccctcctggaggctgagccgccccatgtgctgatcagccgccccagtgcgccc
+ttcaccgaggcctccatgatgatgtccctgaccaagttggccgacaaggagttggtacacatgatcagctgg
+gccaagaagattcccggctttgtggagctcagcctgttcgaccaagtgcggctcttggagagctgttggatg
+gaggtgttaatgatggggctgatgtggcgctcaattgaccaccccggcaagctcatctttgctccagatctt
+gttctggacagggatgaggggaaatgcgtagaaggaattctggaaatctttgacatgctcctggcaactact
+tcaaggtttcgagagttaaaactccaacacaaagaatatctctgtgtcaaggccatgatcctgctcaattcc
+agtatgtaccctctggtcacagcgacccaggatgctgacagcagccggaagctggctcacttgctgaacgcc
+gtgaccgatgctttggtttgggtgattgccaagagcggcatctcctcccagcagcaatccatgcgcctggct
+aacctcctgatgctcctgtcccacgtcaggcatgcgagtaacaagggcatggaacatctgctcaacatgaag
+tgcaaaaatgtggtcccagtgtatgacctgctgctggagatgctgaatgcccacgtgcttcgcgggtgcaag
+tcctccatcacggggtccgagtgcagcccggcagaggacagtaaaagcaaagagggctcccagaacccacag
+tctcag
+>EMBLCDS|BAA75464/1-2547 Anguilla japonica (Japanese eel) androgen receptor alpha
+atggagattccagttgggttaggaggagtttcagatgccacaaacgccgtttttcgcggaccttaccaaaac
+gttttccacagccttcaagtggcatttcagagtcacggtgccgtctccaggagcttagattttccaaataca
+aagtacggttttttacaaaacagacatttctgtgaaatgcgtcaggagaacaagcagccgccatgcaaagga
+ctcggcctattttacgggaaccatcgtaattcggacactgggacaaacgaagacgacatcgcttgtttttcc
+agacagtccgacgctgaagccagacctggtattttttctgaaagctcattggatactggagacgagattact
+tgcaaactccagtcagacaaccaaggggtaagagcgagcggtcctctcctaccgggctctagcggctgcaat
+tcgggacaaaagtcctcccttgcttgtacgtcccaacaaagggagacaacatctcaaagtgacacctgcgca
+ggagagagctgctcggaacatcaagcaactaccatttcggaaactgcgcgcgaattgtgcaacgccgtttcc
+gtgtcgctgggcttgaatttagatcttaatgatatgaatgacctaagttcaaaccaaatatcgtctaccgaa
+agtgacacaagtcaagccatctacttatttgaatcttcacctgggtatactggggtcggactgaacgccttg
+gtaagagactgtaaatgtcagagtgcacgcgaagggacatcgacacaacagtacgaccgcggggcaatgttt
+aagataaaccgtgtaaatgacttgccgcttcagccagcacccccgcgacacaccagcattagcgatgctaaa
+tgggacatggaagcaggtttgtgtgcgcagatggagcacaaagactctgaaaagtgcgcgaatatggatggt
+gcacactccacttctgtcttctcccagttcgaccaactgttgccagtaaacgcgtcgcactacagtcagaac
+gtttcggtcagagtggaaccacaaagtgatttctctccgattttgtacaaatcacctggtattcagaaaaat
+gccgaaaagtacaatgtccaatatgatgccacaattaaatcagaagatgggaaaacgacatctgaacgggaa
+tggggttttcagtacaggtacaatgaaagctgcagcacaccgtcagcacctcctagacattgtgcacatcag
+aacagggccggaccgtacaaccagttcttttttaatccatttgaatatgcgaaaagaggtgttgtctcaagg
+gaaggatattctctcgaacatgggttcccaaacaatctcgctcggacaccctactctggttccttgaaaaac
+gaactaggagatcgtctgagtgggccataccctgacgtcagttacaggtacgagggcgagcgggagaacgtg
+ttccccgtggagttcttctttccgccgcagaggacctgcctgatctgcggggacgaggcctcgggctgtcac
+tatggagccctcacctgcggcagctgcaaggtgttcttcaagagggccgcggaagggaaacagaagtacctg
+tgcgccagcatcaatgattgcaccattgataaacttcgaaggaagaactgcccctcttgccgtctcaaaagg
+tgctttgctgccggaatgacccttggagcgcggaagctgaagaagatcgggcaaatgagggcccccgaggat
+ggccaggggcagggcccggcggaagcggagctgagcgtctcccccaagtacgacctgggcttccacacccag
+tccatgttcctcaacatcctggaggccatcgagccggaggtggtgaacgccgggcacgactatggccagccg
+gactctgcggccagcctgctgaccagcctcaacgagctcggagaacggcaactcgtcaaggtcgtcaagtgg
+gccaagggcatgccaggttttcggagtctgtacgtggatgaccagatgacagtcatccagcactcctggatg
+gcagtgatggtgttcgctctgggctggaggtcatttaagaatgtgaagtccaggatgctttactttgctcct
+gaccttgttttcaacgagcaccgaatgcaggtgtccaccatgtatgaacactgcatccggatgaagaacttc
+tcccaggagtttgctatgctgcaggtctcccaggaagagttcctgtgcatgaaagctctgcttctcttcagc
+accatccccgttgaagggctgaaggggcagaatttctttgacgagctgcggaggagctacattaacgagctg
+gaccggctggttagcttcaggagcaagtccagctgttccgagaggttccagcagctcacccgcctcctggac
+tccctccaacctgttctgaagaagctccaccagtttacgttcgaccttttcgtccagtcccagaacctctcc
+aaccaagtttgctttcccgagatgatctcagagatcatatccgtgcacgtgccaaagattctcgctggcacg
+gtgaagccaatcctcttccacaagtag
+>EMBLCDS|AAK20930/1-1317 Petromyzon marinus (sea lamprey) partial corticoid receptor
+ggggtggagtttcagttgccctactcggcatctgccacatcctttcgtccgtccgttgccacctcgtccgcc
+tcgggcatctccaacttttcaaatgggaataattttggattcctttctcccaatggagtacaacaggatgga
+tttccttaccctggtttcacgagtcccgcacagtcctcagtccctccgcagaaggcgtgtctcatctgtagt
+gatgaggcttcgggctgccactacggagtgctcacctgtggaagctgcaaggtgttcttcaagcgtgccgtg
+gaaggacagcacaattatctgtgcgccggacgaaacgactgcatcattgacaagatccgccgcaagaactgc
+ccagcttgccgtctgcgcaagtgcatccaggctggaatgacgctaggagcacgcaagcttaagaagcaaggc
+cgggtaaagggagagaaccagcgcagcccagcgtcctccacagccaccacctcgtctgccaccccgcaaccc
+tccagcaactcgacggccgtgaccacgttctcgccaccgccgaccggagagcccattttctcacccacactc
+atcgccatcctgcaggcgatcgagcccgaggtggtcatgtccggctatgacaacacgcggtcccagaccacc
+gcctacatgctgtcgagcctcaaccgcctctgcgacaagcagctcgtgtccattgtcaagtgggccaagtct
+ctgccaggtttccgaaacctgcacatcgacgaccagatggtgttaatccagtactcatggatgggcctgatg
+tcatttgccatgagctggaggtccttccagcacaccaacagcaagctgctctactttgctcctgatctggtt
+tttgatgagacgcgcatgcagcartcggcgatgtatcaattgtgcgtggaaatgaggcaagtctcggaggac
+ttcatgaagttgcaagtcacttcagaggagtttctgtgcatgaaagccatcttgctcctgagtactgtccca
+caagagggtctgaagagccagggctgcttcgaggagatgcggatcagctacatccgggaattgaaccggacc
+atcgcgcggacggagaagaatgccgtgcagtgttggcagcgcttctaccagctcaccaagctgctggrctgc
+atgcaggatctcgtgagcaagctcctggagttctgcttcgcaaccttcacgcagacgcaggtgtggagtgtg
+gagtttcctgacatgatggccgagatcatcagtgcgcagcttgcctcgcatcatggccgagaagcccgggca
+ctccacttccacaagaaatga
+>EMBLCDS|AAA17402/1-1032 Serinus canaria (common canary) partial androgen receptor
+gaagcctccgggtgccactacggagccctgacgtgtgggagctgcaaagtgttcttcaaacgggcagctgaa
+ggtaaacagaagtacctctgtgccagccgcaacgactgcaccatcgacaagttccggcggaaaaactgcccc
+tcctgccgcctgcgcaagtgctacgaggccgggatgacgcttggagcccgcaagctgaagaaactgggtaac
+ctgaaggcacaggacgacatagagggagccagctcgtccagcccaacggaggagcaagctcccaagctggtg
+atgacacgcattgatggctacgagtgccagcccatcttcctcaacgtcctggaggccatcgagcctggggtg
+gtgtgtgctggccatgacaacagccagcctgactccttctccaacctgctgaccagcctgaatgagcttggg
+gagaggcagctggtctacgtggtcaaatgggcaaaggctctgccaggatttcgcaacctgcatgtggatgac
+cagatgtcaataatccagtactcttggatgggcctgatggtgtttgctatggggtggagatccttcaccaac
+gtcaattccaggatgctttactttgctccagacctggtcttcaatgagtaccgcatgcacaaatccaggatg
+tacagccagtgcatcaggatgcggcacctctcccaggaattcgggtggcttcagatcacaccccaggggttc
+ctctgtatgaaggctctcctcttcttcagtattattccagtggatggcctgaagaaccagaagctcttcgat
+gagctccgcatgaattacatcaaggaacttgaccgtatcattgcctgcaagaggaagaaccccacctcatgc
+tcccggaggttttaccagctcaccaaggtcctggactccgtgactccgattgccaaggacctgcatcagttt
+acatttgatctcctaatcaaggcacacatggtgagcgtggactacccagaaatgatggctgagatcatctct
+gtgcaggttcccaagatcctgtct
+>EMBLCDS|AAL37553/1-1455 Drosophila melanogaster (fruit fly) estrogen-related receptor
+atgtccgacggcgtcagcatcttgcacatcaaacaggaggtggacactccatcggcgtcctgctttagtccc
+agctccaagtcaacggccacgcagagtggcacaaacggcctgaaatcctcgccctcggtttcgccggaaagg
+cagctctgcagctcgacgacctctctatcctgcgatttgcacaatgtatccttaagcaatgatggcgatagt
+ctgaaaggaagtggtacaagtggcggcaatggcggaggaggaggtggtggtacgagtggtggaaatgcgacc
+aatgcgagtgccggagctggatcgggatccgtcagggacgagctccgccgattgtgtttggtttgtggcgat
+gtggccagtggattccactatggtgtggcgagttgtgaggcttgcaaagcgttctttaaacgcaccatccaa
+ggcaacatcgagtacacgtgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgccaa
+gcgtgtcgcttccagaaatgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgtgga
+ggacggcagaagtaccgaaggaatcctgtatcaaactcttaccagactatgcagctgctataccaatccaac
+accacctcgctgtgcgatgtcaagatactggaggtgctcaattcatatgagccggatgccttgagcgtccaa
+acgccgccgccgcaagtccacacgactagcataactaatgatgaggcctcatcctcctcgggcagcataaaa
+ctggagtccagcgttgttacgcccaatgggacttgcattttccaaaacaacaacaacaatgatcccaatgag
+atactaagcgtccttagtgatatttacgacaaggaattggtcagcgtcattggctgggccaagcagatacct
+ggctttatagatctgccacttaacgaccagatgaagcttctccaggtgtcgtgggcagagatcctgacgctc
+cagctgaccttccggtccctaccgttcaatggcaagttatgcttcgccacggatgtctggatggatgaacat
+ttggccaaggagtgcggttacacggagttctactaccactgcgtccagatcgcacagcgcatggaaagaata
+tcgccacgaagggaggagtactacttgctaaaggcgctcctgctggccaactgcgacattctgctggatgat
+cagagttccctgcgcgcatttcgtgatacgattcttaattctctaaacgatgtggtctacttgctgcgtcat
+tcgtcggccgtgtcgcatcagcaacaattgctgcttttgctgccttcgctgcggcaggcggatgatatcctg
+cgaagattttggcgtggaattgcacgcgatgaagtcattaccatgaagaaactgttcctcgagatgctcgag
+ccgctggccaggtga
+>EMBLCDS|AAK20929/1-1662 Petromyzon marinus (sea lamprey) partial estrogen receptor
+gcacgaggcttcagcgaggcacatggctacgagtactccggggcctcgctctaccagccactgcctccctcg
+tgcacagagttctcaattggagctcatcaacaacaacaacatcagcaccagcatcaccagcaccagcatcag
+cagcaccaccaccagcagcagcagcagcagccacagccgcagcagaatggagttttgggcgaggggcagagt
+tcccatctctcttatcttccgccctcgaccgagctgccccagtacgtgccctccagccccagcgcgccctac
+agcatggagctcggggcagggcgtcctcacggctacgacccagggccacagagcctctacaggggcggtgtg
+gagagcagcgcccccccgtacagcgagcagcagcaggtggtgggcggcggcggagccatgtcggccatgggc
+ttgacagagccacgccacgtcagctccggatcgctacccagcagcacgaggcccgagcgcagcacccagttc
+tgtgccgtgtgcagcgactatgcctcggggtaccactacggcgtgtggtcctgcgagggctgcaaagccttc
+ttcaagcgcagcacgcaaggccacaatgactacatgtgcccggccaccaaccagtgcaccatcgacaggaac
+cgtcgcaagagctgtcaggcttgccgcctgcgtaagtgctacgaagtgggcatggtcaaaggcgttcgcaag
+gaccgcaaaggctttcgaggggtcaagcacaaacgtaagcgccccatcccccaaaagaatgggggagaagga
+ggtgccggcggcggccaagacgtgagcgagacgaggcctcagggtgagaggccctccgggccgagggaccgg
+gagagcgccgtcagctcactcgaggctgaccaggtgatctcggctcttctggaggctgagccacccaccgta
+ctgtcctcgtatgaccccgacaagcctgtgacggaggcctcgctcatggctgctctcaccagcctggctgac
+cgagagctcgtgcacatgatcacctgggctaagaagattccaggattcacggccatcgggctgagtgaccag
+gtgcagctgctggagtgctgctggctggagatcctaatcgtggggctcatctggaggtctatcgatcgccct
+ggtcagctccactttgctccaaacctcatcctaggaagggaggacgcgcgcaatgtggagggcatgctggac
+atgttcgacatgctgctcgtcaccgtgagtcgcttccgtgagctgcatctccgccgggaggaatacgtctgc
+ctcaaggccatgatcctcctcaactcgggggtgtttttctgcctctccaattccgccggggagcagacgaat
+gtgcagctcatccagcagatcctcgagaaggtgatggacgccctgggcagcaccatcggccacattgaggcg
+tccccgccgcaacactcgcgtcgcctctcccagctgctcctgctgctttcacagatccggcacattagcaac
+aagggcatcgagcatctcaacagcatgaagcgtaagaatgtgatcccgctatacgacctgctccttgagctg
+ctggacgctcacagcctgcagaatactggcttacggacgtcgcccccaccgcaggatttcagggcaaccctc
+gtgccg
--- /dev/null
+>UNIPROT|Q7LCB3/1-530 estrogen nuclear receptor beta variant a
+MDIKNSPSSLNSPSSYNCSQSILPLEHGSIYIPSSYVDSHHEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQ
+TTSPNVLWPTPGHLSPLVVHRQLSHLYAEPQKSPWCEARSLEHTLPVNRETLKRKVSGNRCASPVTGPGSKR
+DAHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVK
+CGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLDALSPEQLVLTLLEAEPPHVLISRPSAP
+FTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL
+VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA
+VTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLRGCK
+SSITGSECSPAEDSKSKEGSQNPQSQ
+>UNIPROT|Q9VSE9/1-484 GH28308p
+MSDGVSILHIKQEVDTPSASCFSPSSKSTATQSGTNGLKSSPSVSPERQLCSSTTSLSCDLHNVSLSNDGDS
+LKGSGTSGGNGGGGGGGTSGGNATNASAGAGSGSVRDELRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ
+GNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSYQTMQLLYQSN
+TTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNE
+ILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQVSWAEILTLQLTFRSLPFNGKLCFATDVWMDEH
+LAKECGYTEFYYHCVQIAQRMERISPRREEYYLLKALLLANCDILLDDQSSLRAFRDTILNSLNDVVYLLRH
+SSAVSHQQQLLLLLPSLRQADDILRRFWRGIARDEVITMKKLFLEMLEPLAR
+>UNIPROT|Q9IBD5/1-710 progesterone receptor
+MDNNHQDKMESLYTPARASPTPDAESIKRARNLIKTYSESFGSYVEEIVRDDSNNIQSLSSVPLLMRNFGNM
+DTLTCAPGSGSDSEIWKDFVVPGNSVVSKDTCGHVEISTKAENLSWAAAPLSREETLAKGTVTVPATVPKES
+FTATSNTSSASGISIKDEQQSLLKMEPQSSDFCPYTANIPKLNPSYLTNTASTKQLGYGEQPDTSAHSSPPA
+QKIVLDTARYSADLCSDNPLPQATNIKTDPCSSFSSFVGEGILTRASMGYSQQAIQTLPVHKSEPFRLSASS
+APADSPFWCQSTGPSEDHHLQIDYLSPAGLHSTCKYSSTNAYSSYLGVLPQRVCVICGDEASGCHYGVLTCG
+SCKVFFKRAVEGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMILGGRKLKKLGALKAAGLTQALVAH
+SLTPRRLSGDSQALMPLGCLPGVRELHLSPQIISVLESIEPEVVYSGYDNSQPDMPNMLLNSLNRLCERQLL
+RIVKWSKSLPGFRSLHINDQMALIQYSWMSLMVFSLGWRSFQNVTSDYLYFAPDLILNEEYMRRSPIFDLCM
+AMQFIPQEFANLQVTKEEFLCMKVLLLLNTVPLEGLKSQPQFDEMRQNYIHELTKAIHLRENGVVACSQRFY
+HLTKLMDHMHDIVKKLHLYCLSTFIQADAMRVEFPEMMSEVIASQLPRVLAGMVKPLLFHTK
+>UNIPROT|Q7LCB3/1-530 estrogen receptor 2 isoform A
+MDIKNSPSSLNSPSSYNCSQSILPLEHGSIYIPSSYVDSHHEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQ
+TTSPNVLWPTPGHLSPLVVHRQLSHLYAEPQKSPWCEARSLEHTLPVNRETLKRKVSGNRCASPVTGPGSKR
+DAHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVK
+CGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLDALSPEQLVLTLLEAEPPHVLISRPSAP
+FTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL
+VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA
+VTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLRGCK
+SSITGSECSPAEDSKSKEGSQNPQSQ
+>UNIPROT|Q9YGV9/1-848 androgen receptor alpha
+MEIPVGLGGVSDATNAVFRGPYQNVFHSLQVAFQSHGAVSRSLDFPNTKYGFLQNRHFCEMRQENKQPPCKG
+LGLFYGNHRNSDTGTNEDDIACFSRQSDAEARPGIFSESSLDTGDEITCKLQSDNQGVRASGPLLPGSSGCN
+SGQKSSLACTSQQRETTSQSDTCAGESCSEHQATTISETARELCNAVSVSLGLNLDLNDMNDLSSNQISSTE
+SDTSQAIYLFESSPGYTGVGLNALVRDCKCQSAREGTSTQQYDRGAMFKINRVNDLPLQPAPPRHTSISDAK
+WDMEAGLCAQMEHKDSEKCANMDGAHSTSVFSQFDQLLPVNASHYSQNVSVRVEPQSDFSPILYKSPGIQKN
+AEKYNVQYDATIKSEDGKTTSEREWGFQYRYNESCSTPSAPPRHCAHQNRAGPYNQFFFNPFEYAKRGVVSR
+EGYSLEHGFPNNLARTPYSGSLKNELGDRLSGPYPDVSYRYEGERENVFPVEFFFPPQRTCLICGDEASGCH
+YGALTCGSCKVFFKRAAEGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMTLGARKLKKIGQMRAPED
+GQGQGPAEAELSVSPKYDLGFHTQSMFLNILEAIEPEVVNAGHDYGQPDSAASLLTSLNELGERQLVKVVKW
+AKGMPGFRSLYVDDQMTVIQHSWMAVMVFALGWRSFKNVKSRMLYFAPDLVFNEHRMQVSTMYEHCIRMKNF
+SQEFAMLQVSQEEFLCMKALLLFSTIPVEGLKGQNFFDELRRSYINELDRLVSFRSKSSCSERFQQLTRLLD
+SLQPVLKKLHQFTFDLFVQSQNLSNQVCFPEMISEIISVHVPKILAGTVKPILFHK
+>UNIPROT|Q90ZM7/1-438 corticoid receptor
+GVEFQLPYSASATSFRPSVATSSASGISNFSNGNNFGFLSPNGVQQDGFPYPGFTSPAQSSVPPQKACLICS
+DEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMTLGARKLKKQG
+RVKGENQRSPASSTATTSSATPQPSSNSTAVTTFSPPPTGEPIFSPTLIAILQAIEPEVVMSGYDNTRSQTT
+AYMLSSLNRLCDKQLVSIVKWAKSLPGFRNLHIDDQMVLIQYSWMGLMSFAMSWRSFQHTNSKLLYFAPDLV
+FDETRMQQSAMYQLCVEMRQVSEDFMKLQVTSEEFLCMKAILLLSTVPQEGLKSQGCFEEMRISYIRELNRT
+IARTEKNAVQCWQRFYQLTKLLXCMQDLVSKLLEFCFATFTQTQVWSVEFPDMMAEIISAQLASHHGREARA
+LHFHKK
+>UNIPROT|Q91445/1-344 androgen receptor
+EASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGN
+LKAQDDIEGASSSSPTEEQAPKLVMTRIDGYECQPIFLNVLEAIEPGVVCAGHDNSQPDSFSNLLTSLNELG
+ERQLVYVVKWAKALPGFRNLHVDDQMSIIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRM
+YSQCIRMRHLSQEFGWLQITPQGFLCMKALLFFSIIPVDGLKNQKLFDELRMNYIKELDRIIACKRKNPTSC
+SRRFYQLTKVLDSVTPIAKDLHQFTFDLLIKAHMVSVDYPEMMAEIISVQVPKILS
+>UNIPROT|Q9VSE9/1-484 estrogen-related receptor
+MSDGVSILHIKQEVDTPSASCFSPSSKSTATQSGTNGLKSSPSVSPERQLCSSTTSLSCDLHNVSLSNDGDS
+LKGSGTSGGNGGGGGGGTSGGNATNASAGAGSGSVRDELRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ
+GNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSYQTMQLLYQSN
+TTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNE
+ILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQVSWAEILTLQLTFRSLPFNGKLCFATDVWMDEH
+LAKECGYTEFYYHCVQIAQRMERISPRREEYYLLKALLLANCDILLDDQSSLRAFRDTILNSLNDVVYLLRH
+SSAVSHQQQLLLLLPSLRQADDILRRFWRGIARDEVITMKKLFLEMLEPLAR
+>UNIPROT|Q90ZM8/1-554 estrogen receptor
+ARGFSEAHGYEYSGASLYQPLPPSCTEFSIGAHQQQQHQHQHHQHQHQQHHHQQQQQQPQPQQNGVLGEGQS
+SHLSYLPPSTELPQYVPSSPSAPYSMELGAGRPHGYDPGPQSLYRGGVESSAPPYSEQQQVVGGGGAMSAMG
+LTEPRHVSSGSLPSSTRPERSTQFCAVCSDYASGYHYGVWSCEGCKAFFKRSTQGHNDYMCPATNQCTIDRN
+RRKSCQACRLRKCYEVGMVKGVRKDRKGFRGVKHKRKRPIPQKNGGEGGAGGGQDVSETRPQGERPSGPRDR
+ESAVSSLEADQVISALLEAEPPTVLSSYDPDKPVTEASLMAALTSLADRELVHMITWAKKIPGFTAIGLSDQ
+VQLLECCWLEILIVGLIWRSIDRPGQLHFAPNLILGREDARNVEGMLDMFDMLLVTVSRFRELHLRREEYVC
+LKAMILLNSGVFFCLSNSAGEQTNVQLIQQILEKVMDALGSTIGHIEASPPQHSRRLSQLLLLLSQIRHISN
+KGIEHLNSMKRKNVIPLYDLLLELLDAHSLQNTGLRTSPPPQDFRATLVP
as tabs within a single alignment window. They can be viewed
simultanously by pressing <strong>X</strong> (or via <strong>"View→Expand"</strong>)
to expand each view into its own linked alignment window. Expanded views
-are gathered back into into a single tabbed alignment window by pressing
-<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>).
+are gathered back into a single tabbed alignment window by pressing
+<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>.
</p>
<p><strong>Hidden Sequence Representatives and Multiple
Views</strong></p>
label.above_identity_threshold = Above Identity Threshold
label.show_sequence_features = Show Sequence Features
label.nucleotide = Nucleotide
+label.protein = Protein
label.to_new_alignment = To New Alignment
label.to_this_alignment = Add To This Alignment
label.apply_colour_to_all_groups = Apply Colour To All Groups
label.about = About...
label.show_sequence_limits = Show Sequence Limits
label.feature_settings = Feature Settings...
-label.sequence_features = Sequence Features
label.all_columns = All Columns
label.all_sequences = All Sequences
label.selected_columns = Selected Columns
label.selected_sequences = Selected Sequences
+label.except_selected_sequences = All except selected sequences
label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)
label.selected_region = Selected Region
label.all_sequences_columns = All Sequences and Columns
+label.hide_insertions = Hide columns gapped for selection
+label.hide_selected_annotations = Hide selected annotations
+label.show_selected_annotations = Show selected annotations
label.group_consensus = Group Consensus
label.group_conservation = Group Conservation
label.show_consensus_histogram = Show Consensus Histogram
label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name
label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>
label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
+label.view_name_original = Original
label.enter_view_name = Enter View Name
label.enter_label = Enter label
label.enter_label_for_the_structure = Enter a label for the structure?
label.load_features_annotations = Load Features/Annotations ...
label.export_features = Export Features ...
label.export_annotations = Export Annotations ...
-label.jalview_copy = Copy (Jalview Only)
-label.jalview_cut = Cut (Jalview Only)
label.to_upper_case = To Upper Case
label.to_lower_case = To Lower Case
label.toggle_case = Toggle Case
label.share_selection_across_views = Share selection across views
label.scroll_highlighted_regions = Scroll to highlighted regions
label.gap_symbol = Gap Symbol
-label.alignment_colour = Alignment Colour
+label.prot_alignment_colour = Protein Alignment Colour
+label.nuc_alignment_colour = Nucleotide Alignment Colour
label.address = Address
label.port = Port
label.default_browser_unix = Default Browser (Unix)
label.clustalx_colours = Clustalx colours
label.above_identity_percentage = Above % Identity
label.create_sequence_details_report_annotation_for = Annotation for {0}
-label.sequece_details_for = Sequece Details for {0}
+label.sequence_details_for = Sequence Details for {0}
label.sequence_name = Sequence Name
label.sequence_description = Sequence Description
label.edit_sequence_name_description = Edit Sequence Name/Description
label.load_tree_for_sequence_set = Load a tree for this sequence set
label.export_image = Export Image
label.vamsas_store = VAMSAS store
-label.translate_cDNA = Translate cDNA
+label.translate_cDNA = Translate as cDNA
+label.linked_view_title = Linked cDNA and protein view
+label.align = Align
label.extract_scores = Extract Scores
label.get_cross_refs = Get Cross References
label.sort_alignment_new_tree = Sort Alignment With New Tree
label.add_sequences = Add Sequences
label.new_window = New Window
+label.split_window = Split Window
label.refresh_available_sources = Refresh Available Sources
label.use_registry = Use Registry
label.add_local_source = Add Local Source
label.settings_for_param = Settings for {0}
label.view_params = View {0}
label.select_all_views = Select all views
+label.all_views = All Views
label.align_sequences_to_existing_alignment = Align sequences to an existing alignment
label.realign_with_params = Realign with {0}
label.calcname_with_default_settings = {0} with Defaults
label.use_sequence_id_2 = \nto embed sequence id in URL
label.ws_parameters_for = Parameters for {0}
label.switch_server = Switch server
-label.open_jabaws_web_page = Opens the JABAWS server's homepage in web browser
label.choose_jabaws_server = Choose a server for running this service
label.services_at = Services at {0}
label.rest_client_submit = {0} using {1}
label.normalise_logo = Normalise Logo
label.no_colour_selection_in_scheme = Please, make a colour selection before to apply colour scheme
label.no_colour_selection_warn = Error saving colour scheme
+label.open_split_window? = Would you like to open as a split window, with cDNA and protein linked?
+label.open_split_window = Open split window
+label.no_mappings = No mappings found
+label.mapping_failed = No sequence mapping could be made between the alignments.<br>A mapping requires sequence names to match, and equivalent sequence lengths.
+action.no = No
+action.yes = Yes
+label.for = for
label.select_by_annotation = Select By Annotation
action.select_by_annotation = Select by Annotation...
label.threshold_filter = Threshold Filter
label.display_name = Display Label
label.description = Description
label.include_description= Include Description
+action.back = Back
+label.hide_insertions = Hide Insertions
+label.mark_as_representative = Mark as representative
+label.open_jabaws_web_page = Open JABAWS web page
+label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser
+label.pdb_sequence_getcher = PDB Sequence Fetcher
+label.result = result
+label.results = results
+label.structure_chooser = Structure Chooser
+label.select = Select :
+label.invert = Invert
+label.select_pdb_file = Select PDB File
+info.select_filter_option = Select Filter Option/Manual Entry
+info.associate_wit_sequence = Associate with Sequence
+label.search_result = Search Result
+label.found_structures_summary = Found Structures Summary
+label.configure_displayed_columns = Configure Displayed Columns
+label.start_jalview = Start Jalview
+label.biojs_html_export = BioJS
type="xs:boolean" use="optional" default="true" />
<xs:attribute name="showSequenceLogo"
type="xs:boolean" use="optional" default="false" />
- <xs:attribute name="normaliseSequenceLogo"
- type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="normaliseSequenceLogo"
+ type="xs:boolean" use="optional" default="false" />
<xs:attribute name="ignoreGapsinConsensus"
type="xs:boolean" use="optional" default="true" />
-
- <xs:attribute name="startRes" type="xs:int" />
+ <xs:attribute name="startRes" type="xs:int" />
<xs:attribute name="startSeq" type="xs:int" />
<xs:attribute name="fontName" type="xs:string" />
<xs:attribute name="fontSize" type="xs:int" />
</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="complementId" type="xs:string"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ The viewport id of this viewport's (cdna/protein) coding complement, if any
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="UserColours" minOccurs="0"
*/
package MCview;
-import java.io.*;
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.appletgui.AlignmentPanel;
+import jalview.appletgui.FeatureRenderer;
+import jalview.appletgui.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Event;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-import jalview.appletgui.*;
-import jalview.structure.*;
-import jalview.util.MessageManager;
+import java.awt.Panel;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.io.PrintStream;
+import java.util.List;
+import java.util.Vector;
public class AppletPDBCanvas extends Panel implements MouseListener,
MouseMotionListener, StructureListener
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ {
pdbentry.setFile("INLINE" + pdb.id);
+ }
} catch (Exception ex)
{
{
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + ((PDBChain) pdb.chains.elementAt(i)).sequence
+ + pdb.chains.elementAt(i).sequence
.getSequenceAsString());
mappingDetails.append("\nNo of residues = "
- + ((PDBChain) pdb.chains.elementAt(i)).residues.size()
+ + pdb.chains.elementAt(i).residues.size()
+ "\n\n");
// Now lets compare the sequences to get
// Align the sequence to the pdb
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
- ((PDBChain) pdb.chains.elementAt(i)).sequence,
- ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+ pdb.chains.elementAt(i).sequence,
+ pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
: AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
}
- mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
+ mainchain = pdb.chains.elementAt(maxchain);
mainchain.pdbstart = pdbstart;
mainchain.pdbend = pdbend;
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.chains.elementAt(ii).isVisible)
{
- Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector tmp = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < tmp.size(); i++)
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.chains.elementAt(ii).isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
}
}
- width[0] = (float) Math.abs(max[0] - min[0]);
- width[1] = (float) Math.abs(max[1] - min[1]);
- width[2] = (float) Math.abs(max[2] - min[2]);
+ width[0] = Math.abs(max[0] - min[0]);
+ width[1] = Math.abs(max[1] - min[1]);
+ width[2] = Math.abs(max[2] - min[2]);
maxwidth = width[0];
// Find centre coordinate
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.chains.elementAt(ii).isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
bsize += bonds.size();
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- chain = (PDBChain) pdb.chains.elementAt(ii);
+ chain = pdb.chains.elementAt(ii);
for (int i = 0; i < chain.bonds.size(); i++)
{
repaint();
if (foundchain != -1)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ PDBChain chain = pdb.chains.elementAt(foundchain);
if (chain == mainchain)
{
if (fatom.alignmentMapping != -1)
PDBChain chain = null;
if (foundchain != -1)
{
- chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ chain = pdb.chains.elementAt(foundchain);
if (chain == mainchain)
{
mouseOverStructure(fatom.resNumber, chain.id);
if ((evt.getModifiers() & Event.META_MASK) != 0)
{
- objmat.rotatez((float) ((mx - omx)));
+ objmat.rotatez(((mx - omx)));
}
else
{
- objmat.rotatex((float) ((omy - my)));
- objmat.rotatey((float) ((omx - mx)));
+ objmat.rotatex(((omy - my)));
+ objmat.rotatey(((omx - mx)));
}
// Alter the bonds
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.chains.elementAt(ii);
if (chain.isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.chains.elementAt(ii);
int truex;
Bond tmpBond = null;
if (chain.isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
if (fatom != null) // )&& chain.ds != null)
{
- chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ chain = pdb.chains.elementAt(foundchain);
}
}
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.chains.elementAt(ii);
chain.isVisible = b;
}
mainchain.isVisible = true;
public void mouseOverStructure(int pdbResNum, String chain)
{
if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
+ {
ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
+ }
lastMessage = pdbResNum + chain;
}
StringBuffer eval = new StringBuffer();
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ /**
+ * Highlight the specified atoms in the structure.
+ *
+ * @param atoms
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
if (!seqColoursReady)
{
return;
}
-
- if (highlightRes != null && highlightRes.contains((atomIndex - 1) + ""))
+ for (AtomSpec atom : atoms)
{
- return;
+ int atomIndex = atom.getAtomIndex();
+
+ if (highlightRes != null
+ && highlightRes.contains((atomIndex - 1) + ""))
+ {
+ continue;
+ }
+
+ highlightAtom(atomIndex);
}
+ redrawneeded = true;
+ repaint();
+ }
+
+ /**
+ * @param atomIndex
+ */
+ protected void highlightAtom(int atomIndex)
+ {
int index = -1;
Bond tmpBond;
for (index = 0; index < mainchain.bonds.size(); index++)
break;
}
}
-
- redrawneeded = true;
- repaint();
}
public Color getColour(int atomIndex, int pdbResNum, String chain,
*/
package MCview;
-import java.awt.*;
+import java.awt.Color;
public class Atom
{
chain = str.substring(21, 22);
resNumber = Integer.parseInt(str.substring(22, 26).trim());
- resNumIns = str.substring(22, 27);
+ resNumIns = str.substring(22, 27).trim();
insCode = str.substring(26, 27).charAt(0);
- this.x = (float) (new Float(str.substring(30, 38).trim()).floatValue());
- this.y = (float) (new Float(str.substring(38, 46).trim()).floatValue());
- this.z = (float) (new Float(str.substring(47, 55).trim()).floatValue());
+ this.x = (new Float(str.substring(30, 38).trim()).floatValue());
+ this.y = (new Float(str.substring(38, 46).trim()).floatValue());
+ this.z = (new Float(str.substring(47, 55).trim()).floatValue());
// optional entries - see JAL-730
String tm = str.substring(54, 60).trim();
if (tm.length() > 0)
{
- occupancy = (float) (new Float(tm)).floatValue();
+ occupancy = (new Float(tm)).floatValue();
}
else
{
tm = str.substring(60, 66).trim();
if (tm.length() > 0)
{
- tfactor = (float) (new Float(tm).floatValue());
+ tfactor = (new Float(tm).floatValue());
}
else
{
*/
package MCview;
-import java.io.*;
-import java.util.*;
-
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Event;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.structure.*;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.io.PrintStream;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
public class PDBCanvas extends JPanel implements MouseListener,
MouseMotionListener, StructureListener
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ {
pdbentry.setFile("INLINE" + pdb.id);
+ }
} catch (Exception ex)
{
{
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + ((PDBChain) pdb.chains.elementAt(i)).sequence
+ + pdb.chains.elementAt(i).sequence
.getSequenceAsString());
mappingDetails.append("\nNo of residues = "
- + ((PDBChain) pdb.chains.elementAt(i)).residues.size()
+ + pdb.chains.elementAt(i).residues.size()
+ "\n\n");
// Now lets compare the sequences to get
// the start and end points.
// Align the sequence to the pdb
AlignSeq as = new AlignSeq(sequence,
- ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
+ pdb.chains.elementAt(i).sequence, "pep");
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
}
- mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
+ mainchain = pdb.chains.elementAt(maxchain);
mainchain.pdbstart = pdbstart;
mainchain.pdbend = pdbend;
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.chains.elementAt(ii).isVisible)
{
- Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector tmp = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < tmp.size(); i++)
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.chains.elementAt(ii).isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
* System.out.println("zmax " + max[2] + " min " + min[2]);
*/
- width[0] = (float) Math.abs(max[0] - min[0]);
- width[1] = (float) Math.abs(max[1] - min[1]);
- width[2] = (float) Math.abs(max[2] - min[2]);
+ width[0] = Math.abs(max[0] - min[0]);
+ width[1] = Math.abs(max[1] - min[1]);
+ width[2] = Math.abs(max[2] - min[2]);
maxwidth = width[0];
// Find centre coordinate
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.chains.elementAt(ii).isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
bsize += bonds.size();
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- chain = (PDBChain) pdb.chains.elementAt(ii);
+ chain = pdb.chains.elementAt(ii);
for (int i = 0; i < chain.bonds.size(); i++)
{
repaint();
if (foundchain != -1)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ PDBChain chain = pdb.chains.elementAt(foundchain);
if (chain == mainchain)
{
if (fatom.alignmentMapping != -1)
PDBChain chain = null;
if (foundchain != -1)
{
- chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ chain = pdb.chains.elementAt(foundchain);
if (chain == mainchain)
{
mouseOverStructure(fatom.resNumber, chain.id);
if ((evt.getModifiers() & Event.META_MASK) != 0)
{
- objmat.rotatez((float) ((mx - omx)));
+ objmat.rotatez(((mx - omx)));
}
else
{
- objmat.rotatex((float) ((my - omy)));
- objmat.rotatey((float) ((omx - mx)));
+ objmat.rotatex(((my - omy)));
+ objmat.rotatey(((omx - mx)));
}
// Alter the bonds
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.chains.elementAt(ii);
if (chain.isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.chains.elementAt(ii);
int truex;
Bond tmpBond = null;
if (chain.isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector bonds = pdb.chains.elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
if (fatom != null) // )&& chain.ds != null)
{
- chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ chain = pdb.chains.elementAt(foundchain);
}
}
{
for (int ii = 0; ii < pdb.chains.size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.chains.elementAt(ii);
chain.isVisible = b;
}
mainchain.isVisible = true;
public void mouseOverStructure(int pdbResNum, String chain)
{
if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
+ {
ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
+ }
lastMessage = pdbResNum + chain;
}
StringBuffer eval = new StringBuffer();
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ /**
+ * Highlight the specified atoms in the structure.
+ *
+ * @param atoms
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
if (!seqColoursReady)
{
return;
}
- if (highlightRes != null && highlightRes.contains((atomIndex - 1) + ""))
+ for (AtomSpec atom : atoms)
{
- return;
+ int atomIndex = atom.getAtomIndex();
+ if (highlightRes != null
+ && highlightRes.contains((atomIndex - 1) + ""))
+ {
+ continue;
+ }
+
+ highlightAtom(atomIndex);
}
+ redrawneeded = true;
+ repaint();
+ }
+
+ /**
+ * Highlight the atom at the specified index.
+ *
+ * @param atomIndex
+ */
+ protected void highlightAtom(int atomIndex)
+ {
int index = -1;
Bond tmpBond;
for (index = 0; index < mainchain.bonds.size(); index++)
break;
}
}
-
- redrawneeded = true;
- repaint();
}
public Color getColour(int atomIndex, int pdbResNum, String chain,
List<String> reply = new ArrayList<String>();
BufferedReader response = null;
try {
- response = HttpClientUtils.doHttpUrlPost(restUrl,
- commands);
+ response = HttpClientUtils
+ .doHttpUrlPost(restUrl, commands, 100, 2000);
String line = "";
while ((line = response.readLine()) != null) {
reply.add(line);
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof ServiceHandle))
+ if (obj == null)
{
return false;
}
- ServiceHandle other = (ServiceHandle) obj;
- if (obj == null)
+ if (!(obj instanceof ServiceHandle))
{
return false;
}
+ ServiceHandle other = (ServiceHandle) obj;
if (this == obj)
{
return true;
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof ServiceHandles))
+ if (obj == null)
{
return false;
}
- ServiceHandles other = (ServiceHandles) obj;
- if (obj == null)
+ if (!(obj instanceof ServiceHandles))
{
return false;
}
+ ServiceHandles other = (ServiceHandles) obj;
if (this == obj)
{
return true;
*/
package jalview.analysis;
-import java.util.*;
-
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
import jalview.util.Format;
-import jalview.datamodel.*;
+import jalview.util.MappingUtils;
+import jalview.util.QuickSort;
+
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
/**
* Takes in a vector or array of sequences and column start and column end and
*/
public class AAFrequency
{
- // No need to store 1000s of strings which are not
- // visible to the user.
+ private static final int TO_UPPER_CASE = 'A' - 'a'; // -32
+
public static final String MAXCOUNT = "C";
public static final String MAXRESIDUE = "R";
public static final String PROFILE = "P";
+ public static final String ENCODED_CHARS = "E";
+
+ /*
+ * Quick look-up of String value of char 'A' to 'Z'
+ */
+ private static final String[] CHARS = new String['Z' - 'A' + 1];
+
+ static
+ {
+ for (char c = 'A'; c <= 'Z'; c++)
+ {
+ CHARS[c - 'A'] = String.valueOf(c);
+ }
+ }
+
public static final Hashtable[] calculate(List<SequenceI> list,
int start, int end)
{
}
public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result)
- {
- calculate(sequences, start, end, result, false);
- }
-
- public static final void calculate(SequenceI[] sequences, int start,
int end, Hashtable[] result, boolean profile)
{
Hashtable residueHash;
- int maxCount, nongap, i, j, v, jSize = sequences.length;
+ int maxCount, nongap, i, j, v;
+ int jSize = sequences.length;
String maxResidue;
char c = '-';
float percentage;
}
else if ('a' <= c && c <= 'z')
{
- c -= 32; // ('a' - 'A');
+ c += TO_UPPER_CASE;
}
nongap++;
}
else
{
- for (v = 'A'; v < 'Z'; v++)
+ for (v = 'A'; v <= 'Z'; v++)
{
- if (values[v] < 2 || values[v] < maxCount)
+ // TODO why ignore values[v] == 1?
+ if (values[v] < 1 /* 2 */|| values[v] < maxCount)
{
continue;
}
if (values[v] > maxCount)
{
- maxResidue = String.valueOf((char) v);
+ maxResidue = CHARS[v - 'A'];
}
else if (values[v] == maxCount)
{
- maxResidue += String.valueOf((char) v);
+ maxResidue += CHARS[v - 'A'];
}
maxCount = values[v];
}
}
if (profile)
{
+ // TODO use a 1-dimensional array with jSize, nongap in [0] and [1]
residueHash.put(PROFILE, new int[][]
{ values, new int[]
{ jSize, nongap } });
{
completeConsensus(consensus, hconsensus, iStart, width,
ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
- nseq); // new
- // char[]
- // { 'A', 'C', 'G', 'T', 'U' });
+ nseq);
}
+ /**
+ * Derive the consensus annotations to be added to the alignment for display.
+ * This does not recompute the raw data, but may be called on a change in
+ * display options, such as 'show logo', which may in turn result in a change
+ * in the derived values.
+ *
+ * @param consensus
+ * the annotation row to add annotations to
+ * @param hconsensus
+ * the source consensus data
+ * @param iStart
+ * start column
+ * @param width
+ * end column
+ * @param ignoreGapsInConsensusCalculation
+ * if true, use the consensus calculated ignoring gaps
+ * @param includeAllConsSymbols
+ * if true include all consensus symbols, else just show modal
+ * residue
+ * @param alphabet
+ * @param nseq
+ * number of sequences
+ */
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols, char[] alphabet, long nseq)
{
- float tval, value;
if (consensus == null || consensus.annotations == null
|| consensus.annotations.length < width)
{
// initialised properly
return;
}
- String fmtstr = "%3.1f";
- int precision = 0;
- while (nseq >= 10)
- {
- precision++;
- nseq /= 10;
- }
- final Format fmt;
- if (precision > 1)
- {
- // if (precision>2)
- {
- fmtstr = "%" + (2 + precision) + "." + (precision) + "f";
- }
- fmt = new Format(fmtstr);
- }
- else
- {
- fmt = null;
- }
+
+ final Format fmt = getPercentageFormat(nseq);
+
for (int i = iStart; i < width; i++)
{
Hashtable hci;
consensus.annotations[i] = null;
continue;
}
- value = 0;
- Float fv;
- if (ignoreGapsInConsensusCalculation)
- {
- fv = (Float) hci.get(AAFrequency.PID_NOGAPS);
- }
- else
- {
- fv = (Float) hci.get(AAFrequency.PID_GAPS);
- }
+ Float fv = (Float) hci
+ .get(ignoreGapsInConsensusCalculation ? PID_NOGAPS : PID_GAPS);
if (fv == null)
{
consensus.annotations[i] = null;
// data has changed below us .. give up and
continue;
}
- value = fv.floatValue();
+ float value = fv.floatValue();
String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString();
- String mouseOver = hci.get(AAFrequency.MAXRESIDUE) + " ";
+ StringBuilder mouseOver = new StringBuilder(64);
if (maxRes.length() > 1)
{
- mouseOver = "[" + maxRes + "] ";
+ mouseOver.append("[").append(maxRes).append("] ");
maxRes = "+";
}
+ else
+ {
+ mouseOver.append(hci.get(AAFrequency.MAXRESIDUE) + " ");
+ }
int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
+ int sequenceCount = profile[1][0];
+ int nonGappedCount = profile[1][1];
+ int normalisedBy = ignoreGapsInConsensusCalculation ? nonGappedCount
+ : sequenceCount;
if (profile != null && includeAllConsSymbols)
{
- mouseOver = "";
+ mouseOver.setLength(0);
if (alphabet != null)
{
for (int c = 0; c < alphabet.length; c++)
{
- tval = profile[0][alphabet[c]] * 100f
- / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
- mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + ((fmt != null) ? fmt.form(tval) : ((int) tval)) + "%";
+ float tval = profile[0][alphabet[c]] * 100f / normalisedBy;
+ mouseOver
+ .append(((c == 0) ? "" : "; "))
+ .append(alphabet[c])
+ .append(" ")
+ .append(((fmt != null) ? fmt.form(tval) : ((int) tval)))
+ .append("%");
}
}
else
{
- Object[] ca = new Object[profile[0].length];
+ // TODO do this sort once only in calculate()?
+ // char[][] ca = new char[profile[0].length][];
+ char[] ca = new char[profile[0].length];
float[] vl = new float[profile[0].length];
for (int c = 0; c < ca.length; c++)
{
- ca[c] = new char[]
- { (char) c };
+ ca[c] = (char) c;
+ // ca[c] = new char[]
+ // { (char) c };
vl[c] = profile[0][c];
}
- ;
- jalview.util.QuickSort.sort(vl, ca);
- for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ QuickSort.sort(vl, ca);
+ for (int p = 0, c = ca.length - 1; profile[0][ca[c]] > 0; c--)
{
- if (((char[]) ca[c])[0] != '-')
+ final char residue = ca[c];
+ if (residue != '-')
{
- tval = profile[0][((char[]) ca[c])[0]]
- * 100f
- / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
- mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " "
- + ((fmt != null) ? fmt.form(tval) : ((int) tval))
- + "%";
+ float tval = profile[0][residue] * 100f / normalisedBy;
+ mouseOver
+ .append((((p == 0) ? "" : "; ")))
+ .append(residue)
+ .append(" ")
+ .append(((fmt != null) ? fmt.form(tval)
+ : ((int) tval))).append("%");
p++;
-
}
}
-
}
}
else
{
- mouseOver += ((fmt != null) ? fmt.form(value) : ((int) value))
- + "%";
+ mouseOver.append(
+ (((fmt != null) ? fmt.form(value) : ((int) value))))
+ .append("%");
}
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+ consensus.annotations[i] = new Annotation(maxRes,
+ mouseOver.toString(), ' ',
value);
}
}
/**
- * get the sorted profile for the given position of the consensus
+ * Returns a Format designed to show all significant figures for profile
+ * percentages. For less than 100 sequences, returns null (the integer
+ * percentage value will be displayed). For 100-999 sequences, returns "%3.1f"
+ *
+ * @param nseq
+ * @return
+ */
+ protected static Format getPercentageFormat(long nseq)
+ {
+ int scale = 0;
+ while (nseq >= 10)
+ {
+ scale++;
+ nseq /= 10;
+ }
+ return scale <= 1 ? null : new Format("%3." + (scale - 1) + "f");
+ }
+
+ /**
+ * Returns the sorted profile for the given consensus data. The returned array
+ * contains
+ *
+ * <pre>
+ * [profileType, numberOfValues, nonGapCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * in descending order of percentage value
+ * </pre>
*
* @param hconsensus
+ * the data table from which to extract and sort values
+ * @param ignoreGaps
+ * if true, only non-gapped values are included in percentage
+ * calculations
* @return
*/
public static int[] extractProfile(Hashtable hconsensus,
- boolean ignoreGapsInConsensusCalculation)
+ boolean ignoreGaps)
{
int[] rtnval = new int[64];
int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
if (profile == null)
+ {
return null;
- Object[] ca = new Object[profile[0].length];
+ }
+ char[] ca = new char[profile[0].length];
float[] vl = new float[profile[0].length];
for (int c = 0; c < ca.length; c++)
{
- ca[c] = new char[]
- { (char) c };
+ ca[c] = (char) c;
vl[c] = profile[0][c];
}
- ;
- jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 2;
- rtnval[1] = 0;
- for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ QuickSort.sort(vl, ca);
+ int nextArrayPos = 2;
+ int totalPercentage = 0;
+ int distinctValuesCount = 0;
+ final int divisor = profile[1][ignoreGaps ? 1 : 0];
+ for (int c = ca.length - 1; profile[0][ca[c]] > 0; c--)
+ {
+ if (ca[c] != '-')
+ {
+ rtnval[nextArrayPos++] = ca[c];
+ final int percentage = (int) (profile[0][ca[c]] * 100f / divisor);
+ rtnval[nextArrayPos++] = percentage;
+ totalPercentage += percentage;
+ distinctValuesCount++;
+ }
+ }
+ rtnval[0] = distinctValuesCount;
+ rtnval[1] = totalPercentage;
+ int[] result = new int[rtnval.length + 1];
+ result[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
+ System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+
+ return result;
+ }
+
+ /**
+ * Extract a sorted extract of cDNA codon profile data. The returned array
+ * contains
+ *
+ * <pre>
+ * [profileType, numberOfValues, totalCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * in descending order of percentage value, where the character values encode codon triplets
+ * </pre>
+ *
+ * @param hashtable
+ * @return
+ */
+ public static int[] extractCdnaProfile(Hashtable hashtable, boolean ignoreGaps)
+ {
+ // this holds #seqs, #ungapped, and then codon count, indexed by encoded
+ // codon triplet
+ int[] codonCounts = (int[]) hashtable.get(PROFILE);
+ int[] sortedCounts = new int[codonCounts.length - 2];
+ System.arraycopy(codonCounts, 2, sortedCounts, 0,
+ codonCounts.length - 2);
+
+ int[] result = new int[3 + 2 * sortedCounts.length];
+ // first value is just the type of profile data
+ result[0] = AlignmentAnnotation.CDNA_PROFILE;
+
+ char[] codons = new char[sortedCounts.length];
+ for (int i = 0; i < codons.length; i++)
+ {
+ codons[i] = (char) i;
+ }
+ QuickSort.sort(sortedCounts, codons);
+ int totalPercentage = 0;
+ int distinctValuesCount = 0;
+ int j = 3;
+ int divisor = ignoreGaps ? codonCounts[1] : codonCounts[0];
+ for (int i = codons.length - 1; i >= 0; i--)
+ {
+ final int codonCount = sortedCounts[i];
+ if (codonCount == 0)
+ {
+ break; // nothing else of interest here
+ }
+ distinctValuesCount++;
+ result[j++] = codons[i];
+ final int percentage = codonCount * 100 / divisor;
+ result[j++] = percentage;
+ totalPercentage += percentage;
+ }
+ result[2] = totalPercentage;
+
+ /*
+ * Just return the non-zero values
+ */
+ // todo next value is redundant if we limit the array to non-zero counts
+ result[1] = distinctValuesCount;
+ return Arrays.copyOfRange(result, 0, j);
+ }
+
+ /**
+ * Compute a consensus for the cDNA coding for a protein alignment.
+ *
+ * @param alignment
+ * the protein alignment (which should hold mappings to cDNA
+ * sequences)
+ * @param hconsensus
+ * the consensus data stores to be populated (one per column)
+ */
+ public static void calculateCdna(AlignmentI alignment,
+ Hashtable[] hconsensus)
+ {
+ final char gapCharacter = alignment.getGapCharacter();
+ Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+ if (mappings == null || mappings.isEmpty())
+ {
+ return;
+ }
+
+ int cols = alignment.getWidth();
+ for (int col = 0; col < cols; col++)
+ {
+ // todo would prefer a Java bean for consensus data
+ Hashtable<String, int[]> columnHash = new Hashtable<String, int[]>();
+ // #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
+ int[] codonCounts = new int[66];
+ codonCounts[0] = alignment.getSequences().size();
+ int ungappedCount = 0;
+ for (SequenceI seq : alignment.getSequences())
+ {
+ if (seq.getCharAt(col) == gapCharacter)
+ {
+ continue;
+ }
+ char[] codon = MappingUtils.findCodonFor(seq, col, mappings);
+ int codonEncoded = CodingUtils.encodeCodon(codon);
+ if (codonEncoded >= 0)
+ {
+ codonCounts[codonEncoded + 2]++;
+ ungappedCount++;
+ }
+ }
+ codonCounts[1] = ungappedCount;
+ // todo: sort values here, save counts and codons?
+ columnHash.put(PROFILE, codonCounts);
+ hconsensus[col] = columnHash;
+ }
+ }
+
+ /**
+ * Derive displayable cDNA consensus annotation from computed consensus data.
+ *
+ * @param consensusAnnotation
+ * the annotation row to be populated for display
+ * @param consensusData
+ * the computed consensus data
+ * @param showProfileLogo
+ * if true show all symbols present at each position, else only the
+ * modal value
+ * @param nseqs
+ * the number of sequences in the alignment
+ */
+ public static void completeCdnaConsensus(
+ AlignmentAnnotation consensusAnnotation,
+ Hashtable[] consensusData, boolean showProfileLogo, int nseqs)
+ {
+ if (consensusAnnotation == null
+ || consensusAnnotation.annotations == null
+ || consensusAnnotation.annotations.length < consensusData.length)
+ {
+ // called with a bad alignment annotation row - wait for it to be
+ // initialised properly
+ return;
+ }
+
+ // ensure codon triplet scales with font size
+ consensusAnnotation.scaleColLabel = true;
+ for (int col = 0; col < consensusData.length; col++)
{
- if (((char[]) ca[c])[0] != '-')
+ Hashtable hci = consensusData[col];
+ if (hci == null)
{
- rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
- rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0]);
- rtnval[1] += rtnval[rtnval[0]++];
+ // gapped protein column?
+ continue;
}
+ // array holds #seqs, #ungapped, then codon counts indexed by codon
+ final int[] codonCounts = (int[]) hci.get(PROFILE);
+ int totalCount = 0;
+ StringBuilder mouseOver = new StringBuilder(32);
+
+ /*
+ * First pass - get total count and find the highest
+ */
+ final char[] codons = new char[codonCounts.length - 2];
+ for (int j = 2; j < codonCounts.length; j++)
+ {
+ final int codonCount = codonCounts[j];
+ codons[j - 2] = (char) (j - 2);
+ totalCount += codonCount;
+ }
+
+ /*
+ * Sort array of encoded codons by count ascending - so the modal value
+ * goes to the end; start by copying the count (dropping the first value)
+ */
+ int[] sortedCodonCounts = new int[codonCounts.length - 2];
+ System.arraycopy(codonCounts, 2, sortedCodonCounts, 0,
+ codonCounts.length - 2);
+ QuickSort.sort(sortedCodonCounts, codons);
+
+ int modalCodonEncoded = codons[codons.length - 1];
+ int modalCodonCount = sortedCodonCounts[codons.length - 1];
+ String modalCodon = String.valueOf(CodingUtils
+ .decodeCodon(modalCodonEncoded));
+ if (sortedCodonCounts.length > 1
+ && sortedCodonCounts[codons.length - 2] == modalCodonEncoded)
+ {
+ modalCodon = "+";
+ }
+ float pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100
+ / (float) totalCount;
+
+ /*
+ * todo ? Replace consensus hashtable with sorted arrays of codons and
+ * counts (non-zero only). Include total count in count array [0].
+ */
+
+ /*
+ * Scan sorted array backwards for most frequent values first.
+ */
+ for (int j = codons.length - 1; j >= 0; j--)
+ {
+ int codonCount = sortedCodonCounts[j];
+ if (codonCount == 0)
+ {
+ break;
+ }
+ int codonEncoded = codons[j];
+ final int pct = codonCount * 100 / totalCount;
+ String codon = String
+ .valueOf(CodingUtils.decodeCodon(codonEncoded));
+ Format fmt = getPercentageFormat(nseqs);
+ String formatted = fmt == null ? Integer.toString(pct) : fmt
+ .form(pct);
+ if (showProfileLogo || codonCount == modalCodonCount)
+ {
+ mouseOver.append(codon).append(": ").append(formatted)
+ .append("% ");
+ }
+ }
+
+ consensusAnnotation.annotations[col] = new Annotation(modalCodon,
+ mouseOver.toString(), ' ', pid);
}
- return rtnval;
}
}
}
/**
- * DOCUMENT ME!
+ * Returns the given sequence with all of the given gap characters removed.
*
- * @param gapChar
- * DOCUMENT ME!
+ * @param gapChars
+ * a string of characters to be treated as gaps
* @param seq
- * DOCUMENT ME!
+ * the input sequence
*
- * @return DOCUMENT ME!
+ * @return
*/
- public static String extractGaps(String gapChar, String seq)
+ public static String extractGaps(String gapChars, String seq)
{
- StringTokenizer str = new StringTokenizer(seq, gapChar);
- StringBuffer newString = new StringBuffer();
+ if (gapChars == null || seq == null)
+ {
+ return null;
+ }
+ StringTokenizer str = new StringTokenizer(seq, gapChars);
+ StringBuilder newString = new StringBuilder(seq.length());
while (str.hasMoreTokens())
{
*/
package jalview.analysis;
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.QuickSort;
+
+import java.util.ArrayList;
+import java.util.List;
/**
* Routines for manipulating the order of a multiple sequence alignment TODO:
seqs[i] = align.getSequenceAt(i);
}
- QuickSort.sort(scores, 0, scores.length - 1, seqs);
+ QuickSort.sort(scores, seqs);
setReverseOrder(align, seqs);
}
* @param tmp
* sequences as a vector
*/
- private static void setOrder(AlignmentI align, Vector tmp)
+ private static void setOrder(AlignmentI align, List<SequenceI> tmp)
{
setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
}
{
// MAINTAINS ORIGNAL SEQUENCE ORDER,
// ORDERS BY GROUP SIZE
- Vector groups = new Vector();
+ List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
if (groups.hashCode() != lastGroupHash)
{
{
for (int j = 0; j < groups.size(); j++)
{
- SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+ SequenceGroup sg2 = groups.get(j);
if (sg.getSize() > sg2.getSize())
{
- groups.insertElementAt(sg, j);
+ groups.add(j, sg);
break;
}
if (!groups.contains(sg))
{
- groups.addElement(sg);
+ groups.add(sg);
}
}
// NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
// /////////////////////////////////////////////
- Vector seqs = new Vector();
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
for (int i = 0; i < groups.size(); i++)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ SequenceGroup sg = groups.get(i);
SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
for (int j = 0; j < orderedseqs.length; j++)
{
- seqs.addElement(orderedseqs[j]);
+ seqs.add(orderedseqs[j]);
}
}
}
/**
- * Converts Vector to array. java 1.18 does not have Vector.toArray()
- *
- * @param tmp
- * Vector of SequenceI objects
- *
- * @return array of Sequence[]
- */
- private static SequenceI[] vectorToArray(Vector tmp)
- {
- SequenceI[] seqs = new SequenceI[tmp.size()];
-
- for (int i = 0; i < tmp.size(); i++)
- {
- seqs[i] = (SequenceI) tmp.elementAt(i);
- }
-
- return seqs;
- }
-
- /**
* Select sequences in order from tmp that is present in mask, and any
- * remaining seqeunces in mask not in tmp
+ * remaining sequences in mask not in tmp
*
* @param tmp
* thread safe collection of sequences
private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
List<SequenceI> mask)
{
+ // or?
+ // tmp2 = tmp.retainAll(mask);
+ // return tmp2.addAll(mask.removeAll(tmp2))
+
ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
int i, idx;
boolean[] tmask = new boolean[mask.size()];
public static void sortBy(AlignmentI align, AlignmentOrder order)
{
// Get an ordered vector of sequences which may also be present in align
- Vector tmp = order.getOrder();
+ List<SequenceI> tmp = order.getOrder();
if (lastOrder == order)
{
*
* @return DOCUMENT ME!
*/
- private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+ private static List<SequenceI> getOrderByTree(AlignmentI align,
+ NJTree tree)
{
int nSeq = align.getHeight();
- Vector tmp = new Vector();
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
*/
public static void sortByTree(AlignmentI align, NJTree tree)
{
- Vector tmp = getOrderByTree(align, tree);
+ List<SequenceI> tmp = getOrderByTree(align, tree);
// tmp should properly permute align with tree.
if (lastTree != tree)
*
* @param align
* DOCUMENT ME!
- * @param seqs
+ * @param tmp
* DOCUMENT ME!
*/
- private static void addStrays(AlignmentI align, Vector seqs)
+ private static void addStrays(AlignmentI align, List<SequenceI> tmp)
{
int nSeq = align.getHeight();
for (int i = 0; i < nSeq; i++)
{
- if (!seqs.contains(align.getSequenceAt(i)))
+ if (!tmp.contains(align.getSequenceAt(i)))
{
- seqs.addElement(align.getSequenceAt(i));
+ tmp.add(align.getSequenceAt(i));
}
}
- if (nSeq != seqs.size())
+ if (nSeq != tmp.size())
{
System.err
.println("ERROR: Size still not right even after addStrays");
*
* @return DOCUMENT ME!
*/
- private static Vector _sortByTree(SequenceNode node, Vector tmp,
+ private static List<SequenceI> _sortByTree(SequenceNode node,
+ List<SequenceI> tmp,
List<SequenceI> seqset)
{
if (node == null)
// seqset.size()==0 ||
// seqset.contains(tmp)))
{
- tmp.addElement(node.element());
+ tmp.add((SequenceI) node.element());
}
}
}
for (int i = 0; i < seqs.length; i++)
{
SequenceFeature[] sf = seqs[i].getSequenceFeatures();
- if (sf == null && seqs[i].getDatasetSequence() != null)
- {
- sf = seqs[i].getDatasetSequence().getSequenceFeatures();
- }
if (sf == null)
{
sf = new SequenceFeature[0];
*/
package jalview.analysis;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
+
+import jalview.datamodel.AlignedCodon;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-
-import java.util.ArrayList;
-import java.util.List;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MapList;
/**
* grab bag of useful alignment manipulation operations Expect these to be
}
return result;
}
+
+ /**
+ * Returns a map of lists of sequences in the alignment, keyed by sequence
+ * name. For use in mapping between different alignment views of the same
+ * sequences.
+ *
+ * @see jalview.datamodel.AlignmentI#getSequencesByName()
+ */
+ public static Map<String, List<SequenceI>> getSequencesByName(
+ AlignmentI al)
+ {
+ Map<String, List<SequenceI>> theMap = new LinkedHashMap<String, List<SequenceI>>();
+ for (SequenceI seq : al.getSequences())
+ {
+ String name = seq.getName();
+ if (name != null)
+ {
+ List<SequenceI> seqs = theMap.get(name);
+ if (seqs == null)
+ {
+ seqs = new ArrayList<SequenceI>();
+ theMap.put(name, seqs);
+ }
+ seqs.add(seq);
+ }
+ }
+ return theMap;
+ }
+
+ /**
+ * Build mapping of protein to cDNA alignment. Mappings are made between
+ * sequences where the cDNA translates to the protein sequence. Any new
+ * mappings are added to the protein alignment. Returns true if any mappings
+ * either already exist or were added, else false.
+ *
+ * @param proteinAlignment
+ * @param cdnaAlignment
+ * @return
+ */
+ public static boolean mapProteinToCdna(
+ final AlignmentI proteinAlignment,
+ final AlignmentI cdnaAlignment)
+ {
+ if (proteinAlignment == null || cdnaAlignment == null)
+ {
+ return false;
+ }
+
+ Set<SequenceI> mappedDna = new HashSet<SequenceI>();
+ Set<SequenceI> mappedProtein = new HashSet<SequenceI>();
+
+ /*
+ * First pass - map sequences where cross-references exist. This include
+ * 1-to-many mappings to support, for example, variant cDNA.
+ */
+ boolean mappingPerformed = mapProteinToCdna(proteinAlignment,
+ cdnaAlignment, mappedDna, mappedProtein, true);
+
+ /*
+ * Second pass - map sequences where no cross-references exist. This only
+ * does 1-to-1 mappings and assumes corresponding sequences are in the same
+ * order in the alignments.
+ */
+ mappingPerformed |= mapProteinToCdna(proteinAlignment, cdnaAlignment,
+ mappedDna, mappedProtein, false);
+ return mappingPerformed;
+ }
+
+ /**
+ * Make mappings between compatible sequences (where the cDNA translation
+ * matches the protein).
+ *
+ * @param proteinAlignment
+ * @param cdnaAlignment
+ * @param mappedDna
+ * a set of mapped DNA sequences (to add to)
+ * @param mappedProtein
+ * a set of mapped Protein sequences (to add to)
+ * @param xrefsOnly
+ * if true, only map sequences where xrefs exist
+ * @return
+ */
+ protected static boolean mapProteinToCdna(
+ final AlignmentI proteinAlignment,
+ final AlignmentI cdnaAlignment, Set<SequenceI> mappedDna,
+ Set<SequenceI> mappedProtein, boolean xrefsOnly)
+ {
+ boolean mappingPerformed = false;
+ List<SequenceI> thisSeqs = proteinAlignment.getSequences();
+ for (SequenceI aaSeq : thisSeqs)
+ {
+ boolean proteinMapped = false;
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ for (SequenceI cdnaSeq : cdnaAlignment.getSequences())
+ {
+ /*
+ * Always try to map if sequences have xref to each other; this supports
+ * variant cDNA or alternative splicing for a protein sequence.
+ *
+ * If no xrefs, try to map progressively, assuming that alignments have
+ * mappable sequences in corresponding order. These are not
+ * many-to-many, as that would risk mixing species with similar cDNA
+ * sequences.
+ */
+ if (xrefsOnly && !CrossRef.haveCrossRef(aaSeq, cdnaSeq))
+ {
+ continue;
+ }
+
+ /*
+ * Don't map non-xrefd sequences more than once each. This heuristic
+ * allows us to pair up similar sequences in ordered alignments.
+ */
+ if (!xrefsOnly
+ && (mappedProtein.contains(aaSeq) || mappedDna
+ .contains(cdnaSeq)))
+ {
+ continue;
+ }
+ if (!mappingExists(proteinAlignment.getCodonFrames(),
+ aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence()))
+ {
+ MapList map = mapProteinToCdna(aaSeq, cdnaSeq);
+ if (map != null)
+ {
+ acf.addMap(cdnaSeq, aaSeq, map);
+ mappingPerformed = true;
+ proteinMapped = true;
+ mappedDna.add(cdnaSeq);
+ mappedProtein.add(aaSeq);
+ }
+ }
+ }
+ if (proteinMapped)
+ {
+ proteinAlignment.addCodonFrame(acf);
+ }
+ }
+ return mappingPerformed;
+ }
+
+ /**
+ * Answers true if the mappings include one between the given (dataset)
+ * sequences.
+ */
+ public static boolean mappingExists(Set<AlignedCodonFrame> set,
+ SequenceI aaSeq, SequenceI cdnaSeq)
+ {
+ if (set != null)
+ {
+ for (AlignedCodonFrame acf : set)
+ {
+ if (cdnaSeq == acf.getDnaForAaSeq(aaSeq))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Build a mapping (if possible) of a protein to a cDNA sequence. The cDNA
+ * must be three times the length of the protein, possibly after ignoring
+ * start and/or stop codons, and must translate to the protein. Returns null
+ * if no mapping is determined.
+ *
+ * @param proteinSeqs
+ * @param cdnaSeq
+ * @return
+ */
+ public static MapList mapProteinToCdna(SequenceI proteinSeq,
+ SequenceI cdnaSeq)
+ {
+ /*
+ * Here we handle either dataset sequence set (desktop) or absent (applet).
+ * Use only the char[] form of the sequence to avoid creating possibly large
+ * String objects.
+ */
+ final SequenceI proteinDataset = proteinSeq.getDatasetSequence();
+ char[] aaSeqChars = proteinDataset != null ? proteinDataset
+ .getSequence() : proteinSeq.getSequence();
+ final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence();
+ char[] cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence()
+ : cdnaSeq.getSequence();
+ if (aaSeqChars == null || cdnaSeqChars == null)
+ {
+ return null;
+ }
+
+ /*
+ * cdnaStart/End, proteinStartEnd are base 1 (for dataset sequence mapping)
+ */
+ final int mappedLength = 3 * aaSeqChars.length;
+ int cdnaLength = cdnaSeqChars.length;
+ int cdnaStart = 1;
+ int cdnaEnd = cdnaLength;
+ final int proteinStart = 1;
+ final int proteinEnd = aaSeqChars.length;
+
+ /*
+ * If lengths don't match, try ignoring stop codon.
+ */
+ if (cdnaLength != mappedLength && cdnaLength > 2)
+ {
+ String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - 3, 3)
+ .toUpperCase();
+ for (String stop : ResidueProperties.STOP)
+ {
+ if (lastCodon.equals(stop))
+ {
+ cdnaEnd -= 3;
+ cdnaLength -= 3;
+ break;
+ }
+ }
+ }
+
+ /*
+ * If lengths still don't match, try ignoring start codon.
+ */
+ if (cdnaLength != mappedLength
+ && cdnaLength > 2
+ && String.valueOf(cdnaSeqChars, 0, 3).toUpperCase()
+ .equals(
+ ResidueProperties.START))
+ {
+ cdnaStart += 3;
+ cdnaLength -= 3;
+ }
+
+ if (cdnaLength != mappedLength)
+ {
+ return null;
+ }
+ if (!translatesAs(cdnaSeqChars, cdnaStart - 1, aaSeqChars))
+ {
+ return null;
+ }
+ MapList map = new MapList(new int[]
+ { cdnaStart, cdnaEnd }, new int[]
+ { proteinStart, proteinEnd }, 3, 1);
+ return map;
+ }
+
+ /**
+ * Test whether the given cdna sequence, starting at the given offset,
+ * translates to the given amino acid sequence, using the standard translation
+ * table. Designed to fail fast i.e. as soon as a mismatch position is found.
+ *
+ * @param cdnaSeqChars
+ * @param cdnaStart
+ * @param aaSeqChars
+ * @return
+ */
+ protected static boolean translatesAs(char[] cdnaSeqChars, int cdnaStart,
+ char[] aaSeqChars)
+ {
+ int aaResidue = 0;
+ for (int i = cdnaStart; i < cdnaSeqChars.length - 2
+ && aaResidue < aaSeqChars.length; i += 3, aaResidue++)
+ {
+ String codon = String.valueOf(cdnaSeqChars, i, 3);
+ final String translated = ResidueProperties.codonTranslate(
+ codon);
+ /*
+ * ? allow X in protein to match untranslatable in dna ?
+ */
+ final char aaRes = aaSeqChars[aaResidue];
+ if ((translated == null || "STOP".equals(translated)) && aaRes == 'X')
+ {
+ continue;
+ }
+ if (translated == null
+ || !(aaRes == translated.charAt(0)))
+ {
+ // debug
+ // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
+ // + codon + "(" + translated + ") != " + aaRes));
+ return false;
+ }
+ }
+ // fail if we didn't match all of the aa sequence
+ return (aaResidue == aaSeqChars.length);
+ }
+
+ /**
+ * Align sequence 'seq' to match the alignment of a mapped sequence. Note this
+ * currently assumes that we are aligning cDNA to match protein.
+ *
+ * @param seq
+ * the sequence to be realigned
+ * @param al
+ * the alignment whose sequence alignment is to be 'copied'
+ * @param gap
+ * character string represent a gap in the realigned sequence
+ * @param preserveUnmappedGaps
+ * @param preserveMappedGaps
+ * @return true if the sequence was realigned, false if it could not be
+ */
+ public static boolean alignSequenceAs(SequenceI seq, AlignmentI al,
+ String gap, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
+ {
+ /*
+ * Get any mappings from the source alignment to the target (dataset) sequence.
+ */
+ // TODO there may be one AlignedCodonFrame per dataset sequence, or one with
+ // all mappings. Would it help to constrain this?
+ List<AlignedCodonFrame> mappings = al.getCodonFrame(seq);
+ if (mappings == null || mappings.isEmpty())
+ {
+ return false;
+ }
+
+ /*
+ * Locate the aligned source sequence whose dataset sequence is mapped. We
+ * just take the first match here (as we can't align cDNA like more than one
+ * protein sequence).
+ */
+ SequenceI alignFrom = null;
+ AlignedCodonFrame mapping = null;
+ for (AlignedCodonFrame mp : mappings)
+ {
+ alignFrom = mp.findAlignedSequence(seq.getDatasetSequence(), al);
+ if (alignFrom != null)
+ {
+ mapping = mp;
+ break;
+ }
+ }
+
+ if (alignFrom == null)
+ {
+ return false;
+ }
+ alignSequenceAs(seq, alignFrom, mapping, gap, al.getGapCharacter(),
+ preserveMappedGaps, preserveUnmappedGaps);
+ return true;
+ }
+
+ /**
+ * Align sequence 'alignTo' the same way as 'alignFrom', using the mapping to
+ * match residues and codons. Flags control whether existing gaps in unmapped
+ * (intron) and mapped (exon) regions are preserved or not. Gaps linking intro
+ * and exon are only retained if both flags are set.
+ *
+ * @param alignTo
+ * @param alignFrom
+ * @param mapping
+ * @param myGap
+ * @param sourceGap
+ * @param preserveUnmappedGaps
+ * @param preserveMappedGaps
+ */
+ public static void alignSequenceAs(SequenceI alignTo,
+ SequenceI alignFrom,
+ AlignedCodonFrame mapping, String myGap, char sourceGap,
+ boolean preserveMappedGaps, boolean preserveUnmappedGaps)
+ {
+ // TODO generalise to work for Protein-Protein, dna-dna, dna-protein
+ final char[] thisSeq = alignTo.getSequence();
+ final char[] thatAligned = alignFrom.getSequence();
+ StringBuilder thisAligned = new StringBuilder(2 * thisSeq.length);
+
+ // aligned and dataset sequence positions, all base zero
+ int thisSeqPos = 0;
+ int sourceDsPos = 0;
+
+ int basesWritten = 0;
+ char myGapChar = myGap.charAt(0);
+ int ratio = myGap.length();
+
+ /*
+ * Traverse the aligned protein sequence.
+ */
+ int sourceGapMappedLength = 0;
+ boolean inExon = false;
+ for (char sourceChar : thatAligned)
+ {
+ if (sourceChar == sourceGap)
+ {
+ sourceGapMappedLength += ratio;
+ continue;
+ }
+
+ /*
+ * Found a residue. Locate its mapped codon (start) position.
+ */
+ sourceDsPos++;
+ // Note mapping positions are base 1, our sequence positions base 0
+ int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom,
+ sourceDsPos);
+ if (mappedPos == null)
+ {
+ /*
+ * Abort realignment if unmapped protein. Or could ignore it??
+ */
+ System.err.println("Can't align: no codon mapping to residue "
+ + sourceDsPos + "(" + sourceChar + ")");
+ return;
+ }
+
+ int mappedCodonStart = mappedPos[0]; // position (1...) of codon start
+ int mappedCodonEnd = mappedPos[mappedPos.length - 1]; // codon end pos
+ StringBuilder trailingCopiedGap = new StringBuilder();
+
+ /*
+ * Copy dna sequence up to and including this codon. Optionally, include
+ * gaps before the codon starts (in introns) and/or after the codon starts
+ * (in exons).
+ *
+ * Note this only works for 'linear' splicing, not reverse or interleaved.
+ * But then 'align dna as protein' doesn't make much sense otherwise.
+ */
+ int intronLength = 0;
+ while (basesWritten < mappedCodonEnd && thisSeqPos < thisSeq.length)
+ {
+ final char c = thisSeq[thisSeqPos++];
+ if (c != myGapChar)
+ {
+ basesWritten++;
+
+ if (basesWritten < mappedCodonStart)
+ {
+ /*
+ * Found an unmapped (intron) base. First add in any preceding gaps
+ * (if wanted).
+ */
+ if (preserveUnmappedGaps && trailingCopiedGap.length() > 0)
+ {
+ thisAligned.append(trailingCopiedGap.toString());
+ intronLength += trailingCopiedGap.length();
+ trailingCopiedGap = new StringBuilder();
+ }
+ intronLength++;
+ inExon = false;
+ }
+ else
+ {
+ final boolean startOfCodon = basesWritten == mappedCodonStart;
+ int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
+ preserveUnmappedGaps, sourceGapMappedLength, inExon,
+ trailingCopiedGap.length(), intronLength, startOfCodon);
+ for (int i = 0; i < gapsToAdd; i++)
+ {
+ thisAligned.append(myGapChar);
+ }
+ sourceGapMappedLength = 0;
+ inExon = true;
+ }
+ thisAligned.append(c);
+ trailingCopiedGap = new StringBuilder();
+ }
+ else
+ {
+ if (inExon && preserveMappedGaps)
+ {
+ trailingCopiedGap.append(myGapChar);
+ }
+ else if (!inExon && preserveUnmappedGaps)
+ {
+ trailingCopiedGap.append(myGapChar);
+ }
+ }
+ }
+ }
+
+ /*
+ * At end of protein sequence. Copy any remaining dna sequence, optionally
+ * including (intron) gaps. We do not copy trailing gaps in protein.
+ */
+ while (thisSeqPos < thisSeq.length)
+ {
+ final char c = thisSeq[thisSeqPos++];
+ if (c != myGapChar || preserveUnmappedGaps)
+ {
+ thisAligned.append(c);
+ }
+ }
+
+ /*
+ * All done aligning, set the aligned sequence.
+ */
+ alignTo.setSequence(new String(thisAligned));
+ }
+
+ /**
+ * Helper method to work out how many gaps to insert when realigning.
+ *
+ * @param preserveMappedGaps
+ * @param preserveUnmappedGaps
+ * @param sourceGapMappedLength
+ * @param inExon
+ * @param trailingCopiedGap
+ * @param intronLength
+ * @param startOfCodon
+ * @return
+ */
+ protected static int calculateGapsToInsert(boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps, int sourceGapMappedLength,
+ boolean inExon, int trailingGapLength,
+ int intronLength, final boolean startOfCodon)
+ {
+ int gapsToAdd = 0;
+ if (startOfCodon)
+ {
+ /*
+ * Reached start of codon. Ignore trailing gaps in intron unless we are
+ * preserving gaps in both exon and intron. Ignore them anyway if the
+ * protein alignment introduces a gap at least as large as the intronic
+ * region.
+ */
+ if (inExon && !preserveMappedGaps)
+ {
+ trailingGapLength = 0;
+ }
+ if (!inExon && !(preserveMappedGaps && preserveUnmappedGaps))
+ {
+ trailingGapLength = 0;
+ }
+ if (inExon)
+ {
+ gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength);
+ }
+ else
+ {
+ if (intronLength + trailingGapLength <= sourceGapMappedLength)
+ {
+ gapsToAdd = sourceGapMappedLength - intronLength;
+ }
+ else
+ {
+ gapsToAdd = Math.min(intronLength + trailingGapLength
+ - sourceGapMappedLength, trailingGapLength);
+ }
+ }
+ }
+ else
+ {
+ /*
+ * second or third base of codon; check for any gaps in dna
+ */
+ if (!preserveMappedGaps)
+ {
+ trailingGapLength = 0;
+ }
+ gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength);
+ }
+ return gapsToAdd;
+ }
+
+ /**
+ * Returns a list of sequences mapped from the given sequences and aligned
+ * (gapped) in the same way. For example, the cDNA for aligned protein, where
+ * a single gap in protein generates three gaps in cDNA.
+ *
+ * @param sequences
+ * @param gapCharacter
+ * @param mappings
+ * @return
+ */
+ public static List<SequenceI> getAlignedTranslation(
+ List<SequenceI> sequences, char gapCharacter,
+ Set<AlignedCodonFrame> mappings)
+ {
+ List<SequenceI> alignedSeqs = new ArrayList<SequenceI>();
+
+ for (SequenceI seq : sequences)
+ {
+ List<SequenceI> mapped = getAlignedTranslation(seq, gapCharacter,
+ mappings);
+ alignedSeqs.addAll(mapped);
+ }
+ return alignedSeqs;
+ }
+
+ /**
+ * Returns sequences aligned 'like' the source sequence, as mapped by the
+ * given mappings. Normally we expect zero or one 'mapped' sequences, but this
+ * will support 1-to-many as well.
+ *
+ * @param seq
+ * @param gapCharacter
+ * @param mappings
+ * @return
+ */
+ protected static List<SequenceI> getAlignedTranslation(SequenceI seq,
+ char gapCharacter, Set<AlignedCodonFrame> mappings)
+ {
+ List<SequenceI> result = new ArrayList<SequenceI>();
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ if (mapping.involvesSequence(seq))
+ {
+ SequenceI mapped = getAlignedTranslation(seq, gapCharacter, mapping);
+ if (mapped != null)
+ {
+ result.add(mapped);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns the translation of 'seq' (as held in the mapping) with
+ * corresponding alignment (gaps).
+ *
+ * @param seq
+ * @param gapCharacter
+ * @param mapping
+ * @return
+ */
+ protected static SequenceI getAlignedTranslation(SequenceI seq,
+ char gapCharacter, AlignedCodonFrame mapping)
+ {
+ String gap = String.valueOf(gapCharacter);
+ boolean toDna = false;
+ int fromRatio = 1;
+ SequenceI mapTo = mapping.getDnaForAaSeq(seq);
+ if (mapTo != null)
+ {
+ // mapping is from protein to nucleotide
+ toDna = true;
+ // should ideally get gap count ratio from mapping
+ gap = String.valueOf(new char[]
+ { gapCharacter, gapCharacter, gapCharacter });
+ }
+ else
+ {
+ // mapping is from nucleotide to protein
+ mapTo = mapping.getAaForDnaSeq(seq);
+ fromRatio = 3;
+ }
+ StringBuilder newseq = new StringBuilder(seq.getLength()
+ * (toDna ? 3 : 1));
+
+ int residueNo = 0; // in seq, base 1
+ int[] phrase = new int[fromRatio];
+ int phraseOffset = 0;
+ int gapWidth = 0;
+ boolean first = true;
+ final Sequence alignedSeq = new Sequence("", "");
+
+ for (char c : seq.getSequence())
+ {
+ if (c == gapCharacter)
+ {
+ gapWidth++;
+ if (gapWidth >= fromRatio)
+ {
+ newseq.append(gap);
+ gapWidth = 0;
+ }
+ }
+ else
+ {
+ phrase[phraseOffset++] = residueNo + 1;
+ if (phraseOffset == fromRatio)
+ {
+ /*
+ * Have read a whole codon (or protein residue), now translate: map
+ * source phrase to positions in target sequence add characters at
+ * these positions to newseq Note mapping positions are base 1, our
+ * sequence positions base 0.
+ */
+ SearchResults sr = new SearchResults();
+ for (int pos : phrase)
+ {
+ mapping.markMappedRegion(seq, pos, sr);
+ }
+ newseq.append(sr.toString());
+ if (first)
+ {
+ first = false;
+ // Hack: Copy sequence dataset, name and description from
+ // SearchResults.match[0].sequence
+ // TODO? carry over sequence names from original 'complement'
+ // alignment
+ SequenceI mappedTo = sr.getResultSequence(0);
+ alignedSeq.setName(mappedTo.getName());
+ alignedSeq.setDescription(mappedTo.getDescription());
+ alignedSeq.setDatasetSequence(mappedTo);
+ }
+ phraseOffset = 0;
+ }
+ residueNo++;
+ }
+ }
+ alignedSeq.setSequence(newseq.toString());
+ return alignedSeq;
+ }
+
+ /**
+ * Realigns the given protein to match the alignment of the dna, using codon
+ * mappings to translate aligned codon positions to protein residues.
+ *
+ * @param protein
+ * the alignment whose sequences are realigned by this method
+ * @param dna
+ * the dna alignment whose alignment we are 'copying'
+ * @return the number of sequences that were realigned
+ */
+ public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)
+ {
+ Set<AlignedCodonFrame> mappings = protein.getCodonFrames();
+
+ /*
+ * Map will hold, for each aligned codon position e.g. [3, 5, 6], a map of
+ * {dnaSequence, {proteinSequence, codonProduct}} at that position. The
+ * comparator keeps the codon positions ordered.
+ */
+ Map<AlignedCodon, Map<SequenceI, String>> alignedCodons = new TreeMap<AlignedCodon, Map<SequenceI, String>>(
+ new CodonComparator());
+ for (SequenceI dnaSeq : dna.getSequences())
+ {
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
+ SequenceI prot = mapping.findAlignedSequence(
+ dnaSeq.getDatasetSequence(), protein);
+ if (prot != null)
+ {
+ addCodonPositions(dnaSeq, prot, protein.getGapCharacter(),
+ seqMap, alignedCodons);
+ }
+ }
+ }
+ return alignProteinAs(protein, alignedCodons);
+ }
+
+ /**
+ * Update the aligned protein sequences to match the codon alignments given in
+ * the map.
+ *
+ * @param protein
+ * @param alignedCodons
+ * an ordered map of codon positions (columns), with sequence/peptide
+ * values present in each column
+ * @return
+ */
+ protected static int alignProteinAs(AlignmentI protein,
+ Map<AlignedCodon, Map<SequenceI, String>> alignedCodons)
+ {
+ /*
+ * Prefill aligned sequences with gaps before inserting aligned protein
+ * residues.
+ */
+ int alignedWidth = alignedCodons.size();
+ char[] gaps = new char[alignedWidth];
+ Arrays.fill(gaps, protein.getGapCharacter());
+ String allGaps = String.valueOf(gaps);
+ for (SequenceI seq : protein.getSequences())
+ {
+ seq.setSequence(allGaps);
+ }
+
+ int column = 0;
+ for (AlignedCodon codon : alignedCodons.keySet())
+ {
+ final Map<SequenceI, String> columnResidues = alignedCodons.get(codon);
+ for (Entry<SequenceI, String> entry : columnResidues
+ .entrySet())
+ {
+ // place translated codon at its column position in sequence
+ entry.getKey().getSequence()[column] = entry.getValue().charAt(0);
+ }
+ column++;
+ }
+ return 0;
+ }
+
+ /**
+ * Populate the map of aligned codons by traversing the given sequence
+ * mapping, locating the aligned positions of mapped codons, and adding those
+ * positions and their translation products to the map.
+ *
+ * @param dna
+ * the aligned sequence we are mapping from
+ * @param protein
+ * the sequence to be aligned to the codons
+ * @param gapChar
+ * the gap character in the dna sequence
+ * @param seqMap
+ * a mapping to a sequence translation
+ * @param alignedCodons
+ * the map we are building up
+ */
+ static void addCodonPositions(SequenceI dna, SequenceI protein,
+ char gapChar,
+ Mapping seqMap,
+ Map<AlignedCodon, Map<SequenceI, String>> alignedCodons)
+ {
+ Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar);
+ while (codons.hasNext())
+ {
+ AlignedCodon codon = codons.next();
+ Map<SequenceI, String> seqProduct = alignedCodons.get(codon);
+ if (seqProduct == null)
+ {
+ seqProduct = new HashMap<SequenceI, String>();
+ alignedCodons.put(codon, seqProduct);
+ }
+ seqProduct.put(protein, codon.product);
+ }
+ }
+
+ /**
+ * Returns true if a cDNA/Protein mapping either exists, or could be made,
+ * between at least one pair of sequences in the two alignments. Currently,
+ * the logic is:
+ * <ul>
+ * <li>One alignment must be nucleotide, and the other protein</li>
+ * <li>At least one pair of sequences must be already mapped, or mappable</li>
+ * <li>Mappable means the nucleotide translation matches the protein sequence</li>
+ * <li>The translation may ignore start and stop codons if present in the
+ * nucleotide</li>
+ * </ul>
+ *
+ * @param al1
+ * @param al2
+ * @return
+ */
+ public static boolean isMappable(AlignmentI al1, AlignmentI al2)
+ {
+ /*
+ * Require one nucleotide and one protein
+ */
+ if (al1.isNucleotide() == al2.isNucleotide())
+ {
+ return false;
+ }
+ AlignmentI dna = al1.isNucleotide() ? al1 : al2;
+ AlignmentI protein = dna == al1 ? al2 : al1;
+ Set<AlignedCodonFrame> mappings = protein.getCodonFrames();
+ for (SequenceI dnaSeq : dna.getSequences())
+ {
+ for (SequenceI proteinSeq : protein.getSequences())
+ {
+ if (isMappable(dnaSeq, proteinSeq, mappings))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns true if the dna sequence is mapped, or could be mapped, to the
+ * protein sequence.
+ *
+ * @param dnaSeq
+ * @param proteinSeq
+ * @param mappings
+ * @return
+ */
+ public static boolean isMappable(SequenceI dnaSeq, SequenceI proteinSeq,
+ Set<AlignedCodonFrame> mappings)
+ {
+ SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq.getDatasetSequence();
+ SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
+ : proteinSeq.getDatasetSequence();
+
+ /*
+ * Already mapped?
+ */
+ for (AlignedCodonFrame mapping : mappings) {
+ if ( proteinDs == mapping.getAaForDnaSeq(dnaDs)) {
+ return true;
+ }
+ }
+
+ /*
+ * Just try to make a mapping (it is not yet stored), test whether
+ * successful.
+ */
+ return mapProteinToCdna(proteinDs, dnaDs) != null;
+ }
+
+ /**
+ * Finds any reference annotations associated with the sequences in
+ * sequenceScope, that are not already added to the alignment, and adds them
+ * to the 'candidates' map. Also populates a lookup table of annotation
+ * labels, keyed by calcId, for use in constructing tooltips or the like.
+ *
+ * @param sequenceScope
+ * the sequences to scan for reference annotations
+ * @param labelForCalcId
+ * (optional) map to populate with label for calcId
+ * @param candidates
+ * map to populate with annotations for sequence
+ * @param al
+ * the alignment to check for presence of annotations
+ */
+ public static void findAddableReferenceAnnotations(
+ List<SequenceI> sequenceScope, Map<String, String> labelForCalcId,
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates,
+ AlignmentI al)
+ {
+ if (sequenceScope == null)
+ {
+ return;
+ }
+
+ /*
+ * For each sequence in scope, make a list of any annotations on the
+ * underlying dataset sequence which are not already on the alignment.
+ *
+ * Add to a map of { alignmentSequence, <List of annotations to add> }
+ */
+ for (SequenceI seq : sequenceScope)
+ {
+ SequenceI dataset = seq.getDatasetSequence();
+ if (dataset == null)
+ {
+ continue;
+ }
+ AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
+ if (datasetAnnotations == null)
+ {
+ continue;
+ }
+ final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation dsann : datasetAnnotations)
+ {
+ /*
+ * Find matching annotations on the alignment. If none is found, then
+ * add this annotation to the list of 'addable' annotations for this
+ * sequence.
+ */
+ final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
+ .findAnnotations(seq, dsann.getCalcId(),
+ dsann.label);
+ if (!matchedAlignmentAnnotations.iterator().hasNext())
+ {
+ result.add(dsann);
+ if (labelForCalcId != null)
+ {
+ labelForCalcId.put(dsann.getCalcId(), dsann.label);
+ }
+ }
+ }
+ /*
+ * Save any addable annotations for this sequence
+ */
+ if (!result.isEmpty())
+ {
+ candidates.put(seq, result);
+ }
+ }
+ }
+
+ /**
+ * Adds annotations to the top of the alignment annotations, in the same order
+ * as their related sequences.
+ *
+ * @param annotations
+ * the annotations to add
+ * @param alignment
+ * the alignment to add them to
+ * @param selectionGroup
+ * current selection group (or null if none)
+ */
+ public static void addReferenceAnnotations(
+ Map<SequenceI, List<AlignmentAnnotation>> annotations,
+ final AlignmentI alignment, final SequenceGroup selectionGroup)
+ {
+ for (SequenceI seq : annotations.keySet())
+ {
+ for (AlignmentAnnotation ann : annotations.get(seq))
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ if (selectionGroup != null)
+ {
+ startRes = selectionGroup.getStartRes();
+ endRes = selectionGroup.getEndRes();
+ }
+ copyAnn.restrict(startRes, endRes);
+
+ /*
+ * Add to the sequence (sets copyAnn.datasetSequence), unless the
+ * original annotation is already on the sequence.
+ */
+ if (!seq.hasAnnotation(ann))
+ {
+ seq.addAlignmentAnnotation(copyAnn);
+ }
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ alignment.addAnnotation(copyAnn);
+ copyAnn.visible = true;
+ }
+ }
+ }
+
+ /**
+ * Set visibility of alignment annotations of specified types (labels), for
+ * specified sequences. This supports controls like
+ * "Show all secondary structure", "Hide all Temp factor", etc.
+ *
+ * @al the alignment to scan for annotations
+ * @param types
+ * the types (labels) of annotations to be updated
+ * @param forSequences
+ * if not null, only annotations linked to one of these sequences are
+ * in scope for update; if null, acts on all sequence annotations
+ * @param anyType
+ * if this flag is true, 'types' is ignored (label not checked)
+ * @param doShow
+ * if true, set visibility on, else set off
+ */
+ public static void showOrHideSequenceAnnotations(AlignmentI al,
+ Collection<String> types, List<SequenceI> forSequences,
+ boolean anyType, boolean doShow)
+ {
+ for (AlignmentAnnotation aa : al
+ .getAlignmentAnnotation())
+ {
+ if (anyType || types.contains(aa.label))
+ {
+ if ((aa.sequenceRef != null)
+ && (forSequences == null || forSequences
+ .contains(aa.sequenceRef)))
+ {
+ aa.visible = doShow;
+ }
+ }
+ }
+ }
}
--- /dev/null
+package jalview.analysis;
+
+/**
+ * A utility class to provide encoding/decoding schemes for data.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class CodingUtils
+{
+
+ /*
+ * Number of bits used when encoding codon characters. 2 is enough for ACGT.
+ * To accommodate more (e.g. ambiguity codes), simply increase this number
+ * (and adjust unit tests to match).
+ */
+ private static final int CODON_ENCODING_BITSHIFT = 2;
+
+ /**
+ * Encode a codon from e.g. ['A', 'G', 'C'] to a number in the range 0 - 63.
+ * Converts lower to upper case, U to T, then assembles a binary value by
+ * encoding A/C/G/T as 00/01/10/11 respectively and shifting.
+ *
+ * @param codon
+ * @return the encoded codon, or a negative number if unexpected characters
+ * found
+ */
+ public static int encodeCodon(char[] codon)
+ {
+ if (codon == null)
+ {
+ return -1;
+ }
+ return encodeCodon(codon[2])
+ + (encodeCodon(codon[1]) << CODON_ENCODING_BITSHIFT)
+ + (encodeCodon(codon[0]) << (2 * CODON_ENCODING_BITSHIFT));
+ }
+
+ /**
+ * Encodes aA/cC/gG/tTuU as 0/1/2/3 respectively. Returns Integer.MIN_VALUE (a
+ * large negative value) for any other character.
+ *
+ * @param c
+ * @return
+ */
+ public static int encodeCodon(char c)
+ {
+ int result = Integer.MIN_VALUE;
+ switch (c)
+ {
+ case 'A':
+ case 'a':
+ result = 0;
+ break;
+ case 'C':
+ case 'c':
+ result = 1;
+ break;
+ case 'G':
+ case 'g':
+ result = 2;
+ break;
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ result = 3;
+ break;
+ }
+ return result;
+ }
+
+ /**
+ * Converts a binary encoded codon into an ['A', 'C', 'G'] (or 'T') triplet.
+ *
+ * The two low-order bits encode for A/C/G/T as 0/1/2/3, etc.
+ *
+ * @param encoded
+ * @return
+ */
+ public static char[] decodeCodon(int encoded)
+ {
+ char[] result = new char[3];
+ result[2] = decodeNucleotide(encoded & 3);
+ encoded = encoded >>> CODON_ENCODING_BITSHIFT;
+ result[1] = decodeNucleotide(encoded & 3);
+ encoded = encoded >>> CODON_ENCODING_BITSHIFT;
+ result[0] = decodeNucleotide(encoded & 3);
+ return result;
+ }
+
+ /**
+ * Convert value 0/1/2/3 to 'A'/'C'/'G'/'T'
+ *
+ * @param i
+ * @return
+ */
+ public static char decodeNucleotide(int i)
+ {
+ char result = '0';
+ switch (i)
+ {
+ case 0:
+ result = 'A';
+ break;
+ case 1:
+ result = 'C';
+ break;
+ case 2:
+ result = 'G';
+ break;
+ case 3:
+ result = 'T';
+ break;
+ }
+ return result;
+ }
+
+}
--- /dev/null
+package jalview.analysis;
+
+import jalview.datamodel.AlignedCodon;
+
+import java.util.Comparator;
+
+/**
+ * Implements rules for comparing two aligned codons, i.e. determining whether
+ * they should occupy the same position in a translated protein alignment, or
+ * one or the other should 'follow' (by preceded by a gap).
+ *
+ * @author gmcarstairs
+ *
+ */
+public final class CodonComparator implements Comparator<AlignedCodon>
+{
+
+ @Override
+ public int compare(AlignedCodon ac1, AlignedCodon ac2)
+ {
+ if (ac1 == null || ac2 == null || ac1.equals(ac2))
+ {
+ return 0;
+ }
+
+ /**
+ * <pre>
+ * Case 1: if one starts before the other, and doesn't end after it, then it
+ * precedes. We ignore the middle base position here.
+ * A--GT
+ * -CT-G
+ * </pre>
+ */
+ if (ac1.pos1 < ac2.pos1 && ac1.pos3 <= ac2.pos3)
+ {
+ return -1;
+ }
+ if (ac2.pos1 < ac1.pos1 && ac2.pos3 <= ac1.pos3)
+ {
+ return 1;
+ }
+
+ /**
+ * <pre>
+ * Case 2: if one ends after the other, and doesn't start before it, then it
+ * follows. We ignore the middle base position here.
+ * -TG-A
+ * G-TC
+ * </pre>
+ */
+ if (ac1.pos3 > ac2.pos3 && ac1.pos1 >= ac2.pos1)
+ {
+ return 1;
+ }
+ if (ac2.pos3 > ac1.pos3 && ac2.pos1 >= ac1.pos1)
+ {
+ return -1;
+ }
+
+ /*
+ * Case 3: if start and end match, compare middle base positions.
+ */
+ if (ac1.pos1 == ac2.pos1 && ac1.pos3 == ac2.pos3)
+ {
+ return Integer.compare(ac1.pos2, ac2.pos2);
+ }
+
+ /*
+ * That just leaves the 'enclosing' case - one codon starts after but ends
+ * before the other. If the middle bases don't match, use their comparison
+ * (majority vote).
+ */
+ int compareMiddles = Integer.compare(ac1.pos2, ac2.pos2);
+ if (compareMiddles != 0)
+ {
+ return compareMiddles;
+ }
+
+ /**
+ * <pre>
+ * Finally just leaves overlap with matching middle base, e.g.
+ * -A-A-A
+ * G--GG
+ * In this case the choice is arbitrary whether to compare based on
+ * first or last base position. We pick the first. Note this preserves
+ * symmetricality of the comparison.
+ * </pre>
+ */
+ return Integer.compare(ac1.pos1, ac2.pos1);
+ }
+}
*/
package jalview.analysis;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
-import java.util.Hashtable;
-
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.ws.SequenceFetcher;
import jalview.ws.seqfetcher.ASequenceFetcher;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
/**
* Functions for cross-referencing sequence databases. user must first specify
* if cross-referencing from protein or dna (set dna==true)
{
Vector rseqs = new Vector();
Alignment ral = null;
- AlignedCodonFrame cf = new AlignedCodonFrame(0); // nominal width
+ AlignedCodonFrame cf = new AlignedCodonFrame(); // nominal width
for (int s = 0; s < seqs.length; s++)
{
SequenceI dss = seqs[s];
for (int r = 0; xrfs != null && r < xrfs.length; r++)
{
if (source != null && !source.equals(xrfs[r].getSource()))
+ {
continue;
+ }
if (xrfs[r].hasMap())
{
if (xrfs[r].getMap().getTo() != null)
{
found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
if (found)
+ {
xrfs[r] = null; // we've recovered seqs for this one.
+ }
}
}
}
for (int r = 0; r < xrfs.length; r++)
{
if (xrfs[r] != null)
+ {
t[l++] = xrfs[r];
+ }
}
xrfs = t;
try
{
boolean found = false;
if (lrfs == null)
+ {
return false;
+ }
for (int i = 0; i < lrfs.length; i++)
{
DBRefEntry xref = new DBRefEntry(lrfs[i]);
boolean found = false;
SequenceI[] typer = new SequenceI[1];
if (dataset == null)
+ {
return false;
+ }
if (dataset.getSequences() == null)
{
System.err.println("Empty dataset sequence set - NO VECTOR");
synchronized (ds = dataset.getSequences())
{
for (SequenceI nxt : ds)
+ {
if (nxt != null)
{
if (nxt.getDatasetSequence() != null)
}
}
+ }
}
return found;
}
/**
+ * Returns true if either sequence has a cross-reference to the other
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ public static boolean haveCrossRef(SequenceI seq1, SequenceI seq2)
+ {
+ return hasCrossRef(seq1, seq2) || hasCrossRef(seq2, seq1);
+ }
+
+ /**
+ * Returns true if seq1 has a cross-reference to seq2. Currently this assumes
+ * that sequence name is structured as Source|AccessId.
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ public static boolean hasCrossRef(SequenceI seq1, SequenceI seq2)
+ {
+ if (seq1 == null || seq2 == null)
+ {
+ return false;
+ }
+ String name = seq2.getName();
+ final DBRefEntry[] xrefs = seq1.getDBRef();
+ if (xrefs != null)
+ {
+ for (DBRefEntry xref : xrefs)
+ {
+ String xrefName = xref.getSource() + "|" + xref.getAccessionId();
+ // case-insensitive test, consistent with DBRefEntry.equalRef()
+ if (xrefName.equalsIgnoreCase(name))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
* precalculate different products that can be found for seqs in dataset and
* return them.
*
*/
package jalview.analysis;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Vector;
-
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.ShiftList;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Map;
+
public class Dna
{
- /**
+ private static final String STOP_X = "X";
+
+ private static final Comparator<AlignedCodon> comparator = new CodonComparator();
+
+ /*
+ * 'final' variables describe the inputs to the translation, which should not
+ * be modified.
+ */
+ final private List<SequenceI> selection;
+
+ final private String[] seqstring;
+
+ final private int[] contigs;
+
+ final private char gapChar;
+
+ final private AlignmentAnnotation[] annotations;
+
+ final private int dnaWidth;
+
+ final private Alignment dataset;
+
+ /*
+ * Working variables for the translation.
*
- * @param cdp1
- * @param cdp2
- * @return -1 if cdp1 aligns before cdp2, 0 if in the same column or cdp2 is
- * null, +1 if after cdp2
+ * The width of the translation-in-progress protein alignment.
*/
- private static int compare_codonpos(int[] cdp1, int[] cdp2)
- {
- if (cdp2 == null
- || (cdp1[0] == cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))
- return 0;
- if (cdp1[0] < cdp2[0] || cdp1[1] < cdp2[1] || cdp1[2] < cdp2[2])
- return -1; // one base in cdp1 precedes the corresponding base in the
- // other codon
- return 1; // one base in cdp1 appears after the corresponding base in the
- // other codon.
- }
+ private int aaWidth = 0;
- /**
- * DNA->mapped protein sequence alignment translation given set of sequences
- * 1. id distinct coding regions within selected region for each sequence 2.
- * generate peptides based on inframe (or given) translation or (optionally
- * and where specified) out of frame translations (annotated appropriately) 3.
- * align peptides based on codon alignment
+ /*
+ * This array will be built up so that position i holds the codon positions
+ * e.g. [7, 9, 10] that match column i (base 0) in the aligned translation.
+ * Note this implies a contract that if two codons do not align exactly, their
+ * translated products must occupy different column positions.
*/
+ private AlignedCodon[] alignedCodons;
+
/**
- * id potential products from dna 1. search for distinct products within
- * selected region for each selected sequence 2. group by associated DB type.
- * 3. return as form for input into above function
+ * Constructor given a viewport and the visible contigs.
+ *
+ * @param viewport
+ * @param visibleContigs
*/
+ public Dna(AlignViewportI viewport, int[] visibleContigs)
+ {
+ this.selection = Arrays.asList(viewport.getSequenceSelection());
+ this.seqstring = viewport.getViewAsString(true);
+ this.contigs = visibleContigs;
+ this.gapChar = viewport.getGapCharacter();
+ this.annotations = viewport.getAlignment().getAlignmentAnnotation();
+ this.dnaWidth = viewport.getAlignment().getWidth();
+ this.dataset = viewport.getAlignment().getDataset();
+ }
+
/**
+ * Test whether codon positions cdp1 should align before, with, or after cdp2.
+ * Returns zero if all positions match (or either argument is null). Returns
+ * -1 if any position in the first codon precedes the corresponding position
+ * in the second codon. Else returns +1 (some position in the second codon
+ * precedes the corresponding position in the first).
+ *
+ * Note this is not necessarily symmetric, for example:
+ * <ul>
+ * <li>compareCodonPos([2,5,6], [3,4,5]) returns -1</li>
+ * <li>compareCodonPos([3,4,5], [2,5,6]) also returns -1</li>
+ * </ul>
*
+ * @param ac1
+ * @param ac2
+ * @return
*/
+ public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
+ {
+ return comparator.compare(ac1, ac2);
+ // return jalview_2_8_2compare(ac1, ac2);
+ }
+
/**
- * create a new alignment of protein sequences by an inframe translation of
- * the provided NA sequences
+ * Codon comparison up to Jalview 2.8.2. This rule is sequence order dependent
+ * - see http://issues.jalview.org/browse/JAL-1635
*
- * @param selection
- * @param seqstring
- * @param viscontigs
- * @param gapCharacter
- * @param annotations
- * @param aWidth
- * @param dataset
- * destination dataset for translated sequences and mappings
+ * @param ac1
+ * @param ac2
* @return
*/
- public static AlignmentI CdnaTranslate(SequenceI[] selection,
- String[] seqstring, int viscontigs[], char gapCharacter,
- AlignmentAnnotation[] annotations, int aWidth, Alignment dataset)
+ private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2)
{
- return CdnaTranslate(selection, seqstring, null, viscontigs,
- gapCharacter, annotations, aWidth, dataset);
+ if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
+ {
+ return 0;
+ }
+ if (ac1.pos1 < ac2.pos1 || ac1.pos2 < ac2.pos2 || ac1.pos3 < ac2.pos3)
+ {
+ // one base in cdp1 precedes the corresponding base in the other codon
+ return -1;
+ }
+ // one base in cdp1 appears after the corresponding base in the other codon.
+ return 1;
}
/**
*
- * @param selection
- * @param seqstring
- * @param product
- * - array of DbRefEntry objects from which exon map in seqstring is
- * derived
- * @param viscontigs
- * @param gapCharacter
- * @param annotations
- * @param aWidth
- * @param dataset
* @return
*/
- public static AlignmentI CdnaTranslate(SequenceI[] selection,
- String[] seqstring, DBRefEntry[] product, int viscontigs[],
- char gapCharacter, AlignmentAnnotation[] annotations, int aWidth,
- Alignment dataset)
+ public AlignmentI translateCdna()
{
- AlignedCodonFrame codons = new AlignedCodonFrame(aWidth); // stores hash of
- // subsequent
- // positions for
- // each codon
- // start position
- // in alignment
- int s, sSize = selection.length;
- Vector pepseqs = new Vector();
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ alignedCodons = new AlignedCodon[dnaWidth];
+
+ int s;
+ int sSize = selection.size();
+ List<SequenceI> pepseqs = new ArrayList<SequenceI>();
for (s = 0; s < sSize; s++)
{
- SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
- viscontigs, codons, gapCharacter,
- (product != null) ? product[s] : null, false); // possibly
- // anonymous
- // product
+ SequenceI newseq = translateCodingRegion(selection.get(s),
+ seqstring[s], acf, pepseqs);
+
if (newseq != null)
{
- pepseqs.addElement(newseq);
+ pepseqs.add(newseq);
SequenceI ds = newseq;
if (dataset != null)
{
}
}
}
- if (codons.aaWidth == 0)
- return null;
- SequenceI[] newseqs = new SequenceI[pepseqs.size()];
- pepseqs.copyInto(newseqs);
+
+ SequenceI[] newseqs = pepseqs.toArray(new SequenceI[pepseqs.size()]);
AlignmentI al = new Alignment(newseqs);
- al.padGaps(); // ensure we look aligned.
+ // ensure we look aligned.
+ al.padGaps();
+ // link the protein translation to the DNA dataset
al.setDataset(dataset);
- translateAlignedAnnotations(annotations, al, codons);
- al.addCodonFrame(codons);
+ translateAlignedAnnotations(al, acf);
+ al.addCodonFrame(acf);
return al;
}
for (int gd = 0; gd < selection.length; gd++)
{
SequenceI dna = selection[gd];
- jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
+ DBRefEntry[] dnarefs = DBRefUtils
.selectRefs(dna.getDBRef(),
jalview.datamodel.DBRefSource.DNACODINGDBS);
if (dnarefs != null)
{
// intersect with pep
- // intersect with pep
- Vector mappedrefs = new Vector();
+ List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
DBRefEntry[] refs = dna.getDBRef();
for (int d = 0; d < refs.length; d++)
{
&& refs[d].getMap().getMap().getFromRatio() == 3
&& refs[d].getMap().getMap().getToRatio() == 1)
{
- mappedrefs.addElement(refs[d]); // add translated protein maps
+ mappedrefs.add(refs[d]); // add translated protein maps
}
}
- dnarefs = new DBRefEntry[mappedrefs.size()];
- mappedrefs.copyInto(dnarefs);
+ dnarefs = mappedrefs.toArray(new DBRefEntry[mappedrefs.size()]);
for (int d = 0; d < dnarefs.length; d++)
{
Mapping mp = dnarefs[d].getMap();
}
/**
- * generate a set of translated protein products from annotated sequenceI
+ * Translate nucleotide alignment annotations onto translated amino acid
+ * alignment using codon mapping codons
*
- * @param selection
- * @param viscontigs
- * @param gapCharacter
- * @param dataset
- * destination dataset for translated sequences
- * @param annotations
- * @param aWidth
- * @return
- */
- public static AlignmentI CdnaTranslate(SequenceI[] selection,
- int viscontigs[], char gapCharacter, Alignment dataset)
- {
- int alwidth = 0;
- Vector cdnasqs = new Vector();
- Vector cdnasqi = new Vector();
- Vector cdnaprod = new Vector();
- for (int gd = 0; gd < selection.length; gd++)
- {
- SequenceI dna = selection[gd];
- jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
- .selectRefs(dna.getDBRef(),
- jalview.datamodel.DBRefSource.DNACODINGDBS);
- if (dnarefs != null)
- {
- // intersect with pep
- Vector mappedrefs = new Vector();
- DBRefEntry[] refs = dna.getDBRef();
- for (int d = 0; d < refs.length; d++)
- {
- if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
- && refs[d].getMap().getMap().getFromRatio() == 3
- && refs[d].getMap().getMap().getToRatio() == 1)
- {
- mappedrefs.addElement(refs[d]); // add translated protein maps
- }
- }
- dnarefs = new DBRefEntry[mappedrefs.size()];
- mappedrefs.copyInto(dnarefs);
- for (int d = 0; d < dnarefs.length; d++)
- {
- Mapping mp = dnarefs[d].getMap();
- StringBuffer sqstr = new StringBuffer();
- if (mp != null)
- {
- Mapping intersect = mp.intersectVisContigs(viscontigs);
- // generate seqstring for this sequence based on mapping
-
- if (sqstr.length() > alwidth)
- alwidth = sqstr.length();
- cdnasqs.addElement(sqstr.toString());
- cdnasqi.addElement(dna);
- cdnaprod.addElement(intersect);
- }
- }
- }
- SequenceI[] cdna = new SequenceI[cdnasqs.size()];
- DBRefEntry[] prods = new DBRefEntry[cdnaprod.size()];
- String[] xons = new String[cdnasqs.size()];
- cdnasqs.copyInto(xons);
- cdnaprod.copyInto(prods);
- cdnasqi.copyInto(cdna);
- return CdnaTranslate(cdna, xons, prods, viscontigs, gapCharacter,
- null, alwidth, dataset);
- }
- return null;
- }
-
- /**
- * translate na alignment annotations onto translated amino acid alignment al
- * using codon mapping codons
- *
- * @param annotations
* @param al
- * @param codons
+ * the translated protein alignment
*/
- public static void translateAlignedAnnotations(
- AlignmentAnnotation[] annotations, AlignmentI al,
- AlignedCodonFrame codons)
+ protected void translateAlignedAnnotations(AlignmentI al,
+ AlignedCodonFrame acf)
{
- // //////////////////////////////
- // Copy annotations across
- //
// Can only do this for columns with consecutive codons, or where
// annotation is sequence associated.
- int pos, a, aSize;
if (annotations != null)
{
- for (int i = 0; i < annotations.length; i++)
+ for (AlignmentAnnotation annotation : annotations)
{
- // Skip any autogenerated annotation
- if (annotations[i].autoCalculated)
+ /*
+ * Skip hidden or autogenerated annotation. Also (for now), RNA
+ * secondary structure annotation. If we want to show this against
+ * protein we need a smarter way to 'translate' without generating
+ * invalid (unbalanced) structure annotation.
+ */
+ if (annotation.autoCalculated || !annotation.visible
+ || annotation.isRNA())
{
continue;
}
- aSize = codons.getaaWidth(); // aa alignment width.
- jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null
- : new jalview.datamodel.Annotation[aSize];
+ int aSize = aaWidth;
+ Annotation[] anots = (annotation.annotations == null) ? null
+ : new Annotation[aSize];
if (anots != null)
{
- for (a = 0; a < aSize; a++)
+ for (int a = 0; a < aSize; a++)
{
// process through codon map.
- if (codons.codons[a] != null
- && codons.codons[a][0] == (codons.codons[a][2] - 2))
+ if (a < alignedCodons.length && alignedCodons[a] != null
+ && alignedCodons[a].pos1 == (alignedCodons[a].pos3 - 2))
{
- anots[a] = getCodonAnnotation(codons.codons[a],
- annotations[i].annotations);
+ anots[a] = getCodonAnnotation(alignedCodons[a],
+ annotation.annotations);
}
}
}
- jalview.datamodel.AlignmentAnnotation aa = new jalview.datamodel.AlignmentAnnotation(
- annotations[i].label, annotations[i].description, anots);
- aa.graph = annotations[i].graph;
- aa.graphGroup = annotations[i].graphGroup;
- aa.graphHeight = annotations[i].graphHeight;
- if (annotations[i].getThreshold() != null)
+ AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label,
+ annotation.description, anots);
+ aa.graph = annotation.graph;
+ aa.graphGroup = annotation.graphGroup;
+ aa.graphHeight = annotation.graphHeight;
+ if (annotation.getThreshold() != null)
{
- aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i]
+ aa.setThreshold(new GraphLine(annotation
.getThreshold()));
}
- if (annotations[i].hasScore)
+ if (annotation.hasScore)
{
- aa.setScore(annotations[i].getScore());
+ aa.setScore(annotation.getScore());
}
- if (annotations[i].sequenceRef != null)
+
+ final SequenceI seqRef = annotation.sequenceRef;
+ if (seqRef != null)
{
- SequenceI aaSeq = codons
- .getAaForDnaSeq(annotations[i].sequenceRef);
+ SequenceI aaSeq = acf.getAaForDnaSeq(seqRef);
if (aaSeq != null)
{
// aa.compactAnnotationArray(); // throw away alignment annotation
// positioning
aa.setSequenceRef(aaSeq);
- aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild
- // mapping
+ // rebuild mapping
+ aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true);
aa.adjustForAlignment();
aaSeq.addAlignmentAnnotation(aa);
}
-
}
al.addAnnotation(aa);
}
}
}
- private static Annotation getCodonAnnotation(int[] is,
+ private static Annotation getCodonAnnotation(AlignedCodon is,
Annotation[] annotations)
{
// Have a look at all the codon positions for annotation and put the first
// one found into the translated annotation pos.
int contrib = 0;
Annotation annot = null;
- for (int p = 0; p < 3; p++)
+ for (int p = 1; p <= 3; p++)
{
- if (annotations[is[p]] != null)
+ int dnaCol = is.getBaseColumn(p);
+ if (annotations[dnaCol] != null)
{
if (annot == null)
{
- annot = new Annotation(annotations[is[p]]);
+ annot = new Annotation(annotations[dnaCol]);
contrib = 1;
}
else
{
// merge with last
- Annotation cpy = new Annotation(annotations[is[p]]);
+ Annotation cpy = new Annotation(annotations[dnaCol]);
if (annot.colour == null)
{
annot.colour = cpy.colour;
}
if (contrib > 1)
{
- annot.value /= (float) contrib;
+ annot.value /= contrib;
}
return annot;
}
* sequence displayed under viscontigs visible columns
* @param seqstring
* ORF read in some global alignment reference frame
- * @param viscontigs
- * mapping from global reference frame to visible seqstring ORF read
- * @param codons
- * Definition of global ORF alignment reference frame
- * @param gapCharacter
- * @return sequence ready to be added to alignment.
- * @deprecated Use
- * {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)}
- * instead
- */
- public static SequenceI translateCodingRegion(SequenceI selection,
- String seqstring, int[] viscontigs, AlignedCodonFrame codons,
- char gapCharacter, DBRefEntry product)
- {
- return translateCodingRegion(selection, seqstring, viscontigs, codons,
- gapCharacter, product, false);
- }
-
- /**
- * Translate a na sequence
- *
- * @param selection
- * sequence displayed under viscontigs visible columns
- * @param seqstring
- * ORF read in some global alignment reference frame
- * @param viscontigs
- * mapping from global reference frame to visible seqstring ORF read
- * @param codons
+ * @param acf
* Definition of global ORF alignment reference frame
- * @param gapCharacter
- * @param starForStop
- * when true stop codons will translate as '*', otherwise as 'X'
+ * @param proteinSeqs
* @return sequence ready to be added to alignment.
*/
- public static SequenceI translateCodingRegion(SequenceI selection,
- String seqstring, int[] viscontigs, AlignedCodonFrame codons,
- char gapCharacter, DBRefEntry product, final boolean starForStop)
+ protected SequenceI translateCodingRegion(SequenceI selection,
+ String seqstring, AlignedCodonFrame acf,
+ List<SequenceI> proteinSeqs)
{
- java.util.List skip = new ArrayList();
+ List<int[]> skip = new ArrayList<int[]>();
int skipint[] = null;
ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
// intervals
- int vc, scontigs[] = new int[viscontigs.length];
+ int vc;
+ int[] scontigs = new int[contigs.length];
int npos = 0;
- for (vc = 0; vc < viscontigs.length; vc += 2)
+ for (vc = 0; vc < contigs.length; vc += 2)
{
if (vc == 0)
{
- vismapping.addShift(npos, viscontigs[vc]);
+ vismapping.addShift(npos, contigs[vc]);
}
else
{
// hidden region
- vismapping.addShift(npos, viscontigs[vc] - viscontigs[vc - 1] + 1);
+ vismapping.addShift(npos, contigs[vc] - contigs[vc - 1] + 1);
}
- scontigs[vc] = viscontigs[vc];
- scontigs[vc + 1] = viscontigs[vc + 1];
+ scontigs[vc] = contigs[vc];
+ scontigs[vc + 1] = contigs[vc + 1];
}
- StringBuffer protein = new StringBuffer();
- String seq = seqstring.replace('U', 'T');
+ // allocate a roughly sized buffer for the protein sequence
+ StringBuilder protein = new StringBuilder(seqstring.length() / 2);
+ String seq = seqstring.replace('U', 'T').replace('u', 'T');
char codon[] = new char[3];
- int cdp[] = new int[3], rf = 0, lastnpos = 0, nend;
+ int cdp[] = new int[3];
+ int rf = 0;
+ int lastnpos = 0;
+ int nend;
int aspos = 0;
int resSize = 0;
for (npos = 0, nend = seq.length(); npos < nend; npos++)
{
- if (!jalview.util.Comparison.isGap(seq.charAt(npos)))
+ if (!Comparison.isGap(seq.charAt(npos)))
{
cdp[rf] = npos; // store position
codon[rf++] = seq.charAt(npos); // store base
}
- // filled an RF yet ?
if (rf == 3)
{
+ /*
+ * Filled up a reading frame...
+ */
+ AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
String aa = ResidueProperties.codonTranslate(new String(codon));
rf = 0;
+ final String gapString = String.valueOf(gapChar);
if (aa == null)
{
- aa = String.valueOf(gapCharacter);
+ aa = gapString;
if (skipint == null)
{
skipint = new int[]
- { cdp[0], cdp[2] };
+ { alignedCodon.pos1, alignedCodon.pos3 /* cdp[0], cdp[2] */};
}
- skipint[1] = cdp[2];
+ skipint[1] = alignedCodon.pos3; // cdp[2];
}
else
{
}
if (aa.equals("STOP"))
{
- aa = starForStop ? "*" : "X";
+ aa = STOP_X;
}
resSize++;
}
- // insert/delete gaps prior to this codon - if necessary
boolean findpos = true;
while (findpos)
{
- // first ensure that the codons array is long enough.
- codons.checkCodonFrameWidth(aspos);
- // now check to see if we place the aa at the current aspos in the
- // protein alignment
- switch (Dna.compare_codonpos(cdp, codons.codons[aspos]))
+ /*
+ * Compare this codon's base positions with those currently aligned to
+ * this column in the translation.
+ */
+ final int compareCodonPos = compareCodonPos(alignedCodon,
+ alignedCodons[aspos]);
+ switch (compareCodonPos)
{
case -1:
- codons.insertAAGap(aspos, gapCharacter);
+
+ /*
+ * This codon should precede the mapped positions - need to insert a
+ * gap in all prior sequences.
+ */
+ insertAAGap(aspos, proteinSeqs);
findpos = false;
break;
+
case +1:
- // this aa appears after the aligned codons at aspos, so prefix it
- // with a gap
- aa = "" + gapCharacter + aa;
+
+ /*
+ * This codon belongs after the aligned codons at aspos. Prefix it
+ * with a gap and try the next position.
+ */
+ aa = gapString + aa;
aspos++;
- // if (aspos >= codons.aaWidth)
- // codons.aaWidth = aspos + 1;
- break; // check the next position for alignment
+ break;
+
case 0:
- // codon aligns at aspos position.
+
+ /*
+ * Exact match - codon 'belongs' at this translated position.
+ */
findpos = false;
}
}
- // codon aligns with all other sequence residues found at aspos
protein.append(aa);
lastnpos = npos;
- if (codons.codons[aspos] == null)
+ if (alignedCodons[aspos] == null)
{
// mark this column as aligning to this aligned reading frame
- codons.codons[aspos] = new int[]
- { cdp[0], cdp[1], cdp[2] };
+ alignedCodons[aspos] = alignedCodon;
+ }
+ else if (!alignedCodons[aspos].equals(alignedCodon))
+ {
+ throw new IllegalStateException("Tried to coalign "
+ + alignedCodons[aspos].toString() + " with "
+ + alignedCodon.toString());
}
- if (aspos >= codons.aaWidth)
+ if (aspos >= aaWidth)
{
// update maximum alignment width
- // (we can do this without calling checkCodonFrameWidth because it was
- // already done above)
- codons.setAaWidth(aspos);
+ aaWidth = aspos;
}
// ready for next translated reading frame alignment position (if any)
aspos++;
protein.toString());
if (rf != 0)
{
- if (jalview.bin.Cache.log != null)
+ final String errMsg = "trimming contigs for incomplete terminal codon.";
+ if (Cache.log != null)
{
- jalview.bin.Cache.log
- .debug("trimming contigs for incomplete terminal codon.");
+ Cache.log.debug(errMsg);
}
else
{
- System.err
- .println("trimming contigs for incomplete terminal codon.");
+ System.err.println(errMsg);
}
// map and trim contigs to ORF region
vc = scontigs.length - 1;
scontigs = t;
}
if (vc <= 0)
+ {
scontigs = null;
+ }
}
if (scontigs != null)
{
scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
if (scontigs[vc + 1] == selection.getEnd())
+ {
break;
+ }
}
// trim trailing empty intervals.
if ((vc + 2) < scontigs.length)
MapList map = new MapList(scontigs, new int[]
{ 1, resSize }, 3, 1);
- // update newseq as if it was generated as mapping from product
-
- if (product != null)
- {
- newseq.setName(product.getSource() + "|"
- + product.getAccessionId());
- if (product.getMap() != null)
- {
- // Mapping mp = product.getMap();
- // newseq.setStart(mp.getPosition(scontigs[0]));
- // newseq.setEnd(mp
- // .getPosition(scontigs[scontigs.length - 1]));
- }
- }
transferCodedFeatures(selection, newseq, map, null, null);
- SequenceI rseq = newseq.deriveSequence(); // construct a dataset
- // sequence for our new
- // peptide, regardless.
- // store a mapping (this actually stores a mapping between the dataset
- // sequences for the two sequences
- codons.addMap(selection, rseq, map);
+
+ /*
+ * Construct a dataset sequence for our new peptide.
+ */
+ SequenceI rseq = newseq.deriveSequence();
+
+ /*
+ * Store a mapping (between the dataset sequences for the two
+ * sequences).
+ */
+ // SIDE-EFFECT: acf stores the aligned sequence reseq; to remove!
+ acf.addMap(selection, rseq, map);
return rseq;
}
}
}
/**
+ * Insert a gap into the aligned proteins and the codon mapping array.
+ *
+ * @param pos
+ * @param proteinSeqs
+ * @return
+ */
+ protected void insertAAGap(int pos,
+ List<SequenceI> proteinSeqs)
+ {
+ aaWidth++;
+ for (SequenceI seq : proteinSeqs)
+ {
+ seq.insertCharAt(pos, gapChar);
+ }
+
+ checkCodonFrameWidth();
+ if (pos < aaWidth)
+ {
+ aaWidth++;
+
+ /*
+ * Shift from [pos] to the end one to the right, and null out [pos]
+ */
+ System.arraycopy(alignedCodons, pos, alignedCodons, pos + 1,
+ alignedCodons.length - pos - 1);
+ alignedCodons[pos] = null;
+ }
+ }
+
+ /**
+ * Check the codons array can accommodate a single insertion, if not resize
+ * it.
+ */
+ protected void checkCodonFrameWidth()
+ {
+ if (alignedCodons[alignedCodons.length - 1] != null)
+ {
+ /*
+ * arraycopy insertion would bump a filled slot off the end, so expand.
+ */
+ AlignedCodon[] c = new AlignedCodon[alignedCodons.length + 10];
+ System.arraycopy(alignedCodons, 0, c, 0, alignedCodons.length);
+ alignedCodons = c;
+ }
+ }
+
+ /**
* Given a peptide newly translated from a dna sequence, copy over and set any
* features on the peptide from the DNA. If featureTypes is null, all features
* on the dna sequence are searched (rather than just the displayed ones), and
* @param pep
* @param map
* @param featureTypes
- * hash who's keys are the displayed feature type strings
+ * hash whose keys are the displayed feature type strings
* @param featureGroups
* hash where keys are feature groups and values are Boolean objects
* indicating if they are displayed.
*/
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
- MapList map, Hashtable featureTypes, Hashtable featureGroups)
+ MapList map, Map<String, Object> featureTypes,
+ Map<String, Boolean> featureGroups)
{
- SequenceFeature[] sf = (dna.getDatasetSequence() != null ? dna
- .getDatasetSequence() : dna).getSequenceFeatures();
+ SequenceFeature[] sfs = dna.getSequenceFeatures();
Boolean fgstate;
- jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
- .selectRefs(dna.getDBRef(),
- jalview.datamodel.DBRefSource.DNACODINGDBS);
+ DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+ DBRefSource.DNACODINGDBS);
if (dnarefs != null)
{
// intersect with pep
}
}
}
- if (sf != null)
+ if (sfs != null)
{
- for (int f = 0; f < sf.length; f++)
+ for (SequenceFeature sf : sfs)
{
- fgstate = (featureGroups == null) ? null : ((Boolean) featureGroups
- .get(sf[f].featureGroup));
- if ((featureTypes == null || featureTypes.containsKey(sf[f]
- .getType())) && (fgstate == null || fgstate.booleanValue()))
+ fgstate = (featureGroups == null) ? null : featureGroups
+ .get(sf.featureGroup);
+ if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
+ && (fgstate == null || fgstate.booleanValue()))
{
- if (FeatureProperties.isCodingFeature(null, sf[f].getType()))
+ if (FeatureProperties.isCodingFeature(null, sf.getType()))
{
// if (map.intersectsFrom(sf[f].begin, sf[f].end))
{
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* Routines for approximate Sequence Id resolution by name using string
}
}
+ @Override
public int hashCode()
{
return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
.hashCode());
}
+ @Override
public boolean equals(Object s)
{
+ if (s == null)
+ {
+ return false;
+ }
if (s instanceof SeqIdName)
{
return this.equals((SeqIdName) s);
*/
package jalview.analysis;
-import java.util.*;
-
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.util.Format;
-import jalview.datamodel.*;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
/**
* Takes in a vector or array of sequences and column start and column end and
*/
public class StructureFrequency
{
+ public static final int STRUCTURE_PROFILE_LENGTH = 74;
+
// No need to store 1000s of strings which are not
// visible to the user.
public static final String MAXCOUNT = "C";
// UPDATE this for new values
if (profile)
{
+ // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
residueHash.put(PROFILE, new int[][]
{ values, new int[]
{ jSize, (jSize - values['-']) } });
* ((c == 0) ? "" : "; ") + alphabet[c] + " " + ((int) tval) + "%"; } }
* else {
*/
- Object[] ca = new Object[625];
+ int[][] ca = new int[625][];
float[] vl = new float[625];
int x = 0;
for (int c = 65; c < 90; c++)
jalview.util.QuickSort.sort(vl, ca);
int p = 0;
+ /*
+ * profile[1] is {total, ungappedTotal}
+ */
+ final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)
{
- tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0]);
- mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
- + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval)
+ tval = (vl[c] * 100f / divisor);
+ mouseOver += ((p == 0) ? "" : "; ") + (char) ca[c][0]
+ + (char) ca[c][1] + " " + fmt.form(tval)
+ "%";
p++;
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
- int[] rtnval = new int[74]; // 2*(5*5)+2
+ int[] rtnval = new int[STRUCTURE_PROFILE_LENGTH]; // 2*(5*5)+2
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
if (profile == null)
+ {
return null;
+ }
// TODO fix the object length, also do it in completeConsensus
- Object[] ca = new Object[625];
+ // Object[] ca = new Object[625];
+ int[][] ca = new int[625][];
float[] vl = new float[625];
int x = 0;
for (int c = 65; c < 90; c++)
}
jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 2;
+ int valuesCount = 0;
rtnval[1] = 0;
+ int offset = 2;
+ final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)
{
- rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
- rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
- rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0]);
- rtnval[1] += rtnval[rtnval[0]++];
+ rtnval[offset++] = ca[c][0];
+ rtnval[offset++] = ca[c][1];
+ rtnval[offset] = (int) (vl[c] * 100f / divisor);
+ rtnval[1] += rtnval[offset++];
+ valuesCount++;
}
}
+ rtnval[0] = valuesCount;
- return rtnval;
+ // insert profile type code in position 0
+ int[] result = new int[rtnval.length + 1];
+ result[0] = AlignmentAnnotation.STRUCTURE_PROFILE;
+ System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+ return result;
}
public static void main(String args[])
* @author jimp
*
*/
-public interface AlignViewportI
+public interface AlignViewportI extends ViewStyleI
{
int getCharWidth();
Hashtable[] getSequenceConsensusHash();
- Hashtable[] getRnaStructureConsensusHash();
+ /**
+ * Get consensus data table for the cDNA complement of this alignment (if any)
+ *
+ * @return
+ */
+ Hashtable[] getComplementConsensusHash();
- boolean getIgnoreGapsConsensus();
+ Hashtable[] getRnaStructureConsensusHash();
- boolean getCentreColumnLabels();
+ boolean isIgnoreGapsConsensus();
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for cDNA complement consensus annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getComplementConsensusAnnotation();
+
+ /**
* Test to see if viewport is still open and active
*
* @return true indicates that all references to viewport should be dropped
void setSequenceConsensusHash(Hashtable[] hconsensus);
/**
+ * Set the cDNA complement consensus for the viewport
+ *
+ * @param hconsensus
+ */
+ void setComplementConsensusHash(Hashtable[] hconsensus);
+
+ /**
*
* @return the alignment annotatino row for the structure consensus
* calculation
* first column (inclusive, from 0)
* @param max
* last column (exclusive)
- * @return int[][] range of {start,end} visible positions TODO: change to list
- * of int ranges
+ * @return int[][] range of {start,end} visible positions
*/
- int[][] getVisibleRegionBoundaries(int min, int max);
+ List<int[]> getVisibleRegionBoundaries(int min, int max);
/**
* This method returns an array of new SequenceI objects derived from the
boolean hasHiddenRows();
+ /**
+ *
+ * @return a copy of this view's current display settings
+ */
+ public ViewStyleI getViewStyle();
+
+ /**
+ * update the view's display settings with the given style set
+ *
+ * @param settingsForView
+ */
+ public void setViewStyle(ViewStyleI settingsForView);
+
+ /**
+ * Returns a viewport which holds the cDna for this (protein), or vice versa,
+ * or null if none is set.
+ *
+ * @return
+ */
+ AlignViewportI getCodingComplement();
+
+ /**
+ * Sets the viewport which holds the cDna for this (protein), or vice versa.
+ * Implementation should guarantee that the reciprocal relationship is always
+ * set, i.e. each viewport is the complement of the other.
+ */
+ void setCodingComplement(AlignViewportI sl);
+
+ /**
+ * Answers true if viewport hosts DNA/RNA, else false.
+ *
+ * @return
+ */
+ boolean isNucleotide();
+
+ /**
+ * Returns an id guaranteed to be unique for this viewport.
+ *
+ * @return
+ */
+ String getViewId();
}
public interface AlignmentViewPanel extends OOMHandlerI
{
+ AlignViewportI getAlignViewport();
+
AlignmentI getAlignment();
StructureSelectionManager getStructureSelectionManager();
--- /dev/null
+package jalview.api;
+
+import jalview.datamodel.AlignmentI;
+
+/**
+ * Describes a visual container that can show two alignments.
+ *
+ * @author gmcarstairs
+ *
+ */
+public interface SplitContainerI
+{
+
+ /**
+ * Set visibility of the specified split view component.
+ *
+ * @param alignFrame
+ * @param show
+ */
+ // TODO need an interface for AlignFrame?
+ void setComplementVisible(Object alignFrame, boolean show);
+
+ /**
+ * Returns the alignment that is complementary to the one in the given
+ * AlignFrame, or null.
+ */
+ AlignmentI getComplement(Object af);
+
+ /**
+ * Returns the frame title for the alignment that is complementary to the one
+ * in the given AlignFrame, or null.
+ *
+ * @param af
+ * @return
+ */
+ String getComplementTitle(Object af);
+
+}
--- /dev/null
+package jalview.api;
+
+import java.awt.Color;
+
+public interface ViewStyleI
+{
+
+ void setColourAppliesToAllGroups(boolean b);
+
+ boolean getColourAppliesToAllGroups();
+
+ boolean getAbovePIDThreshold();
+
+ void setIncrement(int inc);
+
+ int getIncrement();
+
+ boolean getConservationSelected();
+
+ void setConservationSelected(boolean b);
+
+ void setShowHiddenMarkers(boolean show);
+
+ boolean getShowHiddenMarkers();
+
+ void setScaleRightWrapped(boolean b);
+
+ void setScaleLeftWrapped(boolean b);
+
+ void setScaleAboveWrapped(boolean b);
+
+ boolean getScaleLeftWrapped();
+
+ boolean getScaleAboveWrapped();
+
+ boolean getScaleRightWrapped();
+
+ void setAbovePIDThreshold(boolean b);
+
+ void setThreshold(int thresh);
+
+ int getThreshold();
+
+ boolean getShowJVSuffix();
+
+ void setShowJVSuffix(boolean b);
+
+ void setWrapAlignment(boolean state);
+
+ void setShowText(boolean state);
+
+ void setRenderGaps(boolean state);
+
+ boolean getColourText();
+
+ void setColourText(boolean state);
+
+ void setShowBoxes(boolean state);
+
+ boolean getWrapAlignment();
+
+ boolean getShowText();
+
+ int getWrappedWidth();
+
+ void setWrappedWidth(int w);
+
+ int getCharHeight();
+
+ void setCharHeight(int h);
+
+ int getCharWidth();
+
+ void setCharWidth(int w);
+
+ boolean getShowBoxes();
+
+ boolean getShowUnconserved();
+
+ void setShowUnconserved(boolean showunconserved);
+
+ boolean isDisplayReferenceSeq();
+
+ void setDisplayReferenceSeq(boolean displayReferenceSeq);
+
+ boolean isColourByReferenceSeq();
+
+ void setSeqNameItalics(boolean default1);
+
+ void setShowSequenceFeatures(boolean b);
+
+ boolean isShowSequenceFeatures();
+
+ boolean isRightAlignIds();
+
+ void setRightAlignIds(boolean rightAlignIds);
+
+ boolean isShowAnnotation();
+
+ void setShowAnnotation(boolean b);
+
+ void setShowSeqFeaturesHeight(boolean selected);
+
+ boolean isShowSequenceFeaturesHeight();
+
+ void setColourByReferenceSeq(boolean colourByReferenceSeq);
+
+ Color getTextColour();
+
+ Color getTextColour2();
+
+ int getThresholdTextColour();
+
+ boolean isConservationColourSelected();
+
+ boolean isRenderGaps();
+
+ boolean isShowColourText();
+
+ boolean isShowSeqFeaturesHeight();
+
+ void setConservationColourSelected(boolean conservationColourSelected);
+
+ void setShowColourText(boolean showColourText);
+
+ void setTextColour(Color textColour);
+
+ void setThresholdTextColour(int thresholdTextColour);
+
+ void setTextColour2(Color textColour2);
+
+ boolean isSeqNameItalics();
+
+ void setUpperCasebold(boolean upperCasebold);
+
+ boolean isUpperCasebold();
+
+ boolean sameStyle(ViewStyleI them);
+
+ void setFontName(String name);
+
+ void setFontStyle(int style);
+
+ void setFontSize(int size);
+
+ int getFontStyle();
+
+ String getFontName();
+
+ int getFontSize();
+
+ /**
+ * @return width of Sequence and Annotation ID margin. If less than zero, then
+ * width will be autocalculated
+ */
+ int getIdWidth();
+
+ /**
+ * Set width if
+ *
+ * @param i
+ */
+
+ void setIdWidth(int i);
+
+ /**
+ * centre columnar annotation labels in displayed alignment annotation
+ */
+ boolean isCentreColumnLabels();
+
+ /**
+ * centre columnar annotation labels in displayed alignment annotation
+ */
+ void setCentreColumnLabels(boolean centreColumnLabels);
+
+ /**
+ * enable or disable the display of Database Cross References in the sequence
+ * ID tooltip
+ */
+ void setShowDBRefs(boolean showdbrefs);
+
+ /**
+ *
+ * @return true if Database References are to be displayed on tooltips.
+ */
+ boolean isShowDBRefs();
+
+ /**
+ *
+ * @return true if Non-positional features are to be displayed on tooltips.
+ */
+ boolean isShowNPFeats();
+
+ /**
+ * enable or disable the display of Non-Positional sequence features in the
+ * sequence ID tooltip
+ *
+ * @param show
+ */
+ void setShowNPFeats(boolean shownpfeats);
+
+}
*/
package jalview.appletgui;
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.Vector;
-
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
{
+ private static final String ALL_ANNOTATIONS = "All";
+
Menu groupMenu = new Menu();
MenuItem editGroupName = new MenuItem();
CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
+ Menu seqShowAnnotationsMenu = new Menu(
+ MessageManager.getString("label.show_annotations"));
+
+ Menu seqHideAnnotationsMenu = new Menu(
+ MessageManager.getString("label.hide_annotations"));
+
+ MenuItem seqAddReferenceAnnotations = new MenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
+ Menu groupShowAnnotationsMenu = new Menu(
+ MessageManager.getString("label.show_annotations"));
+
+ Menu groupHideAnnotationsMenu = new Menu(
+ MessageManager.getString("label.hide_annotations"));
+
+ MenuItem groupAddReferenceAnnotations = new MenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
Menu editMenu = new Menu(MessageManager.getString("action.edit"));
- MenuItem copy = new MenuItem(
- MessageManager.getString("label.jalview_copy"));
+ MenuItem copy = new MenuItem(MessageManager.getString("action.copy"));
- MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
+ MenuItem cut = new MenuItem(MessageManager.getString("action.cut"));
MenuItem toUpper = new MenuItem(
MessageManager.getString("label.to_upper_case"));
MenuItem makeReferenceSeq = new MenuItem();
- Sequence seq;
+ SequenceI seq;
MenuItem revealAll = new MenuItem();
Menu menu1 = new Menu();
- public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
+ public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
+ Vector<String> links)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
outputmenu.add(item);
}
- SequenceGroup sg = ap.av.getSelectionGroup();
+ buildAnnotationSubmenus();
+ SequenceGroup sg = ap.av.getSelectionGroup();
if (sg != null && sg.getSize() > 0)
{
editGroupName.setLabel(MessageManager.formatMessage(
- "label.name_param", new String[]
+ "label.name_param", new Object[]
{ sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
if (links != null && links.size() > 0)
{
Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- String link;
for (int i = 0; i < links.size(); i++)
{
- link = links.elementAt(i).toString();
+ String link = links.elementAt(i);
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
.getString("action.set_as_reference")); // );
}
repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
+ "label.represent_group_with", new Object[]
{ seq.getName() }));
}
else
}
/**
+ * Build menus for annotation types that may be shown or hidden, and for
+ * 'reference annotations' that may be added to the alignment.
+ */
+ private void buildAnnotationSubmenus()
+ {
+ /*
+ * First for the currently selected sequence (if there is one):
+ */
+ final List<SequenceI> selectedSequence = (seq == null ? Collections
+ .<SequenceI> emptyList() : Arrays.asList(seq));
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * and repeat for the current selection group (if there is one):
+ */
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
+ .<SequenceI> emptyList() : ap.av.getSelectionGroup()
+ .getSequences());
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,
+ groupHideAnnotationsMenu, selectedGroup);
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
+ selectedGroup);
+ }
+
+ /**
+ * Determine whether or not to enable 'add reference annotations' menu item.
+ * It is enable if there are any annotations, on any of the selected
+ * sequences, which are not yet on the alignment (visible or not).
+ *
+ * @param menu
+ * @param forSequences
+ */
+ private void configureReferenceAnnotationsMenu(MenuItem menuItem,
+ List<SequenceI> forSequences)
+ {
+ menuItem.setEnabled(false);
+
+ /*
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.
+ * Using TreeMap means calcIds are shown in alphabetical order.
+ */
+ Map<String, String> tipEntries = new TreeMap<String, String>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences,
+ tipEntries, candidates, al);
+ if (!candidates.isEmpty())
+ {
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its action.
+ */
+ menuItem.setEnabled(true);
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
+ }
+
+ /**
+ * Add annotations to the sequences and to the alignment.
+ *
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
+ */
+ protected void addReferenceAnnotations_actionPerformed(
+ Map<SequenceI, List<AlignmentAnnotation>> candidates)
+ {
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
+ refresh();
+ }
+
+ /**
* add a show URL menu item to the given linkMenu
*
* @param linkMenu
{
if (seq == null)
{
- seq = (Sequence) sg.getSequenceAt(0);
+ seq = sg.getSequenceAt(0);
}
EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
else if (source == toUpper || source == toLower || source == toggleCase)
{
SequenceGroup sg = ap.av.getSelectionGroup();
- Vector regions = new Vector();
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
sg.getStartRes(), sg.getEndRes() + 1);
String description;
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.selection_output_command", new String[]
+ "label.selection_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(),
- ap.av.showJVSuffix, ap.av, true));
+ e.getActionCommand(), ap.av.getShowJVSuffix(), ap.av, true));
}
for (SequenceI seq : sequences)
{
contents.append(MessageManager.formatMessage(
- "label.annotation_for_displayid", new String[]
+ "label.annotation_for_displayid", new Object[]
{ seq.getDisplayId(true) }));
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
+ (sequences.length == 1 ? sequences[0].getDisplayId(true)
: "Selection"), 600, 500);
cap.setText(MessageManager.formatMessage("label.html_content",
- new String[]
+ new Object[]
{ contents.toString() }));
}
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new Sequence[]
+ new jalview.appletgui.AppletJmol(entry, new SequenceI[]
{ seq }, null, ap, AppletFormatAdapter.URL);
}
else
{
- new MCview.AppletPDBViewer(entry, new Sequence[]
+ new MCview.AppletPDBViewer(entry, new SequenceI[]
{ seq }, null, ap, AppletFormatAdapter.URL);
}
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.paste_pdb_file_for_sequence", new String[]
+ "label.paste_pdb_file_for_sequence", new Object[]
{ seq.getName() }), 400, 300);
}
}
pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
+ "label.represent_group_with", new Object[]
{ "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
this.add(revealSeq);
this.add(revealAll);
// groupMenu.add(selSeqDetails);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputmenu);
groupMenu.add(sequenceFeature);
editMenu.add(toLower);
toLower.addActionListener(this);
editMenu.add(toggleCase);
+ seqMenu.add(seqShowAnnotationsMenu);
+ seqMenu.add(seqHideAnnotationsMenu);
+ seqMenu.add(seqAddReferenceAnnotations);
seqMenu.add(sequenceName);
seqMenu.add(makeReferenceSeq);
// seqMenu.add(sequenceDetails);
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
else
// remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
refresh();
ap.av.sendSelection();
}
+ /**
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection. Separate menus are built for
+ * the selected sequence group (if any), and the selected sequence.
+ * <p>
+ * Some annotation rows are always rendered together - these can be identified
+ * by a common graphGroup property > -1. Only one of each group will be marked
+ * as visible (to avoid duplication of the display). For such groups we add a
+ * composite type name, e.g.
+ * <p>
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(Menu showMenu, Menu hideMenu,
+ List<SequenceI> forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
+ false);
+ showMenu.addSeparator();
+ hideMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
+ * the insertion order, which is the order of the annotations on the
+ * alignment.
+ */
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
+ hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations),
+ forSequences);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List<String> type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showMenu, forSequences,
+ calcId, type, false, true);
+ }
+ }
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
+
+ for (String calcId : shownTypes.keySet())
+ {
+ for (List<String> type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideMenu, forSequences,
+ calcId, type, false, false);
+ }
+ }
+ // grey out 'hide annotations' if none are shown
+ hideMenu.setEnabled(!shownTypes.isEmpty());
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @param forSequences
+ * the sequences whose annotations may be shown or hidden
+ * @param calcId
+ * @param types
+ * the label to add
+ * @param allTypes
+ * if true this is a special label meaning 'All'
+ * @param actionIsShow
+ * if true, the select menu item action is to show the annotation
+ * type, else hide
+ */
+ protected void addAnnotationTypeToShowHide(Menu showOrHideMenu,
+ final List<SequenceI> forSequences, String calcId,
+ final List<String> types, final boolean allTypes,
+ final boolean actionIsShow)
+ {
+ String label = types.toString(); // [a, b, c]
+ label = label.substring(1, label.length() - 1);
+ final MenuItem item = new MenuItem(label);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
+ forSequences, allTypes, actionIsShow);
+ refresh();
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
}
*/
package jalview.appletgui;
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
-import java.awt.BorderLayout;
-import java.awt.Canvas;
-import java.awt.CheckboxMenuItem;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Label;
-import java.awt.Menu;
-import java.awt.MenuBar;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
String jalviewServletURL;
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
+ /*
+ * Flag for showing autocalculated consensus above or below other consensus
+ * rows
+ */
+ private boolean showAutoCalculatedAbove;
+
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ /**
+ * Constructor that creates the frame and adds it to the display.
+ *
+ * @param al
+ * @param applet
+ * @param title
+ * @param embedded
+ */
+ public AlignFrame(AlignmentI al, JalviewLite applet,
String title, boolean embedded)
{
+ this(al, applet, title, embedded, true);
+ }
+
+ /**
+ * Constructor that optionally allows the frame to be displayed or only
+ * created.
+ *
+ * @param al
+ * @param applet
+ * @param title
+ * @param embedded
+ * @param addToDisplay
+ */
+ public AlignFrame(AlignmentI al, JalviewLite applet,
+ String title, boolean embedded, boolean addToDisplay)
+ {
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
- annotationPanelMenuItem.setState(viewport.showAnnotation);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.getFollowHighlight());
showGroupConsensus.setState(viewport.isShowGroupConsensus());
showSequenceLogo.setState(viewport.isShowSequenceLogo());
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+ showAlignmentAnnotations.setState(viewport.isShowAnnotation());
+ showSequenceAnnotations.setState(viewport.isShowAnnotation());
- seqLimits.setState(viewport.showJVSuffix);
+ seqLimits.setState(viewport.getShowJVSuffix());
if (applet != null)
{
alignPanel.annotationPanelHolder.addKeyListener(this);
alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
alignPanel.alabels.addKeyListener(this);
- createAlignFrameWindow(embedded, title);
+ if (addToDisplay)
+ {
+ addToDisplay(embedded);
+ }
+ }
+
+ /**
+ * @param embedded
+ */
+ public void addToDisplay(boolean embedded)
+ {
+ createAlignFrameWindow(embedded);
validate();
alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true);
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(true);
}
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(false);
}
@Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == displayNonconservedMenuItem)
+ final Object source = evt.getSource();
+ if (source == displayNonconservedMenuItem)
{
displayNonconservedMenuItem_actionPerformed();
}
- else if (evt.getSource() == colourTextMenuItem)
+ else if (source == colourTextMenuItem)
{
colourTextMenuItem_actionPerformed();
}
- else if (evt.getSource() == wrapMenuItem)
+ else if (source == wrapMenuItem)
{
wrapMenuItem_actionPerformed();
}
- else if (evt.getSource() == scaleAbove)
+ else if (source == scaleAbove)
{
viewport.setScaleAboveWrapped(scaleAbove.getState());
}
- else if (evt.getSource() == scaleLeft)
+ else if (source == scaleLeft)
{
viewport.setScaleLeftWrapped(scaleLeft.getState());
}
- else if (evt.getSource() == scaleRight)
+ else if (source == scaleRight)
{
viewport.setScaleRightWrapped(scaleRight.getState());
}
- else if (evt.getSource() == seqLimits)
+ else if (source == seqLimits)
{
seqLimits_itemStateChanged();
}
- else if (evt.getSource() == viewBoxesMenuItem)
+ else if (source == viewBoxesMenuItem)
{
viewport.setShowBoxes(viewBoxesMenuItem.getState());
}
- else if (evt.getSource() == viewTextMenuItem)
+ else if (source == viewTextMenuItem)
{
viewport.setShowText(viewTextMenuItem.getState());
}
- else if (evt.getSource() == renderGapsMenuItem)
+ else if (source == renderGapsMenuItem)
{
viewport.setRenderGaps(renderGapsMenuItem.getState());
}
- else if (evt.getSource() == annotationPanelMenuItem)
+ else if (source == annotationPanelMenuItem)
{
viewport.setShowAnnotation(annotationPanelMenuItem.getState());
alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
}
- else if (evt.getSource() == sequenceFeatures)
+ else if (source == sequenceFeatures)
{
viewport.setShowSequenceFeatures(sequenceFeatures.getState());
alignPanel.seqPanel.seqCanvas.repaint();
}
- else if (evt.getSource() == conservationMenuItem)
+ else if (source == showAlignmentAnnotations)
+ {
+ setAnnotationsVisibility();
+ }
+ else if (source == showSequenceAnnotations)
+ {
+ setAnnotationsVisibility();
+ }
+ else if (source == sortAnnBySequence)
+ {
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setState(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ setViewportAnnotationOrder();
+ }
+ else if (source == sortAnnByLabel)
+ {
+ boolean newState = sortAnnByLabel.getState();
+ sortAnnBySequence.setState(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ setViewportAnnotationOrder();
+ }
+ else if (source == showAutoFirst)
+ {
+ showAutoLast.setState(!showAutoFirst.getState());
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
+ setViewportAnnotationOrder();
+ }
+ else if (source == showAutoLast)
+ {
+ showAutoFirst.setState(!showAutoLast.getState());
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
+ setViewportAnnotationOrder();
+ }
+ else if (source == conservationMenuItem)
{
conservationMenuItem_actionPerformed();
}
- else if (evt.getSource() == abovePIDThreshold)
+ else if (source == abovePIDThreshold)
{
abovePIDThreshold_actionPerformed();
}
- else if (evt.getSource() == applyToAllGroups)
+ else if (source == applyToAllGroups)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
}
- else if (evt.getSource() == autoCalculate)
+ else if (source == autoCalculate)
{
viewport.autoCalculateConsensus = autoCalculate.getState();
}
- else if (evt.getSource() == sortByTree)
+ else if (source == sortByTree)
{
viewport.sortByTree = sortByTree.getState();
}
- else if (evt.getSource() == this.centreColumnLabelFlag)
+ else if (source == this.centreColumnLabelFlag)
{
centreColumnLabelFlag_stateChanged();
}
- else if (evt.getSource() == this.followMouseOverFlag)
+ else if (source == this.followMouseOverFlag)
{
mouseOverFlag_stateChanged();
}
- else if (evt.getSource() == showGroupConsensus)
+ else if (source == showGroupConsensus)
{
showGroupConsensus_actionPerformed();
}
- else if (evt.getSource() == showGroupConservation)
+ else if (source == showGroupConservation)
{
showGroupConservation_actionPerformed();
}
- else if (evt.getSource() == showSequenceLogo)
+ else if (source == showSequenceLogo)
{
showSequenceLogo_actionPerformed();
}
- else if (evt.getSource() == normSequenceLogo)
+ else if (source == normSequenceLogo)
{
normSequenceLogo_actionPerformed();
}
- else if (evt.getSource() == showConsensusHistogram)
+ else if (source == showConsensusHistogram)
{
showConsensusHistogram_actionPerformed();
}
- else if (evt.getSource() == applyAutoAnnotationSettings)
+ else if (source == applyAutoAnnotationSettings)
{
applyAutoAnnotationSettings_actionPerformed();
}
alignPanel.paintAlignment(true);
}
+ /**
+ * Set the visibility state of sequence-related and/or alignment-related
+ * annotations depending on checkbox selections. Repaint after calling.
+ *
+ * @param visible
+ */
+ private void setAnnotationsVisibility()
+ {
+ boolean showForAlignment = showAlignmentAnnotations.getState();
+ boolean showForSequences = showSequenceAnnotations.getState();
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ boolean visible = (aa.sequenceRef == null ? showForAlignment
+ : showForSequences);
+ aa.visible = visible;
+ }
+ alignPanel.validateAnnotationDimensions(false);
+ }
+
+ private void setAnnotationSortOrder(SequenceAnnotationOrder order)
+ {
+ this.annotationSortOrder = order;
+ }
+
+ /**
+ * Set flags on the viewport that control annotation ordering
+ */
+ private void setViewportAnnotationOrder()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
+ }
+
+ private void setShowAutoCalculatedAbove(boolean showAbove)
+ {
+ this.showAutoCalculatedAbove = showAbove;
+ }
+
private void mouseOverFlag_stateChanged()
{
viewport.followHighlight = followMouseOverFlag.getState();
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.alignment_output_command", new String[]
+ "label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
cap.setText(new AppletFormatAdapter().formatSequences(
e.getActionCommand(), viewport.getAlignment(),
- viewport.showJVSuffix));
+ viewport.getShowJVSuffix()));
}
public void loadAnnotations()
void updateEditMenuBar()
{
- if (viewport.historyList.size() > 0)
+ if (viewport.getHistoryList().size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
+ CommandI command = viewport.getHistoryList().peek();
undoMenuItem.setLabel(MessageManager.formatMessage(
- "label.undo_command", new String[]
+ "label.undo_command", new Object[]
{ command.getDescription() }));
}
else
undoMenuItem.setLabel(MessageManager.getString("action.undo"));
}
- if (viewport.redoList.size() > 0)
+ if (viewport.getRedoList().size() > 0)
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
+ CommandI command = viewport.getRedoList().peek();
redoMenuItem.setLabel(MessageManager.formatMessage(
- "label.redo_command", new String[]
+ "label.redo_command", new Object[]
{ command.getDescription() }));
}
else
{
if (command.getSize() > 0)
{
- viewport.historyList.push(command);
- viewport.redoList.removeAllElements();
+ viewport.addToHistoryList(command);
+ viewport.clearRedoList();
updateEditMenuBar();
viewport.updateHiddenColumns();
}
*/
protected void undoMenuItem_actionPerformed()
{
- if (viewport.historyList.size() < 1)
+ if (viewport.getHistoryList().isEmpty())
{
return;
}
- CommandI command = (CommandI) viewport.historyList.pop();
- viewport.redoList.push(command);
+ CommandI command = viewport.getHistoryList().pop();
+ viewport.addToRedoList(command);
command.undoCommand(null);
AlignViewport originalSource = getOriginatingSource(command);
*/
protected void redoMenuItem_actionPerformed()
{
- if (viewport.redoList.size() < 1)
+ if (viewport.getRedoList().isEmpty())
{
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
- viewport.historyList.push(command);
+ CommandI command = viewport.getRedoList().pop();
+ viewport.addToHistoryList(command);
command.doCommand(null);
AlignViewport originalSource = getOriginatingSource(command);
return originalSource;
}
+ /**
+ * Move the currently selected sequences up or down one position in the
+ * alignment
+ *
+ * @param up
+ */
public void moveSelectedSequences(boolean up)
{
SequenceGroup sg = viewport.getSelectionGroup();
viewport.getAlignment().moveSelectedSequencesByOne(sg,
up ? null : viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
+
+ /*
+ * Also move cDNA/protein complement sequences
+ */
+ AlignViewportI complement = viewport.getCodingComplement();
+ if (complement != null)
+ {
+ SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
+ viewport, complement);
+ complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
+ up ? null : complement.getHiddenRepSequences(), up);
+ // TODO need to trigger a repaint of the complementary panel - how?
+ // would prefer to handle in SplitFrame but it is not overriding key
+ // listener chiz
+ }
}
synchronized void slideSequences(boolean right, int size)
}
boolean appendHistoryItem = false;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ Deque<CommandI> historyList = viewport.getHistoryList();
+ if (historyList != null && historyList.size() > 0
+ && historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .appendSlideCommand((SlideSequencesCommand) historyList
.peek());
}
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
- Hashtable orderedSeqs = new Hashtable();
+ Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
int index = viewport.getAlignment().findIndex(seq);
- orderedSeqs.put(index + "", seq);
+ orderedSeqs.put(index, seq);
}
int index = 0, startRes, endRes;
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
for (int[] region : viewport.getColumnSelection().getHiddenColumns())
{
-
copiedHiddenColumns.addElement(new int[]
{ region[0] - hiddenOffset, region[1] - hiddenOffset });
}
while (seq == null)
{
- if (orderedSeqs.containsKey(index + ""))
+ if (orderedSeqs.containsKey(index))
{
- seq = (SequenceI) orderedSeqs.get(index + "");
+ seq = orderedSeqs.get(index);
index++;
-
break;
}
else
newaf.setTitle(title.toString());
- newaf.viewport.historyList = viewport.historyList;
- newaf.viewport.redoList = viewport.redoList;
+ newaf.viewport.setHistoryList(viewport.getHistoryList());
+ newaf.viewport.setRedoList(viewport.getRedoList());
return newaf;
}
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- List gps = fr.getFeatureGroups();
- int p=0;
- String[] _gps = new String[gps.size()];
- for (Object gp:gps)
- {
- _gps[p++] = gp.toString();
- }
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
return _gps;
}
return null;
if (alignPanel != null
&& (fr = alignPanel.getFeatureRenderer()) != null)
{
- List gps = fr.getGroups(visible);
- int p=0;
- String[] _gps = new String[gps.size()];
- for (Object gp:gps)
- {
- _gps[p++] = gp.toString();
- }
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
return _gps;
}
return null;
protected void displayNonconservedMenuItem_actionPerformed()
{
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+ viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
alignPanel.paintAlignment(true);
}
MenuItem closeMenuItem = new MenuItem(
MessageManager.getString("action.close"));
- Menu editMenu = new Menu(MessageManager.getString("action.edit"));
-
- Menu viewMenu = new Menu(MessageManager.getString("action.view"));
-
- Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
-
- Menu calculateMenu = new Menu(
- MessageManager.getString("action.calculate"));
-
MenuItem selectAllSequenceMenuItem = new MenuItem(
MessageManager.getString("action.select_all"));
public Label statusBar = new Label();
- Menu outputTextboxMenu = new Menu();
-
MenuItem clustalColour = new MenuItem();
MenuItem zappoColour = new MenuItem();
MenuItem modifyConservation = new MenuItem();
- CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
- "Autocalculate Consensus", true);
+ CheckboxMenuItem autoCalculate = null;
CheckboxMenuItem sortByTree = new CheckboxMenuItem(
"Sort Alignment With New Tree", true);
Menu sortByTreeMenu = new Menu();
- Menu sort = new Menu();
-
- Menu calculate = new Menu();
-
MenuItem inputText = new MenuItem();
- Menu helpMenu = new Menu();
-
MenuItem documentation = new MenuItem();
MenuItem about = new MenuItem();
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
- Menu autoAnnMenu = new Menu();
-
CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
+ /**
+ * Initialise menus and other items
+ *
+ * @throws Exception
+ */
private void jbInit() throws Exception
{
-
setMenuBar(alignFrameMenuBar);
- MenuItem item;
-
- // dynamically fill save as menu with available formats
+ /*
+ * Configure File menu items and actions
+ */
+ inputText
+ .setLabel(MessageManager.getString("label.input_from_textbox"));
+ inputText.addActionListener(this);
+ Menu outputTextboxMenu = new Menu(
+ MessageManager.getString("label.out_to_textbox"));
for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- item = new MenuItem(
+ MenuItem item = new MenuItem(
jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
item.addActionListener(new java.awt.event.ActionListener()
}
closeMenuItem.addActionListener(this);
loadApplication.addActionListener(this);
-
loadTree.addActionListener(this);
loadAnnotations.addActionListener(this);
outputFeatures.addActionListener(this);
outputAnnotations.addActionListener(this);
- selectAllSequenceMenuItem.addActionListener(this);
- deselectAllSequenceMenuItem.addActionListener(this);
- invertSequenceMenuItem.addActionListener(this);
+
+ /*
+ * Configure Edit menu items and actions
+ */
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
+ undoMenuItem.addActionListener(this);
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
+ redoMenuItem.addActionListener(this);
+ copy.setLabel(MessageManager.getString("action.copy"));
+ copy.addActionListener(this);
+ cut.setLabel(MessageManager.getString("action.cut"));
+ cut.addActionListener(this);
+ delete.setLabel(MessageManager.getString("action.delete"));
+ delete.addActionListener(this);
+ pasteMenu.setLabel(MessageManager.getString("action.paste"));
+ pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
+ pasteNew.addActionListener(this);
+ pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
+ pasteThis.addActionListener(this);
remove2LeftMenuItem.setLabel(MessageManager
.getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
removeAllGapsMenuItem.setLabel(MessageManager
.getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel(MessageManager
- .getString("action.by_pairwise_id"));
- sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
- sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel(MessageManager
- .getString("action.by_length"));
- sortLengthMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
- sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel(MessageManager
- .getString("action.remove_redundancy").concat("..."));
+ removeRedundancyMenuItem.setLabel(MessageManager.getString(
+ "action.remove_redundancy").concat("..."));
removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel(MessageManager
- .getString("action.pairwise_alignment"));
- pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel(MessageManager
- .getString("label.principal_component_analysis"));
- PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem.setLabel(MessageManager
- .getString("label.average_distance_identity"));
- averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel(MessageManager
- .getString("label.neighbour_joining_identity"));
- neighbourTreeMenuItem.addActionListener(this);
- statusBar.setBackground(Color.white);
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setLabel(MessageManager
- .getString("label.out_to_textbox"));
- clustalColour.setLabel(MessageManager.getString("label.clustalx"));
- clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(this);
- helixColour
- .setLabel(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(this);
- strandColour.setLabel(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(this);
- purinePyrimidineColour.setLabel(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(this);
- RNAInteractionColour.setLabel(MessageManager
- .getString("label.rna_interaction"));
- RNAInteractionColour.addActionListener(this);
- RNAHelixColour.setLabel(MessageManager
- .getString("action.by_rna_helixes"));
- RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager
- .getString("label.percentage_identity"));
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel(MessageManager
- .getString("label.blosum62_score"));
- BLOSUM62Colour.addActionListener(this);
- tcoffeeColour
- .setLabel(MessageManager.getString("label.tcoffee_scores"));
- tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
- // provided
- tcoffeeColour.addActionListener(this);
- avDistanceTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.average_distance_bloslum62"));
- avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.neighbour_blosum62"));
- njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel(MessageManager
- .getString("label.show_annotations"));
- annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel(MessageManager
- .getString("label.colour_text"));
- colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel(MessageManager
- .getString("label.show_non_conversed"));
- displayNonconservedMenuItem.addItemListener(this);
- alProperties.addActionListener(this);
- overviewMenuItem.setLabel(MessageManager
- .getString("label.overview_window"));
- overviewMenuItem.addActionListener(this);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel(MessageManager.getString("action.undo"));
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel(MessageManager.getString("action.redo"));
- redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
- .getString("action.by_conservation"));
- conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
- wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel(MessageManager
- .getString("action.show_gaps"));
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addItemListener(this);
+ /*
+ * Configure Select menu items and actions
+ */
findMenuItem.setLabel(MessageManager.getString("action.find"));
findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel(MessageManager
- .getString("label.above_identity_threshold"));
- abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(this);
+ selectAllSequenceMenuItem.addActionListener(this);
+ deselectAllSequenceMenuItem.addActionListener(this);
+ invertSequenceMenuItem.setLabel(MessageManager
+ .getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.addActionListener(this);
+ invertColSel.setLabel(MessageManager
+ .getString("action.invert_column_selection"));
+ invertColSel.addActionListener(this);
deleteGroups.setLabel(MessageManager
.getString("action.undefine_groups"));
deleteGroups.addActionListener(this);
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
unGroup.setLabel(MessageManager.getString("action.remove_group"));
- copy.setLabel(MessageManager.getString("action.copy"));
- copy.addActionListener(this);
- cut.setLabel(MessageManager.getString("action.cut"));
- cut.addActionListener(this);
- delete.setLabel(MessageManager.getString("action.delete"));
- delete.addActionListener(this);
- pasteMenu.setLabel(MessageManager.getString("action.paste"));
- pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
- pasteNew.addActionListener(this);
- pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
- pasteThis.addActionListener(this);
- applyToAllGroups.setLabel(MessageManager
- .getString("label.apply_colour_to_all_groups"));
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel(MessageManager.getString("action.font"));
- font.addActionListener(this);
- scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
- scaleAbove.setState(true);
- scaleAbove.setEnabled(false);
- scaleAbove.addItemListener(this);
- scaleLeft.setEnabled(false);
- scaleLeft.setState(true);
- scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
- scaleLeft.addItemListener(this);
- scaleRight.setEnabled(false);
- scaleRight.setState(true);
- scaleRight.setLabel(MessageManager.getString("action.scale_right"));
- scaleRight.addItemListener(this);
- modifyPID.setLabel(MessageManager
- .getString("label.modify_identity_thereshold"));
- modifyPID.addActionListener(this);
- modifyConservation.setLabel(MessageManager
- .getString("label.modify_conservation_thereshold"));
- modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel(MessageManager
- .getString("action.by_tree_order"));
- sort.setLabel(MessageManager.getString("action.sort"));
- calculate.setLabel(MessageManager.getString("action.calculate_tree"));
- autoCalculate.addItemListener(this);
- sortByTree.addItemListener(this);
- inputText
- .setLabel(MessageManager.getString("label.input_from_textbox"));
- inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel(MessageManager
- .getString("label.centre_column_labels"));
- centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel(MessageManager
- .getString("label.automatic_scrolling"));
- followMouseOverFlag.addItemListener(this);
- helpMenu.setLabel(MessageManager.getString("action.help"));
- documentation.setLabel(MessageManager.getString("label.documentation"));
- documentation.addActionListener(this);
-
- about.setLabel(MessageManager.getString("label.about"));
- about.addActionListener(this);
- seqLimits.setState(true);
- seqLimits.setLabel(MessageManager
- .getString("label.show_sequence_limits"));
- seqLimits.addItemListener(this);
- featureSettings.setLabel(MessageManager
- .getString("label.feature_settings"));
- featureSettings.addActionListener(this);
- sequenceFeatures.setLabel(MessageManager
- .getString("label.sequence_features"));
- sequenceFeatures.addItemListener(this);
- sequenceFeatures.setState(false);
- annotationColour.setLabel(MessageManager
- .getString("action.by_annotation"));
- annotationColour.addActionListener(this);
-
annotationColumnSelection.setLabel("Select by Annotation");
annotationColumnSelection.addActionListener(this);
- invertSequenceMenuItem.setLabel(MessageManager
- .getString("action.invert_sequence_selection"));
- invertColSel.setLabel(MessageManager
- .getString("action.invert_column_selection"));
- menu1.setLabel(MessageManager.getString("action.show"));
+ /*
+ * Configure View menu items and actions
+ */
+ newView.setLabel(MessageManager.getString("action.new_view"));
+ newView.addActionListener(this);
+ Menu showMenu = new Menu(MessageManager.getString("action.show"));
showColumns.setLabel(MessageManager.getString("label.all_columns"));
showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
- menu2.setLabel(MessageManager.getString("action.hide"));
+ Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
hideColumns
.setLabel(MessageManager.getString("label.selected_columns"));
hideSequences.setLabel(MessageManager
.getString("label.selected_region"));
showAllHidden.setLabel(MessageManager
.getString("label.all_sequences_columns"));
+ showColumns.addActionListener(this);
+ showSeqs.addActionListener(this);
+ hideColumns.addActionListener(this);
+ hideSequences.addActionListener(this);
+ hideAllButSelection.addActionListener(this);
+ hideAllSelection.addActionListener(this);
+ showAllHidden.addActionListener(this);
+ featureSettings.setLabel(MessageManager
+ .getString("label.feature_settings"));
+ featureSettings.addActionListener(this);
+ sequenceFeatures.setLabel(MessageManager
+ .getString("label.show_sequence_features"));
+ sequenceFeatures.addItemListener(this);
+ sequenceFeatures.setState(false);
+ followMouseOverFlag.setLabel(MessageManager
+ .getString("label.automatic_scrolling"));
+ followMouseOverFlag.addItemListener(this);
+ alProperties.addActionListener(this);
+ overviewMenuItem.setLabel(MessageManager
+ .getString("label.overview_window"));
+ overviewMenuItem.addActionListener(this);
+
+ /*
+ * Configure Annotations menu items and actions
+ */
+ annotationPanelMenuItem.setLabel(MessageManager
+ .getString("label.show_annotations"));
+ annotationPanelMenuItem.addItemListener(this);
showGroupConsensus.setLabel(MessageManager
.getString("label.group_consensus"));
showGroupConservation.setLabel(MessageManager
applyAutoAnnotationSettings.setLabel(MessageManager
.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel(MessageManager
- .getString("label.autocalculated_annotation"));
-
- invertColSel.addActionListener(this);
- showColumns.addActionListener(this);
- showSeqs.addActionListener(this);
- hideColumns.addActionListener(this);
- hideSequences.addActionListener(this);
- hideAllButSelection.addActionListener(this);
- hideAllSelection.addActionListener(this);
- showAllHidden.addActionListener(this);
+ Menu autoAnnMenu = new Menu(
+ MessageManager.getString("label.autocalculated_annotation"));
showGroupConsensus.addItemListener(this);
showGroupConservation.addItemListener(this);
showConsensusHistogram.addItemListener(this);
showSequenceLogo.addItemListener(this);
normSequenceLogo.addItemListener(this);
-
applyAutoAnnotationSettings.addItemListener(this);
- formatMenu.setLabel(MessageManager.getString("action.format"));
- selectMenu.setLabel(MessageManager.getString("action.select"));
- newView.setLabel(MessageManager.getString("action.new_view"));
- newView.addActionListener(this);
+ showAlignmentAnnotations = new CheckboxMenuItem(
+ MessageManager.getString("label.show_all_al_annotations"));
+ showSequenceAnnotations = new CheckboxMenuItem(
+ MessageManager.getString("label.show_all_seq_annotations"));
+ sortAnnBySequence = new CheckboxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_sequence"));
+ sortAnnByLabel = new CheckboxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_label"));
+ showAutoFirst = new CheckboxMenuItem(
+ MessageManager.getString("label.show_first"));
+ showAutoLast = new CheckboxMenuItem(
+ MessageManager.getString("label.show_last"));
+ showAlignmentAnnotations.addItemListener(this);
+ showSequenceAnnotations.addItemListener(this);
+ sortAnnBySequence.addItemListener(this);
+ sortAnnByLabel.addItemListener(this);
+ showAutoFirst.addItemListener(this);
+ showAutoLast.addItemListener(this);
+
+ /*
+ * Configure Format menu items and actions
+ */
+ font.setLabel(MessageManager.getString("action.font"));
+ font.addActionListener(this);
+ scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
+ scaleAbove.setState(true);
+ scaleAbove.setEnabled(false);
+ scaleAbove.addItemListener(this);
+ scaleLeft.setEnabled(false);
+ scaleLeft.setState(true);
+ scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
+ scaleLeft.addItemListener(this);
+ scaleRight.setEnabled(false);
+ scaleRight.setState(true);
+ scaleRight.setLabel(MessageManager.getString("action.scale_right"));
+ scaleRight.addItemListener(this);
+ viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addItemListener(this);
+ viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addItemListener(this);
+ colourTextMenuItem.setLabel(MessageManager
+ .getString("label.colour_text"));
+ colourTextMenuItem.addItemListener(this);
+ displayNonconservedMenuItem.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
+ displayNonconservedMenuItem.addItemListener(this);
+ wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
+ wrapMenuItem.addItemListener(this);
+ renderGapsMenuItem.setLabel(MessageManager
+ .getString("action.show_gaps"));
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addItemListener(this);
+ centreColumnLabelFlag.setLabel(MessageManager
+ .getString("label.centre_column_labels"));
+ centreColumnLabelFlag.addItemListener(this);
+ seqLimits.setState(true);
+ seqLimits.setLabel(MessageManager
+ .getString("label.show_sequence_limits"));
+ seqLimits.addItemListener(this);
+
+ /*
+ * Configure Colour menu items and actions
+ */
+ applyToAllGroups.setLabel(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setState(true);
+ applyToAllGroups.addItemListener(this);
+ clustalColour.setLabel(MessageManager.getString("label.clustalx"));
+ clustalColour.addActionListener(this);
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
+ zappoColour.addActionListener(this);
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
+ taylorColour.addActionListener(this);
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
+ hydrophobicityColour.addActionListener(this);
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour.addActionListener(this);
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
+ strandColour.addActionListener(this);
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+ turnColour.addActionListener(this);
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+ buriedColour.addActionListener(this);
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.addActionListener(this);
+ RNAInteractionColour.setLabel(MessageManager
+ .getString("label.rna_interaction"));
+ RNAInteractionColour.addActionListener(this);
+ RNAHelixColour.setLabel(MessageManager
+ .getString("action.by_rna_helixes"));
+ RNAHelixColour.addActionListener(this);
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
+ userDefinedColour.addActionListener(this);
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.setLabel(MessageManager
+ .getString("label.blosum62_score"));
+ BLOSUM62Colour.addActionListener(this);
+ tcoffeeColour
+ .setLabel(MessageManager.getString("label.tcoffee_scores"));
+ // it will be enabled only if a score file is provided
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener(this);
+ conservationMenuItem.setLabel(MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addItemListener(this);
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(this);
+ abovePIDThreshold.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDThreshold.addItemListener(this);
+ nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(this);
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_thereshold"));
+ modifyPID.addActionListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_thereshold"));
+ modifyConservation.addActionListener(this);
+ annotationColour.setLabel(MessageManager
+ .getString("action.by_annotation"));
+ annotationColour.addActionListener(this);
+
+ /*
+ * Configure Calculate menu items and actions
+ */
+ sortPairwiseMenuItem.setLabel(MessageManager
+ .getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(this);
+ sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel(MessageManager
+ .getString("action.by_length"));
+ sortLengthMenuItem.addActionListener(this);
+ sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(this);
+ pairwiseAlignmentMenuItem.setLabel(MessageManager
+ .getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(this);
+ PCAMenuItem.setLabel(MessageManager
+ .getString("label.principal_component_analysis"));
+ PCAMenuItem.addActionListener(this);
+ autoCalculate = new CheckboxMenuItem(
+ MessageManager.getString("label.autocalculate_consensus"), true);
+ averageDistanceTreeMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.addActionListener(this);
+ neighbourTreeMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.addActionListener(this);
+ avDistanceTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.addActionListener(this);
+ njTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.addActionListener(this);
+ sortByTreeMenu.setLabel(MessageManager
+ .getString("action.by_tree_order"));
+ Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
+ Menu calculateTreeMenu = new Menu(
+ MessageManager.getString("action.calculate_tree"));
+ autoCalculate.addItemListener(this);
+ sortByTree.addItemListener(this);
+
+ /*
+ * Configure Help menu items and actions
+ */
+ Menu helpMenu = new Menu(MessageManager.getString("action.help"));
+ documentation.setLabel(MessageManager.getString("label.documentation"));
+ documentation.addActionListener(this);
+ about.setLabel(MessageManager.getString("label.about"));
+ about.addActionListener(this);
+
+ /*
+ * Add top level menus to frame
+ */
alignFrameMenuBar.add(fileMenu);
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
alignFrameMenuBar.add(editMenu);
+ Menu selectMenu = new Menu(MessageManager.getString("action.select"));
alignFrameMenuBar.add(selectMenu);
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
alignFrameMenuBar.add(viewMenu);
+ Menu annotationsMenu = new Menu(
+ MessageManager.getString("action.annotations"));
+ alignFrameMenuBar.add(annotationsMenu);
+ Menu formatMenu = new Menu(MessageManager.getString("action.format"));
alignFrameMenuBar.add(formatMenu);
+ Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
alignFrameMenuBar.add(colourMenu);
+ Menu calculateMenu = new Menu(
+ MessageManager.getString("action.calculate"));
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(helpMenu);
+ /*
+ * File menu
+ */
fileMenu.add(inputText);
fileMenu.add(loadTree);
fileMenu.add(loadAnnotations);
-
fileMenu.addSeparator();
fileMenu.add(outputTextboxMenu);
fileMenu.add(outputFeatures);
fileMenu.add(outputAnnotations);
-
if (jalviewServletURL != null)
{
fileMenu.add(loadApplication);
}
-
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
+ /*
+ * Edit menu
+ */
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
editMenu.add(cut);
editMenu.add(copy);
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
editMenu.add(pasteMenu);
editMenu.add(delete);
editMenu.addSeparator();
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
+
+ /*
+ * Select menu
+ */
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
+ selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumnSelection);
+
+ /*
+ * View menu
+ */
viewMenu.add(newView);
viewMenu.addSeparator();
- viewMenu.add(menu1);
- viewMenu.add(menu2);
+ showMenu.add(showColumns);
+ showMenu.add(showSeqs);
+ showMenu.add(showAllHidden);
+ viewMenu.add(showMenu);
+ hideMenu.add(hideColumns);
+ hideMenu.add(hideSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+ viewMenu.add(hideMenu);
viewMenu.addSeparator();
viewMenu.add(followMouseOverFlag);
- viewMenu.add(annotationPanelMenuItem);
- autoAnnMenu.add(applyAutoAnnotationSettings);
- autoAnnMenu.add(showConsensusHistogram);
- autoAnnMenu.add(showSequenceLogo);
- autoAnnMenu.add(normSequenceLogo);
- autoAnnMenu.addSeparator();
- autoAnnMenu.add(showGroupConservation);
- autoAnnMenu.add(showGroupConsensus);
- viewMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
viewMenu.add(featureSettings);
viewMenu.add(alProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
+
+ /*
+ * Annotations menu
+ */
+ // annotationsMenu.add(annotationPanelMenuItem);
+ // annotationsMenu.addSeparator();
+ annotationsMenu.add(showAlignmentAnnotations);
+ annotationsMenu.add(showSequenceAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ annotationsMenu.add(autoAnnMenu);
+
+ /*
+ * Format menu
+ */
+ formatMenu.add(font);
+ formatMenu.add(seqLimits);
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(displayNonconservedMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelFlag);
+
+ /*
+ * Colour menu
+ */
colourMenu.add(applyToAllGroups);
colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
colourMenu.add(RNAHelixColour);
- calculateMenu.add(sort);
- calculateMenu.add(calculate);
+
+ /*
+ * Calculate menu
+ */
+ sortMenu.add(sortIDMenuItem);
+ sortMenu.add(sortLengthMenuItem);
+ sortMenu.add(sortByTreeMenu);
+ sortMenu.add(sortGroupMenuItem);
+ sortMenu.add(sortPairwiseMenuItem);
+ calculateMenu.add(sortMenu);
+ calculateTreeMenu.add(averageDistanceTreeMenuItem);
+ calculateTreeMenu.add(neighbourTreeMenuItem);
+ calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
+ calculateTreeMenu.add(njTreeBlosumMenuItem);
+ calculateMenu.add(calculateTreeMenu);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.add(autoCalculate);
calculateMenu.add(sortByTree);
- this.add(statusBar, BorderLayout.SOUTH);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortLengthMenuItem);
- sort.add(sortByTreeMenu);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
+
+ /*
+ * Help menu
+ */
helpMenu.add(documentation);
helpMenu.add(about);
- menu1.add(showColumns);
- menu1.add(showSeqs);
- menu1.add(showAllHidden);
- menu2.add(hideColumns);
- menu2.add(hideSequences);
- menu2.add(hideAllSelection);
- menu2.add(hideAllButSelection);
- formatMenu.add(font);
- formatMenu.add(seqLimits);
- formatMenu.add(wrapMenuItem);
- formatMenu.add(scaleAbove);
- formatMenu.add(scaleLeft);
- formatMenu.add(scaleRight);
- formatMenu.add(viewBoxesMenuItem);
- formatMenu.add(viewTextMenuItem);
- formatMenu.add(colourTextMenuItem);
- formatMenu.add(displayNonconservedMenuItem);
- formatMenu.add(renderGapsMenuItem);
- formatMenu.add(centreColumnLabelFlag);
- selectMenu.add(findMenuItem);
- selectMenu.addSeparator();
- selectMenu.add(selectAllSequenceMenuItem);
- selectMenu.add(deselectAllSequenceMenuItem);
- selectMenu.add(invertSequenceMenuItem);
- selectMenu.add(invertColSel);
- selectMenu.add(createGroup);
- selectMenu.add(unGroup);
- selectMenu.add(grpsFromSelection);
- selectMenu.add(deleteGroups);
- selectMenu.add(annotationColumnSelection);
+ /*
+ * Status bar
+ */
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setText(MessageManager.getString("label.status_bar"));
+ this.add(statusBar, BorderLayout.SOUTH);
}
public void setStatus(String string)
MenuItem invertColSel = new MenuItem();
- Menu menu1 = new Menu();
-
MenuItem showColumns = new MenuItem();
MenuItem showSeqs = new MenuItem();
- Menu menu2 = new Menu();
-
MenuItem hideColumns = new MenuItem();
MenuItem hideSequences = new MenuItem();
MenuItem showAllHidden = new MenuItem();
- Menu formatMenu = new Menu();
+ MenuItem newView = new MenuItem();
- Menu selectMenu = new Menu();
+ private CheckboxMenuItem showAlignmentAnnotations;
- MenuItem newView = new MenuItem();
+ private CheckboxMenuItem showSequenceAnnotations;
+
+ private CheckboxMenuItem sortAnnBySequence;
+
+ private CheckboxMenuItem sortAnnByLabel;
+
+ private CheckboxMenuItem showAutoFirst;
+
+ private CheckboxMenuItem showAutoLast;
/**
* Attach the alignFrame panels after embedding menus, if necessary. This used
* true to attach the view to the applet area on the page rather than
* in a new window
*/
- public void createAlignFrameWindow(boolean reallyEmbedded, String title)
+ public void createAlignFrameWindow(boolean reallyEmbedded)
{
if (reallyEmbedded)
{
- // ////
- // Explicly build the embedded menu panel for the on-page applet
- //
- // view cannot be closed if its actually on the page
- fileMenu.remove(closeMenuItem);
- fileMenu.remove(3); // Remove Seperator
- embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
- Font.PLAIN, 11, false); // use our own fonts.
- // and actually add the components to the applet area
- viewport.applet.setLayout(new BorderLayout());
- viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
- viewport.applet.add(statusBar, BorderLayout.SOUTH);
- alignPanel.setSize(viewport.applet.getSize().width,
- viewport.applet.getSize().height - embeddedMenu.HEIGHT
- - statusBar.HEIGHT);
- viewport.applet.add(alignPanel, BorderLayout.CENTER);
- final AlignFrame me = this;
- viewport.applet.addFocusListener(new FocusListener()
- {
-
- @Override
- public void focusLost(FocusEvent e)
- {
- if (me.viewport.applet.currentAlignFrame == me)
- {
- me.viewport.applet.currentAlignFrame = null;
- }
- }
-
- @Override
- public void focusGained(FocusEvent e)
- {
- me.viewport.applet.currentAlignFrame = me;
- }
- });
- viewport.applet.validate();
+ embedAlignFrameInApplet(viewport.applet);
}
else
{
//
if (embedMenuIfNeeded(alignPanel))
{
- // adjust for status bar height too
- alignPanel.setSize(getSize().width, getSize().height
- - statusBar.HEIGHT);
+ /*
+ * adjust for status bar height too. ? pointless as overridden by layout
+ * manager
+ */
+ alignPanel.setSize(getSize().width,
+ getSize().height - statusBar.getHeight());
}
add(statusBar, BorderLayout.SOUTH);
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
- jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
+ jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
+ DEFAULT_WIDTH,
DEFAULT_HEIGHT);
}
}
/**
+ * Add the components of this AlignFrame to the applet container.
+ *
+ * @param theApplet
+ */
+ public void embedAlignFrameInApplet(final JalviewLite theApplet)
+ {
+ // ////
+ // Explicitly build the embedded menu panel for the on-page applet
+ //
+ // view cannot be closed if its actually on the page
+ fileMenu.remove(closeMenuItem);
+ fileMenu.remove(3); // Remove Separator
+ // construct embedded menu, using default font
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
+ // and actually add the components to the applet area
+ theApplet.setLayout(new BorderLayout());
+ theApplet.add(embeddedMenu, BorderLayout.NORTH);
+ theApplet.add(statusBar, BorderLayout.SOUTH);
+ // TODO should size be left to the layout manager?
+ alignPanel.setSize(theApplet.getSize().width,
+ theApplet.getSize().height - embeddedMenu.getHeight()
+ - statusBar.getHeight());
+ theApplet.add(alignPanel, BorderLayout.CENTER);
+ final AlignFrame me = this;
+ theApplet.addFocusListener(new FocusListener()
+ {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ if (theApplet.currentAlignFrame == me)
+ {
+ theApplet.currentAlignFrame = null;
+ }
+ }
+
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ theApplet.currentAlignFrame = me;
+ }
+ });
+ theApplet.validate();
+ }
+
+ /**
* create a new binding between structures in an existing jmol viewer instance
* and an alignpanel with sequences that have existing PDBFile entries. Note,
* this does not open a new Jmol window, or modify the display of the
*/
package jalview.appletgui;
+import java.awt.Font;
+
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.JalviewLite;
+import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
-import java.awt.Font;
-import java.util.Stack;
-
public class AlignViewport extends AlignmentViewport implements
- AlignViewportI, SelectionSource, VamsasSource
+ AlignViewportI, SelectionSource, VamsasSource, CommandListener
{
int startRes;
boolean cursorMode = false;
- boolean showJVSuffix = true;
-
- boolean showText = true;
-
- boolean showColourText = false;
-
- boolean showBoxes = true;
-
- boolean wrapAlignment = false;
-
- boolean renderGaps = true;
-
- boolean showAnnotation = true;
-
- boolean upperCasebold = false;
-
- int charHeight;
-
- int charWidth;
-
- int wrappedWidth;
-
Font font = new Font("SansSerif", Font.PLAIN, 10);
boolean validCharWidth = true;
- int threshold;
-
- int increment;
-
NJTree currentTree = null;
- boolean scaleAboveWrapped = true;
-
- boolean scaleLeftWrapped = true;
-
- boolean scaleRightWrapped = true;
-
- boolean showHiddenMarkers = true;
-
public jalview.bin.JalviewLite applet;
boolean MAC = false;
- Stack historyList = new Stack();
-
- Stack redoList = new Stack();
-
private AnnotationColumnChooser annotationColumnSelectionState;
public void finalize()
public AlignViewport(AlignmentI al, JalviewLite applet)
{
+ super();
calculator = new jalview.workers.AlignCalcManager();
this.applet = applet;
- setAlignment(al);
+ alignment = al;
// we always pad gaps
this.setPadGaps(true);
this.startRes = 0;
if (applet != null)
{
- showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
+ setShowJVSuffix(applet.getDefaultParameter("showFullId",
+ getShowJVSuffix()));
- showAnnotation = applet.getDefaultParameter("showAnnotation",
- showAnnotation);
+ setShowAnnotation(applet.getDefaultParameter("showAnnotation",
+ isShowAnnotation()));
showConservation = applet.getDefaultParameter("showConservation",
showConservation);
showConsensus = applet.getDefaultParameter("showConsensus",
showConsensus);
- showUnconserved = applet.getDefaultParameter("showUnconserved",
- showUnconserved);
+ setShowUnconserved(applet.getDefaultParameter("showUnconserved",
+ getShowUnconserved()));
String param = applet.getParameter("upperCase");
if (param != null)
{
if (param.equalsIgnoreCase("bold"))
{
- upperCasebold = true;
+ setUpperCasebold(true);
}
}
sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
{
return null;
}
- StringBuffer seqs = new StringBuffer();
+ StringBuilder seqs = new StringBuilder(consensus.annotations.length);
for (int i = 0; i < consensus.annotations.length; i++)
{
if (consensus.annotations[i] != null)
java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
setCharHeight((int) (heightScale * fm.getHeight()));
- charWidth = (int) (widthScale * fm.charWidth('M'));
+ setCharWidth((int) (widthScale * fm.charWidth('M')));
- if (upperCasebold)
+ if (isUpperCasebold())
{
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
fm = nullFrame.getGraphics().getFontMetrics(f2);
- charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
+ setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
}
}
return font;
}
- public int getCharWidth()
- {
- return charWidth;
- }
-
- public void setCharHeight(int h)
- {
- this.charHeight = h;
- }
-
- public int getCharHeight()
- {
- return charHeight;
- }
-
- public void setWrappedWidth(int w)
- {
- this.wrappedWidth = w;
- }
-
- public int getwrappedWidth()
- {
- return wrappedWidth;
- }
-
- public AlignmentI getAlignment()
- {
- return alignment;
- }
-
- public void setAlignment(AlignmentI align)
- {
- this.alignment = align;
- }
-
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- public boolean getColourText()
- {
- return showColourText;
- }
-
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- public boolean getShowText()
- {
- return showText;
- }
-
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
-
- public char getGapCharacter()
- {
- return getAlignment().getGapCharacter();
- }
-
- public void setGapCharacter(char gap)
- {
- if (getAlignment() != null)
- {
- getAlignment().setGapCharacter(gap);
- }
- }
public void resetSeqLimits(int height)
{
return currentTree;
}
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- public void setIgnoreGapsConsensus(boolean b)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(null);
- if (globalColourScheme != null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
-
- }
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
boolean centreColumnLabels;
public void sendSelection()
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(applet).sendSelection(
+ getStructureSelectionManager().sendSelection(
new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()), this);
}
/**
+ * Returns an instance of the StructureSelectionManager scoped to this applet
+ * instance.
+ *
+ * @return
+ */
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(applet);
+ }
+
+ /**
* synthesize a column selection if none exists so it covers the given
* selection group. if wholewidth is false, no column selection is made if the
* selection group covers the whole alignment width.
this.annotationColumnSelectionState = annotationColumnSelectionState;
}
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
+ {
+ // TODO refactor so this can be pulled up to superclass or controller
+ /*
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
+ */
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
+ {
+ // ok to continue;
+ }
+ else
+ {
+ return;
+ }
+
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
+ {
+ mappedCommand.doCommand(null);
+ firePropertyChange("alignment", null, getAlignment().getSequences());
+
+ // ap.scalePanelHolder.repaint();
+ // ap.repaint();
+ }
+ }
+
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ return this;
+ }
+
}
*/
package jalview.appletgui;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureSelectionManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+
public class AlignmentPanel extends Panel implements AdjustmentListener,
AlignmentViewPanel
{
sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
alabels = new AnnotationLabels(this);
- setAnnotationVisible(av.showAnnotation);
+ setAnnotationVisible(av.isShowAnnotation());
idPanelHolder.add(idPanel, BorderLayout.CENTER);
idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
});
}
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
public SequenceRenderer getSequenceRenderer()
{
return seqPanel.seqCanvas.sr;
idPanel.idCanvas.image = null;
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
- idwidthAdjuster.setSize(new Dimension(10, av.charHeight
+ scalePanel.setSize(new Dimension(10, av.getCharHeight()
+ + fm.getDescent()));
+ idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
av.updateSequenceIdColours();
annotationPanel.image = null;
{
start = ostart;
}
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
/*
* int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
public void setAnnotationVisible(boolean b)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
annotationSpaceFillerHolder.setVisible(b);
annotationPanelHolder.setVisible(b);
// this is called after loading new annotation onto alignment
if (alignFrame.getSize().height == 0)
{
- System.out.println("NEEDS FIXING");
+ System.out
+ .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
}
fontChanged();
validateAnnotationDimensions(true);
annotationPanelHolder.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
- else if (av.showAnnotation)
+ else if (av.isShowAnnotation())
{
annotationPanelHolder.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
}
;
- hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
- vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
+ hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
+ vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
if (hextent > width)
{
av.setEndSeq(endSeq);
av.setStartRes(x);
- av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+ av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+ .getCharWidth())) - 1);
hscroll.setValues(x, hextent, 0, width);
vscroll.setValues(y, vextent, 0, height);
seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
scalePanel.repaint();
- if (av.getShowAnnotation())
+ if (av.isShowAnnotation())
{
annotationPanel.fastPaint(av.getStartRes() - oldX);
}
av.endSeq);
}
+ /**
+ * Repaint the alignment and annotations, and, optionally, any overview window
+ */
public void paintAlignment(boolean updateOverview)
{
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
repaint();
if (updateOverview)
seqPanel.seqCanvas.repaint();
idPanel.idCanvas.repaint();
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
alabels.repaint();
annotationPanel.repaint();
*/
package jalview.appletgui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.util.ParseHtmlBodyAndLinks;
-
import java.awt.Checkbox;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.util.Arrays;
+import java.util.Collections;
import java.util.Vector;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
public class AnnotationLabels extends Panel implements ActionListener,
MouseListener, MouseMotionListener
{
}
}
+ refresh();
+ }
+
+ /**
+ * Adjust size and repaint
+ */
+ protected void refresh()
+ {
ap.annotationPanel.adjustPanelHeight();
setSize(getSize().width, ap.annotationPanel.getSize().height);
ap.validate();
.getSize(), f = ap.seqPanelHolder.getSize();
int dif = evt.getY() - oldY;
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
if ((d.height - dif) > 20 && (f.height + dif) > 20)
{
item = new MenuItem(HIDE);
item.addActionListener(this);
popup.add(item);
+
+ /*
+ * Hide all <label>:
+ */
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].sequenceRef != null)
+ {
+ final String label = aa[selectedRow].label;
+ MenuItem hideType = new MenuItem(
+ MessageManager.getString("label.hide_all") + " " + label);
+ hideType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ ap.av.getAlignment(), Collections.singleton(label),
+ null, false, false);
+ refresh();
+ }
+ });
+ popup.add(hideType);
+ }
+ }
+
if (hasHiddenRows)
{
item = new MenuItem(SHOWALL);
MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
- .getIgnoreGapsConsensus());
+ .isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addItemListener(new ItemListener()
{
}
else
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
ap.paintAlignment(true);
}
dragEvent.getY());
}
- if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
g.setColor(Color.black);
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
AdjustmentListener, ActionListener, MouseListener,
MouseMotionListener
int activeRow = -1;
- Vector activeRes;
-
final String HELIX = "Helix";
final String SHEET = "Sheet";
if (av.getColumnSelection() != null
&& av.getColumnSelection().size() > 0
&& anot[av.getColumnSelection().getMin()] != null)
+ {
label = anot[av.getColumnSelection().getMin()].displayCharacter;
+ }
if (evt.getActionCommand().equals(REMOVE))
{
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", type, 0);
}
-
anot[index].secondaryStructure = type != 'S' ? type : label
.length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
ap.alignFrame, "Enter Label", 400, 200, true);
if (dialog.accept)
+ {
return dialog.getName();
+ }
else
+ {
return null;
+ }
}
@Override
return;
}
- if (aa == null)
- {
- return;
- }
-
ap.scalePanel.mousePressed(evt);
}
}
}
}
-
- if (activeRes == null)
- {
- activeRes = new Vector();
- activeRes.addElement(String.valueOf(i));
- return;
- }
-
- activeRes.addElement(String.valueOf(i));
}
@Override
return;
}
- gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal
- * av.charWidth, 0);
+ gg.copyArea(0, 0, imgWidth, getSize().height,
+ -horizontal * av.getCharWidth(), 0);
int sr = av.startRes, er = av.endRes + 1, transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * av.getCharWidth();
sr = er - horizontal;
}
else if (horizontal < 0)
g.setFont(ofont);
g.setColor(Color.white);
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(),
+ getSize().height);
if (fm == null)
{
return bounds;
}
else
+ {
return null;
+ }
}
}
*/
package jalview.appletgui;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.io.AnnotationFile;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.TCoffeeScoreFile;
-import jalview.schemes.TCoffeeColourScheme;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Button;
import java.awt.Dialog;
import java.awt.Font;
import java.awt.Frame;
+import java.awt.Label;
import java.awt.Panel;
import java.awt.TextArea;
import java.awt.event.ActionEvent;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
+import jalview.analysis.AlignmentUtils;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.MessageManager;
+
public class CutAndPasteTransfer extends Panel implements ActionListener,
MouseListener
{
boolean annotationImport = false;
- Sequence seq;
+ SequenceI seq;
AlignFrame alignFrame;
textarea.setText(text);
}
- public void setPDBImport(Sequence seq)
+ public void setPDBImport(SequenceI seq)
{
this.seq = seq;
accept.setLabel(MessageManager.getString("action.accept"));
if (pdbImport)
{
- PDBEntry pdb = new PDBEntry();
- pdb.setFile(text);
+ openPdbViewer(text);
- if (alignFrame.alignPanel.av.applet.jmolAvailable)
- {
- new jalview.appletgui.AppletJmol(pdb, new Sequence[]
- { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
- }
- else
+ }
+ else if (treeImport)
+ {
+ if (!loadTree())
{
- new MCview.AppletPDBViewer(pdb, new Sequence[]
- { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+ return;
}
+ }
+ else if (annotationImport)
+ {
+ loadAnnotations();
+ }
+ else if (alignFrame != null)
+ {
+ loadAlignment(text, newWindow);
+ }
+ // TODO: dialog should indicate if data was parsed correctly or not - see
+ // JAL-1102
+ if (this.getParent() instanceof Frame)
+ {
+ ((Frame) this.getParent()).setVisible(false);
}
- else if (treeImport)
+ else
{
- try
- {
- jalview.io.NewickFile fin = new jalview.io.NewickFile(
- textarea.getText(), "Paste");
+ ((Dialog) this.getParent()).setVisible(false);
+ }
+ }
- fin.parse();
- if (fin.getTree() != null)
- {
- alignFrame.loadTree(fin, "Pasted tree file");
- }
+ /**
+ * Parses text as Newick Tree format, and loads on to the alignment. Returns
+ * true if successful, else false.
+ */
+ protected boolean loadTree()
+ {
+ try
+ {
+ NewickFile fin = new NewickFile(textarea.getText(), "Paste");
- } catch (Exception ex)
+ fin.parse();
+ if (fin.getTree() != null)
{
- // TODO: JAL-1102 - should have a warning message in dialog, not simply
- // overwrite the broken input data with the exception
- textarea.setText(MessageManager.formatMessage(
- "label.could_not_parse_newick_file", new String[]
- { ex.getMessage() }));
- return;
+ alignFrame.loadTree(fin, "Pasted tree file");
+ return true;
}
+ } catch (Exception ex)
+ {
+ // TODO: JAL-1102 - should have a warning message in dialog, not simply
+ // overwrite the broken input data with the exception
+ textarea.setText(MessageManager.formatMessage(
+ "label.could_not_parse_newick_file", new Object[]
+ { ex.getMessage() }));
+ return false;
}
- else if (annotationImport)
+ return false;
+ }
+
+ /**
+ * Parse text as an alignment file and add to the current or a new window.
+ *
+ * @param text
+ * @param newWindow
+ */
+ protected void loadAlignment(String text, boolean newWindow)
+ {
+ Alignment al = null;
+
+ String format = new IdentifyFile().Identify(text,
+ AppletFormatAdapter.PASTE);
+ try
+ {
+ al = new AppletFormatAdapter().readFile(text,
+ AppletFormatAdapter.PASTE, format);
+ } catch (java.io.IOException ex)
{
- TCoffeeScoreFile tcf = null;
- try
+ ex.printStackTrace();
+ }
+
+ if (al != null)
+ {
+ al.setDataset(null); // set dataset on alignment/sequences
+ if (openSplitFrame(al, format))
{
- tcf = new TCoffeeScoreFile(textarea.getText(),
- jalview.io.AppletFormatAdapter.PASTE);
- if (tcf.isValid())
- {
- if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
- true))
- {
- alignFrame.tcoffeeColour.setEnabled(true);
- alignFrame.alignPanel.fontChanged();
- alignFrame.changeColour(new TCoffeeColourScheme(
- alignFrame.viewport.getAlignment()));
- alignFrame.statusBar
- .setText(MessageManager
- .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
- }
- else
- {
- // file valid but didn't get added to alignment for some reason
- alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.failed_add_tcoffee_scores",
- new String[]
- { (tcf.getWarningMessage() != null ? tcf
- .getWarningMessage() : "") }));
- }
- }
- else
- {
- tcf = null;
- }
- } catch (Exception x)
+ return;
+ }
+ if (newWindow)
{
- tcf = null;
+ AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
+ "Cut & Paste input - " + format, false);
+ af.statusBar
+ .setText(MessageManager
+ .getString("label.successfully_pasted_annotation_to_alignment"));
}
- if (tcf == null)
+ else
{
- if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
- textarea.getText(),
- jalview.io.AppletFormatAdapter.PASTE))
+ alignFrame.addSequences(al.getSequencesArray());
+ alignFrame.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
+ }
+ }
+ }
+
+ /**
+ * Check whether the new alignment could be mapped to the current one as
+ * cDNA/protein, if so offer the option to open as split frame view. Returns
+ * true if a split frame view is opened, false if not.
+ *
+ * @param al
+ * @return
+ */
+ protected boolean openSplitFrame(Alignment al, String format)
+ {
+ final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
+ if (thisAlignment.isNucleotide() == al.isNucleotide())
+ {
+ // both nucleotide or both protein
+ return false;
+ }
+ AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
+ AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
+ boolean mapped = AlignmentUtils.mapProteinToCdna(protein, dna);
+ if (!mapped)
+ {
+ return false;
+ }
+
+ /*
+ * A mapping is possible; ask user if they want a split frame.
+ */
+ String title = MessageManager.getString("label.open_split_window");
+ final JVDialog dialog = new JVDialog((Frame) this.getParent(), title,
+ true, 100, 400);
+ dialog.ok.setLabel(MessageManager.getString("action.yes"));
+ dialog.cancel.setLabel(MessageManager.getString("action.no"));
+ Panel question = new Panel(new BorderLayout());
+ final String text = MessageManager
+ .getString("label.open_split_window?");
+ question.add(new Label(text, Label.CENTER), BorderLayout.CENTER);
+ dialog.setMainPanel(question);
+ dialog.setVisible(true);
+ dialog.toFront();
+
+ if (!dialog.accept)
+ {
+ return false;
+ }
+
+ /*
+ * Open SplitFrame with DNA above and protein below, including the alignment
+ * from textbox and a copy of the original.
+ */
+ final JalviewLite applet = this.alignFrame.viewport.applet;
+ AlignFrame copyFrame = new AlignFrame(
+ this.alignFrame.viewport.getAlignment(), applet,
+ alignFrame.getTitle(), false, false);
+ AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
+ "Cut & Paste input - " + format, false, false);
+ AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
+ AlignFrame proteinFrame = al.isNucleotide() ? copyFrame
+ : newFrame;
+ SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
+ sf.addToDisplay(false, applet);
+ return true;
+ }
+
+ /**
+ * Parse the text as a TCoffee score file, if successful add scores as
+ * alignment annotations.
+ */
+ protected void loadAnnotations()
+ {
+ TCoffeeScoreFile tcf = null;
+ try
+ {
+ tcf = new TCoffeeScoreFile(textarea.getText(),
+ jalview.io.AppletFormatAdapter.PASTE);
+ if (tcf.isValid())
+ {
+ if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
+ true))
{
+ alignFrame.tcoffeeColour.setEnabled(true);
alignFrame.alignPanel.fontChanged();
- alignFrame.alignPanel.setScrollValues(0, 0);
+ alignFrame.changeColour(new TCoffeeColourScheme(
+ alignFrame.viewport.getAlignment()));
alignFrame.statusBar
.setText(MessageManager
- .getString("label.successfully_pasted_annotation_to_alignment"));
-
+ .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
- if (!alignFrame.parseFeaturesFile(textarea.getText(),
- jalview.io.AppletFormatAdapter.PASTE))
- {
- alignFrame.statusBar
- .setText(MessageManager
- .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
- }
+ // file valid but didn't get added to alignment for some reason
+ alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.failed_add_tcoffee_scores",
+ new Object[]
+ { (tcf.getWarningMessage() != null ? tcf
+ .getWarningMessage() : "") }));
}
}
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
+ {
+ tcf = null;
}
- else if (alignFrame != null)
+ if (tcf == null)
{
- Alignment al = null;
-
- String format = new IdentifyFile().Identify(text,
- AppletFormatAdapter.PASTE);
- try
- {
- al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE, format);
- } catch (java.io.IOException ex)
+ if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+ textarea.getText(),
+ jalview.io.AppletFormatAdapter.PASTE))
{
- ex.printStackTrace();
- }
+ alignFrame.alignPanel.fontChanged();
+ alignFrame.alignPanel.setScrollValues(0, 0);
+ alignFrame.statusBar
+ .setText(MessageManager
+ .getString("label.successfully_pasted_annotation_to_alignment"));
- if (al != null)
+ }
+ else
{
- if (newWindow)
+ if (!alignFrame.parseFeaturesFile(textarea.getText(),
+ jalview.io.AppletFormatAdapter.PASTE))
{
- AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
- "Cut & Paste input - " + format, false);
- af.statusBar
+ alignFrame.statusBar
.setText(MessageManager
- .getString("label.successfully_pasted_annotation_to_alignment"));
- }
- else
- {
- alignFrame.addSequences(al.getSequencesArray());
- alignFrame.statusBar.setText(MessageManager
- .getString("label.successfully_pasted_alignment_file"));
+ .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
}
}
}
- // TODO: dialog should indicate if data was parsed correctly or not - see
- // JAL-1102
- if (this.getParent() instanceof Frame)
+ }
+
+ /**
+ * Open a Jmol viewer (if available), failing that the built-in PDB viewer,
+ * passing the input text as the PDB file data.
+ *
+ * @param text
+ */
+ protected void openPdbViewer(String text)
+ {
+ PDBEntry pdb = new PDBEntry();
+ pdb.setFile(text);
+
+ if (alignFrame.alignPanel.av.applet.jmolAvailable)
{
- ((Frame) this.getParent()).setVisible(false);
+ new jalview.appletgui.AppletJmol(pdb, new SequenceI[]
+ { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
}
else
{
- ((Dialog) this.getParent()).setVisible(false);
+ new MCview.AppletPDBViewer(pdb, new SequenceI[]
+ { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
}
}
*/
package jalview.appletgui;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.FlowLayout;
import java.awt.PopupMenu;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.HashMap;
+import java.util.Map;
/**
- * This class implements a pattern form embedding toolbars as a panel with
- * popups for situations where the system menu bar is either invisible or
+ * This class implements a pattern for embedding toolbars as a panel with popups
+ * for situations where the system menu bar is either invisible or
* inappropriate. It was derived from the code for embedding the jalview applet
* alignFrame as a component on the web-page, which requires the local
* alignFrame menu to be attached to that panel rather than placed on the parent
*/
public class EmbmenuFrame extends Frame implements MouseListener
{
+ protected static final Font FONT_ARIAL_PLAIN_11 = new Font(
+ "Arial", Font.PLAIN, 11);
+
+ public static final Font DEFAULT_MENU_FONT = FONT_ARIAL_PLAIN_11;
+
/**
* map from labels to popup menus for the embedded menubar
*/
- protected Hashtable embeddedPopup;
+ protected Map<Label, PopupMenu> embeddedPopup = new HashMap<Label, PopupMenu>();
/**
* the embedded menu is built on this and should be added to the frame at the
// DEBUG Hint: can test embedded menus by inserting true here.
if (new jalview.util.Platform().isAMac())
{
- // Build the embedded menu panel
- embeddedMenu = makeEmbeddedPopupMenu(topMenuBar, "Arial", Font.PLAIN,
- 11, true); // try to pickup system font.
+ // Build the embedded menu panel, allowing override with system font
+ embeddedMenu = makeEmbeddedPopupMenu(topMenuBar, true, false);
setMenuBar(null);
- // add the components to the TreePanel area.
+ // add the components to the Panel area.
add(embeddedMenu, BorderLayout.NORTH);
- tobeAdjusted.setSize(getSize().width, getSize().height
- - embeddedMenu.HEIGHT);
+ tobeAdjusted.setSize(getSize().width,
+ getSize().height - embeddedMenu.getHeight());
return true;
}
return false;
}
/**
- * move all menus on menuBar onto embeddedMenu. embeddedPopup is used to store
- * the popups for each menu removed from the menuBar and added to the panel.
- * NOTE: it is up to the caller to remove menuBar from the Frame if it is
- * already attached.
- *
- * @param menuBar
- * @param fn
- * @param fstyle
- * @param fsz
- * @param overrideFonts
- * true if we take the menuBar fonts in preference to the supplied
- * defaults
- * @return the embedded menu instance to be added to the frame.
- */
- protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, String fn,
- int fstyle, int fsz, boolean overrideFonts)
- {
- return makeEmbeddedPopupMenu(menuBar, fn, fstyle, fsz, overrideFonts,
- false);
- }
-
- /**
* Create or add elements to the embedded menu from menuBar. This removes all
* menu from menuBar and it is up to the caller to remove the now useless
* menuBar from the Frame if it is already attached.
*
* @param menuBar
- * @param fn
- * @param fstyle
- * @param fsz
* @param overrideFonts
* @param append
* true means existing menu will be emptied before adding new
* elements
* @return
*/
- protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, String fn,
- int fstyle, int fsz, boolean overrideFonts, boolean append)
+ protected Panel makeEmbeddedPopupMenu(MenuBar menuBar,
+ boolean overrideFonts, boolean append)
{
if (!append)
{
- if (embeddedPopup != null)
- {
- embeddedPopup.clear(); // TODO: check if j1.1
- }
+ embeddedPopup.clear(); // TODO: check if j1.1
if (embeddedMenu != null)
{
embeddedMenu.removeAll();
}
}
- if (embeddedPopup == null)
- {
- embeddedPopup = new Hashtable();
- }
-
- embeddedMenu = makeEmbeddedPopupMenu(menuBar, fn, fstyle, fsz,
- overrideFonts, embeddedPopup, new Panel(), this);
+ embeddedMenu = makeEmbeddedPopupMenu(menuBar, DEFAULT_MENU_FONT,
+ overrideFonts, new Panel(), this);
return embeddedMenu;
}
*
* @param menuBar
* must be non-null
- * @param fn
- * @param fstyle
- * @param fsz
+ * @param font
* @param overrideFonts
- * @param embeddedPopup
- * must be non-null
* @param embeddedMenu
* if null, a new panel will be created and returned
* @param clickHandler
* embeddedPopup and embeddedMenu
* @return the panel instance for convenience.
*/
- protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, String fn,
- int fstyle, int fsz, boolean overrideFonts,
- Hashtable embeddedPopup, Panel embeddedMenu,
+ protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, Font font,
+ boolean overrideFonts,
+ Panel embeddedMenu,
MouseListener clickHandler)
{
- if (embeddedPopup == null)
- {
- throw new Error(MessageManager.getString("error.implementation_error_embeddedpopup_not_null"));
- }
if (overrideFonts)
{
Font mbf = menuBar.getFont();
if (mbf != null)
{
- fn = mbf.getName();
- fstyle = mbf.getStyle();
- fsz = mbf.getSize();
+ font = mbf;
}
}
if (embeddedMenu == null)
+ {
embeddedMenu = new Panel();
+ }
FlowLayout flowLayout1 = new FlowLayout();
embeddedMenu.setBackground(Color.lightGray);
embeddedMenu.setLayout(flowLayout1);
{
Menu mi = menuBar.getMenu(mbi);
Label elab = new Label(mi.getLabel());
- elab.setFont(new java.awt.Font(fn, fstyle, fsz));
+ elab.setFont(font);
// add the menu entries
PopupMenu popup = new PopupMenu();
int m, mSize = mi.getItemCount();
*/
PopupMenu getPopupMenu(Label source)
{
- return (PopupMenu) embeddedPopup.get(source);
+ return embeddedPopup.get(source);
}
public void mouseClicked(MouseEvent evt)
{
if (embeddedPopup != null)
{
- Enumeration e = embeddedPopup.keys();
- while (e.hasMoreElements())
+ for (Label lb : embeddedPopup.keySet())
{
- Label lb = (Label) e.nextElement();
lb.removeMouseListener(this);
}
embeddedPopup.clear();
*/
package jalview.appletgui;
+import jalview.api.ViewStyleI;
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
public class FontChooser extends Panel implements ActionListener,
ItemListener
Font oldFont;
+ int oldCharWidth = 0;
+
boolean init = true;
Frame frame;
this.ap = ap;
oldFont = ap.av.getFont();
+ oldCharWidth = ap.av.getViewStyle().getCharWidth();
init();
}
if (ap != null)
{
ap.av.setFont(oldFont);
+ ViewStyleI style = ap.av.getViewStyle();
+ if (style.getCharWidth() != oldCharWidth)
+ {
+ style.setCharWidth(oldCharWidth);
+ ap.av.setViewStyle(style);
+ }
ap.paintAlignment(true);
}
else if (tp != null)
*/
package jalview.appletgui;
-import java.awt.*;
-import java.util.List;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.util.List;
public class IdCanvas extends Panel
{
((i - starty) * charHeight) + ypos + charHeight
- (charHeight / 5));
- if (av.hasHiddenRows() && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.getShowHiddenMarkers())
{
drawMarker(i, starty, ypos);
}
return;
}
- gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical
- * av.charHeight);
+ gg.copyArea(0, 0, getSize().width, imgHeight, 0,
+ -vertical * av.getCharHeight());
int ss = av.startSeq, es = av.endSeq, transY = 0;
if (vertical > 0) // scroll down
}
else
{
- transY = imgHeight - vertical * av.charHeight;
+ transY = imgHeight - vertical * av.getCharHeight();
}
}
else if (vertical < 0)
}
imgHeight = getSize().height;
- imgHeight -= imgHeight % av.charHeight;
+ imgHeight -= imgHeight % av.getCharHeight();
if (imgHeight < 1)
{
g.drawImage(image, 0, 0, this);
}
+ /**
+ * local copy of av.getCharHeight set at top of drawIds
+ */
+ private int avcharHeight;
void drawIds(int starty, int endy)
{
+ // hardwired italic IDs in applet currently
Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
.getFont().getSize());
+ // temp variable for speed
+ avcharHeight = av.getCharHeight();
gg.setFont(italic);
int annotationHeight = 0;
AnnotationLabels labels = null;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
AnnotationPanel ap = new AnnotationPanel(av);
annotationHeight = ap.adjustPanelHeight();
labels = new AnnotationLabels(av);
}
-
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = avcharHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += avcharHeight;
}
- int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+ int cHeight = alheight * avcharHeight + hgap + annotationHeight;
int rowSize = av.getEndRes() - av.getStartRes();
if (labels != null)
{
- gg.translate(0, ypos + (alheight * av.charHeight));
+ gg.translate(0, ypos + (alheight * avcharHeight));
labels.drawComponent(gg, getSize().width);
- gg.translate(0, -ypos - (alheight * av.charHeight));
+ gg.translate(0, -ypos - (alheight * avcharHeight));
}
}
gg.setColor(currentColor);
// TODO: isrep could be used to highlight the representative in a
// different way
- gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,
- av.charHeight);
+ gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
+ avcharHeight);
gg.setColor(currentTextColor);
gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
- (((i - starty) * av.charHeight) + av.charHeight)
- - (av.charHeight / 5));
+ (((i - starty) * avcharHeight) + avcharHeight)
+ - (avcharHeight / 5));
- if (av.hasHiddenRows() && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.getShowHiddenMarkers())
{
drawMarker(i, starty, 0);
}
if (below)
{
gg.fillPolygon(new int[]
- { getSize().width - av.charHeight, getSize().width - av.charHeight,
+ { getSize().width - avcharHeight, getSize().width - avcharHeight,
getSize().width }, new int[]
- { (i - starty) * av.charHeight + yoffset,
- (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
- (i - starty) * av.charHeight + yoffset }, 3);
+ { (i - starty) * avcharHeight + yoffset,
+ (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
+ (i - starty) * avcharHeight + yoffset }, 3);
}
if (above)
{
gg.fillPolygon(new int[]
- { getSize().width - av.charHeight, getSize().width - av.charHeight,
+ { getSize().width - avcharHeight, getSize().width - avcharHeight,
getSize().width }, new int[]
- { (i - starty + 1) * av.charHeight + yoffset,
- (i - starty + 1) * av.charHeight + yoffset - av.charHeight / 4,
- (i - starty + 1) * av.charHeight + yoffset }, 3);
+ { (i - starty + 1) * avcharHeight + yoffset,
+ (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
+ (i - starty + 1) * avcharHeight + yoffset }, 3);
}
}
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.UrlLink;
+
+import java.awt.BorderLayout;
+import java.awt.Panel;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
import java.util.List;
import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
-
public class IdPanel extends Panel implements MouseListener,
MouseMotionListener
{
int y = e.getY();
if (av.getWrapAlignment())
{
- y -= 2 * av.charHeight;
+ y -= 2 * av.getCharHeight();
}
int seq = alignPanel.seqPanel.findSeq(e);
CommandI command = (CommandI) historyList.pop();
command.undoCommand(null);
- if (ap.av.historyList.contains(command))
+ if (ap.av.getHistoryList().contains(command))
{
- ap.av.historyList.removeElement(command);
+ ap.av.getHistoryList().remove(command);
ap.alignFrame.updateEditMenuBar();
ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
}
int height)
{
gg.setFont(av.getFont());
-
// Fill in the background
gg.setColor(Color.white);
gg.fillRect(0, 0, width, height);
// Fill the selected columns
ColumnSelection cs = av.getColumnSelection();
gg.setColor(new Color(220, 0, 0));
-
+ int avcharWidth = av.getCharWidth(), avcharHeight = av.getCharHeight();
for (int i = 0; i < cs.size(); i++)
{
int sel = cs.columnAt(i);
if ((sel >= startx) && (sel <= endx))
{
- gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
+ gg.fillRect((sel - startx) * avcharWidth, 0, avcharWidth,
getSize().height);
}
}
int scalestartx = (startx / 10) * 10;
FontMetrics fm = gg.getFontMetrics(av.getFont());
- int y = av.charHeight - fm.getDescent();
+ int y = avcharHeight - fm.getDescent();
if ((scalestartx % 10) == 0)
{
{
string = String.valueOf(av.getColumnSelection()
.adjustForHiddenColumns(i));
- if ((i - startx - 1) * av.charWidth > maxX)
+ if ((i - startx - 1) * avcharWidth > maxX)
{
- gg.drawString(string, (i - startx - 1) * av.charWidth, y);
- maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
+ gg.drawString(string, (i - startx - 1) * avcharWidth, y);
+ maxX = (i - startx + 1) * avcharWidth + fm.stringWidth(string);
}
gg.drawLine(
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
y + 2,
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
y + (fm.getDescent() * 2));
}
else
{
gg.drawLine(
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
y + fm.getDescent(),
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ ((i - startx - 1) * avcharWidth)
+ + (avcharWidth / 2),
y + (fm.getDescent() * 2));
}
}
}
gg.fillPolygon(new int[]
- { res * av.charWidth - av.charHeight / 4,
- res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+ { res * avcharWidth - avcharHeight / 4,
+ res * avcharWidth + avcharHeight / 4, res * avcharWidth },
new int[]
- { y - av.charHeight / 2, y - av.charHeight / 2, y + 8 },
+ { y - avcharHeight / 2, y - avcharHeight / 2, y + 8 },
3);
}
if (reveal != null && reveal[0] > startx && reveal[0] < endx)
{
gg.drawString(MessageManager.getString("label.reveal_columns"),
- reveal[0] * av.charWidth, 0);
+ reveal[0] * avcharWidth, 0);
}
}
fr = new FeatureRenderer(av);
sr = new SequenceRenderer(av);
PaintRefresher.Register(this, av.getSequenceSetId());
+ updateViewport();
+ }
+
+ int avcharHeight = 0, avcharWidth = 0;
+
+ private void updateViewport()
+ {
+ avcharHeight = av.getCharHeight();
+ avcharWidth = av.getCharWidth();
}
public AlignViewport getViewport()
return sr;
}
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
int scalestartx = startx - startx % 10 + 10;
value = av.getColumnSelection().adjustForHiddenColumns(value);
}
- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
- ypos - (av.charHeight / 2));
+ g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth,
+ ypos - (avcharHeight / 2));
- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- (ypos + 2) - (av.charHeight / 2),
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
+ (ypos + 2) - (avcharHeight / 2),
+ ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
ypos - 2);
}
}
- void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ private void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
+ ypos += avcharHeight;
if (av.hasHiddenColumns())
{
startx = av.getColumnSelection().adjustForHiddenColumns(startx);
if (value != -1)
{
int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- - av.charWidth / 2;
- g.drawString(value + "", x, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ - avcharWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * avcharHeight))
+ - (avcharHeight / 5));
}
}
}
- void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ private void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
- ypos += av.charHeight;
+ ypos += avcharHeight;
if (av.hasHiddenColumns())
{
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight))
+ - (avcharHeight / 5));
}
}
}
return;
}
+ updateViewport();
+
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
lastsr = av.startRes;
fastPaint = true;
- gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
- imgWidth - horizontal * av.charWidth, imgHeight - vertical
- * av.charHeight, -horizontal * av.charWidth, -vertical
- * av.charHeight);
+ gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
+ - horizontal * avcharWidth,
+ imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
+ -vertical * avcharHeight);
int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * avcharWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
}
else
{
- transY = imgHeight - vertical * av.charHeight;
+ transY = imgHeight - vertical * avcharHeight;
}
}
else if (vertical < 0)
paint(g);
}
+ @Override
public void paint(Graphics g)
{
return;
}
+ updateViewport();
// this draws the whole of the alignment
imgWidth = this.getSize().width;
imgHeight = this.getSize().height;
- imgWidth -= imgWidth % av.charWidth;
- imgHeight -= imgHeight % av.charHeight;
+ imgWidth -= imgWidth % avcharWidth;
+ imgHeight -= imgHeight % avcharHeight;
if (imgWidth < 1 || imgHeight < 1)
{
public int getWrappedCanvasWidth(int cwidth)
{
- cwidth -= cwidth % av.charWidth;
+ cwidth -= cwidth % av.getCharWidth();
FontMetrics fm = getFontMetrics(av.getFont());
LABEL_EAST = 0;
LABEL_WEST = 0;
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.getCharWidth();
}
/**
return mask;
}
- public void drawWrappedPanel(Graphics g, int canvasWidth,
+ private void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
AlignmentI al = av.getAlignment();
FontMetrics fm = getFontMetrics(av.getFont());
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = avcharHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += avcharHeight;
}
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- int cHeight = av.getAlignment().getHeight() * av.charHeight;
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
+ int cHeight = av.getAlignment().getHeight() * avcharHeight;
av.setWrappedWidth(cWidth);
g.setColor(Color.black);
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
drawWestScale(g, startRes, endx, ypos);
}
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
g.translate(canvasWidth - LABEL_EAST, 0);
drawEastScale(g, startRes, endx, ypos);
g.translate(LABEL_WEST, 0);
- if (av.scaleAboveWrapped)
+ if (av.getScaleAboveWrapped())
{
drawNorthScale(g, startRes, endx, ypos);
}
- if (av.hasHiddenColumns() && av.showHiddenMarkers)
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
g.setColor(Color.blue);
int res;
}
gg.fillPolygon(new int[]
- { res * av.charWidth - av.charHeight / 4,
- res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+ { res * avcharWidth - avcharHeight / 4,
+ res * avcharWidth + avcharHeight / 4, res * avcharWidth },
new int[]
- { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
- ypos - (av.charHeight / 2) + 8 }, 3);
+ { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
+ ypos - (avcharHeight / 2) + 8 }, 3);
}
}
if (g.getClip() == null)
{
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+ g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
g.setClip(null);
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 4);
if (annotations == null)
int getAnnotationHeight()
{
- if (!av.showAnnotation)
+ if (!av.isShowAnnotation())
{
return 0;
}
return annotations.adjustPanelHeight();
}
- void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+ private void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq,
int endSeq, int offset)
{
blockEnd = hideStart - 1;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * avcharWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
if (av.getShowHiddenMarkers())
{
g1.setColor(Color.blue);
- g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
- 0 + offset, (blockEnd - blockStart + 1) * av.charWidth
- - 1, (endSeq - startSeq) * av.charHeight
+ g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
+ - 1, (endSeq - startSeq) * avcharHeight
+ offset);
}
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * avcharWidth, 0);
screenY += blockEnd - blockStart + 1;
blockStart = hideEnd + 1;
}
if (screenY <= (endRes - startRes))
{
blockEnd = blockStart + (endRes - startRes) - screenY;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * avcharWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * avcharWidth, 0);
}
}
int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.renderGaps);
-
+ sr.prepare(g, av.isRenderGaps());
+ updateViewport();
SequenceI nextSeq;
// / First draw the sequences
}
sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+ startRes, endRes, offset + ((i - startSeq) * avcharHeight));
if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * av.charHeight));
+ + ((i - startSeq) * avcharHeight));
}
// / Highlight search Results once all sequences have been drawn
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
visibleResults[r + 1], (visibleResults[r] - startRes)
- * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ * avcharWidth, offset
+ + ((i - startSeq) * avcharHeight));
}
}
}
if (av.cursorMode && cursorY == i && cursorX >= startRes
&& cursorX <= endRes)
{
- sr.drawCursor(nextSeq, cursorX,
- (cursorX - startRes) * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
+ offset + ((i - startSeq) * avcharHeight));
}
}
}
- void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
+ private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
int startSeq, int endSeq, int offset)
{
//
for (i = startSeq; i < endSeq; i++)
{
- sx = (group.getStartRes() - startRes) * av.charWidth;
- sy = offset + ((i - startSeq) * av.charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
+ sx = (group.getStartRes() - startRes) * avcharWidth;
+ sy = offset + ((i - startSeq) * avcharHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;
if (sx + ex < 0 || sx > imgWidth)
{
continue;
}
- if ((sx <= (endRes - startRes) * av.charWidth)
+ if ((sx <= (endRes - startRes) * avcharWidth)
&& group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i)))
{
.contains(
av.getAlignment().getSequenceAt(i + 1))))
{
- bottom = sy + av.charHeight;
+ bottom = sy + avcharHeight;
}
if (!inGroup)
ex = imgWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * avcharWidth;
}
if (top != -1)
if (inGroup)
{
- sy = offset + ((i - startSeq) * av.charHeight);
+ sy = offset + ((i - startSeq) * avcharHeight);
if (sx >= 0 && sx < imgWidth)
{
g.drawLine(sx, oldY, sx, sy);
{
ex = imgWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * avcharWidth;
}
if (top != -1)
*/
package jalview.appletgui;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.api.AlignViewportI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
+import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
-import java.awt.BorderLayout;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Panel;
-import java.awt.Point;
-import java.awt.event.InputEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.util.Vector;
-
public class SeqPanel extends Panel implements MouseMotionListener,
- MouseListener, SequenceListener
+ MouseListener, SequenceListener, SelectionListener
{
public SeqCanvas seqCanvas;
seqCanvas.addMouseListener(this);
ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
seqCanvas.repaint();
}
void setCursorPosition()
{
- SequenceI sequence = av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
endEditing();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
ap.scrollToWrappedVisible(seqCanvas.cursorX);
}
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
return 1;
}
+ /**
+ * Set status message in alignment panel
+ *
+ * @param sequence
+ * aligned sequence object
+ * @param res
+ * alignment column
+ * @param seq
+ * index of sequence in alignment
+ * @return position of res in sequence
+ */
void setStatusMessage(SequenceI sequence, int res, int seq)
{
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
- + sequence.getName());
-
- Object obj = null;
+ // TODO remove duplication of identical gui method
+ StringBuilder text = new StringBuilder(32);
+ String seqno = seq == -1 ? "" : " " + (seq + 1);
+ text.append("Sequence" + seqno + " ID: " + sequence.getName());
+
+ String residue = null;
+ /*
+ * Try to translate the display character to residue name (null for gap).
+ */
+ final String displayChar = String.valueOf(sequence.getCharAt(res));
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
- + "");
- if (obj != null)
+ residue = ResidueProperties.nucleotideName.get(displayChar);
+ if (residue != null)
{
- text.append(" Nucleotide: ");
+ text.append(" Nucleotide: ").append(residue);
}
}
else
{
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
- if (obj != null)
- {
- text.append(" Residue: ");
- }
- }
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ResidueProperties.aa2Triplet.get(displayChar);
+ if (residue != null)
+ {
+ text.append(" Residue: ").append(residue);
+ }
+ }
+
+ int pos = -1;
+ if (residue != null)
+ {
+ pos = sequence.findPosition(res);
+ text.append(" (").append(Integer.toString(pos)).append(")");
+ }
+ // Object obj = null;
+ // if (av.getAlignment().isNucleotide())
+ // {
+ // obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ // + "");
+ // if (obj != null)
+ // {
+ // text.append(" Nucleotide: ");
+ // }
+ // }
+ // else
+ // {
+ // obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ // if (obj != null)
+ // {
+ // text.append(" Residue: ");
+ // }
+ // }
+ //
+ // if (obj != null)
+ // {
+ //
+ // if (obj != "")
+ // {
+ // text.append(obj + " (" + sequence.findPosition(res) + ")");
+ // }
+ // }
- if (obj != null)
- {
+ ap.alignFrame.statusBar.setText(text.toString());
- if (obj != "")
- {
- text.append(obj + " (" + sequence.findPosition(res) + ")");
- }
- }
+ }
- ap.alignFrame.statusBar.setText(text.toString());
+ /**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ */
+ private void setStatusMessage(SearchResults results)
+ {
+ List<Match> matches = results.getResults();
+ if (!matches.isEmpty())
+ {
+ Match m = matches.get(0);
+ SequenceI seq = m.getSequence();
+ int sequenceIndex = this.av.getAlignment().findIndex(seq);
+ /*
+ * Convert position in sequence (base 1) to sequence character array index
+ * (base 0)
+ */
+ int start = m.getStart() - 1;
+ setStatusMessage(seq, start, sequenceIndex);
+ }
}
public void mousePressed(MouseEvent evt)
int res = 0;
int x = evt.getX();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap
+ seqCanvas.getAnnotationHeight();
int y = evt.getY();
int seq = 0;
int y = evt.getY();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap
+ seqCanvas.getAnnotationHeight();
y -= hgap;
ap.alignFrame.repaint();
}
}
+ setStatusMessage(results);
seqCanvas.highlightSearchResults(results);
}
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ return this.ap == null ? null : this.ap.av;
+ }
+
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
mouseOverSequence(sequence, res, respos);
}
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
- + sequence.getName());
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(Integer.toString(seq + 1))
+ .append(" ID: ").append(sequence.getName());
- Object obj = null;
+ String obj = null;
+ final String ch = String.valueOf(sequence.getCharAt(res));
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
- + "");
+ obj = ResidueProperties.nucleotideName.get(ch);
if (obj != null)
{
- text.append(" Nucleotide: ");
+ text.append(" Nucleotide: ").append(obj);
}
}
else
{
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ obj = "X".equalsIgnoreCase(ch) ? "X"
+ : ResidueProperties.aa2Triplet.get(ch);
if (obj != null)
{
- text.append(" Residue: ");
+ text.append(" Residue: ").append(obj);
}
}
if (obj != null)
{
- if (obj != "")
- {
- text.append(obj + " (" + respos + ")");
- }
+ text.append(" (").append(Integer.toString(respos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
- StringBuffer tooltipText = new StringBuffer();
+ StringBuilder tooltipText = new StringBuilder();
SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
{
- tooltipText.append(groups[g].getName() + " ");
+ tooltipText.append(groups[g].getName()).append(" ");
}
if (groups[g].getDescription() != null)
{
{
if (mouseWheelPressed)
{
- int oldWidth = av.charWidth;
+ int oldWidth = av.getCharWidth();
// Which is bigger, left-right or up-down?
if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
{
int fontSize = av.font.getSize();
- if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+ if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
{
fontSize--;
}
}
av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
+ av.setCharWidth(oldWidth);
}
else
{
- if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+ if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
{
- av.charWidth--;
+ av.setCharWidth(av.getCharWidth() - 1);
}
else if (evt.getX() > lastMousePress.x)
{
- av.charWidth++;
+ av.setCharWidth(av.getCharWidth() + 1);
}
- if (av.charWidth < 1)
+ if (av.getCharWidth() < 1)
{
- av.charWidth = 1;
+ av.setCharWidth(1);
}
}
ap.fontChanged();
FontMetrics fm = getFontMetrics(av.getFont());
- av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
lastMousePress = evt.getPoint();
StringBuffer message = new StringBuffer();
if (groupEditing)
{
- message.append(MessageManager.getString("action.edit_group")).append(":");
+ message.append(MessageManager.getString("action.edit_group")).append(
+ ":");
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+ editCommand = new EditCommand(
+ MessageManager.getString("action.edit_group"));
}
}
else
{
- message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName());
+ message.append(MessageManager.getString("label.edit_sequence"))
+ .append(" " + seq.getName());
String label = seq.getName();
if (label.length() > 10)
{
}
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
+ editCommand = new EditCommand(MessageManager.formatMessage(
+ "label.edit_params", new String[]
+ { label }));
}
}
}
else
{
- editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.getAlignment(), true);
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - lastres, av.getAlignment(), true);
}
}
else
}
else
{
- editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.getAlignment(), true);
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ lastres - startres, av.getAlignment(), true);
}
}
editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
av.getAlignment(), true);
- editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
- av.getAlignment(), true);
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
+ true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
- av.getAlignment(), true);
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
+ true);
editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
av.getAlignment(), true);
SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
sequence.findPosition(res));
- Vector links = null;
+ Vector<String> links = null;
if (allFeatures != null)
{
for (int i = 0; i < allFeatures.length; i++)
{
if (links == null)
{
- links = new Vector();
+ links = new Vector<String>();
}
for (int j = 0; j < allFeatures[i].links.size(); j++)
{
{
return;
}
+
+ /*
+ * Check for selection in a view of which this one is a dna/protein
+ * complement.
+ */
+ if (selectionFromTranslation(seqsel, colsel, source))
+ {
+ return;
+ }
+
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
// rules are: colsel is copied if there is a real intersection between
ap.scrollTo(column, column, ap.av.startSeq, true, true);
}
+ /**
+ * If this panel is a cdna/protein translation view of the selection source,
+ * tries to map the source selection to a local one, and returns true. Else
+ * returns false.
+ *
+ * @param seqsel
+ * @param colsel
+ * @param source
+ */
+ protected boolean selectionFromTranslation(SequenceGroup seqsel,
+ ColumnSelection colsel, SelectionSource source)
+ {
+ if (!(source instanceof AlignViewportI)) {
+ return false;
+ }
+ final AlignViewportI sourceAv = (AlignViewportI) source;
+ if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+ {
+ return false;
+ }
+
+ /*
+ * Map sequence selection
+ */
+ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
+ av.setSelectionGroup(sg);
+ av.isSelectionGroupChanged(true);
+
+ /*
+ * Map column selection
+ */
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+ av);
+ av.setColumnSelection(cs);
+ av.isColSelChanged(true);
+
+ ap.scalePanelHolder.repaint();
+ ap.repaint();
+
+ return true;
+ }
+
}
package jalview.appletgui;
import jalview.api.FeatureRenderer;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
int length = seq.getLength();
int curStart = -1;
- int curWidth = av.charWidth;
+ int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av
+ .getCharHeight();
Color tempColour = null;
while (i <= end)
{
if (tempColour != null)
{
- graphics.fillRect(av.charWidth * (curStart - start), y1,
- curWidth, av.charHeight);
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+ avCharHeight);
}
graphics.setColor(resBoxColour);
curStart = i;
- curWidth = av.charWidth;
+ curWidth = avCharWidth;
tempColour = resBoxColour;
}
else
{
- curWidth += av.charWidth;
+ curWidth += avCharWidth;
}
i++;
}
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
- av.charHeight);
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+ avCharHeight);
}
public void drawText(SequenceI seq, int start, int end, int y1)
{
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
Font boldFont = null;
boolean bold = false;
- if (av.upperCasebold)
+ if (av.isUpperCasebold())
{
- boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+ boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);
graphics.setFont(av.getFont());
}
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+ y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady
int charOffset = 0;
}
}
- if (av.upperCasebold)
+ if (av.isUpperCasebold())
{
fm = graphics.getFontMetrics();
if ('A' <= s && s <= 'Z')
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+ charOffset = (avCharWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + avCharWidth
* (i - start), y1);
}
public void drawHighlightedText(SequenceI seq, int start, int end,
int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+ int pady = avCharHeight / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
- av.charHeight);
+ graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight);
graphics.setColor(Color.white);
char s = '~';
s = seq.getCharAt(i);
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (avCharWidth - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1
- + av.charWidth * (i - start), y1 + av.charHeight - pady);
+ + avCharWidth * (i - start), y1 + avCharHeight - pady);
}
}
}
public void drawCursor(SequenceI seq, int res, int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
graphics.setColor(Color.white);
graphics.setColor(Color.white);
if (av.validCharWidth)
{
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ (y1 + av.getCharHeight()) - pady);
}
}
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Iterator;
+
public class SliderPanel extends Panel implements ActionListener,
AdjustmentListener, MouseListener
{
}
else
{
- toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+ toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
}
if (allGroups != null && allGroups.hasNext())
{
while ((toChange = allGroups.next().cs) == null
&& allGroups.hasNext())
+ {
;
+ }
}
else
{
--- /dev/null
+package jalview.appletgui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.api.ViewStyleI;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Panel;
+
+public class SplitFrame extends EmbmenuFrame
+{
+ private static final long serialVersionUID = 1L;
+
+ private AlignFrame topFrame;
+
+ private AlignFrame bottomFrame;
+
+ private Panel outermost;
+
+ /**
+ * Constructor
+ */
+ public SplitFrame(AlignFrame af1, AlignFrame af2)
+ {
+ topFrame = af1;
+ bottomFrame = af2;
+ init();
+ }
+
+ /**
+ * Creates a Panel containing two Panels, and adds the first and second
+ * AlignFrame's components to each. At this stage we have not yet committed to
+ * whether the enclosing panel will be added to this frame, for display as a
+ * separate frame, or added to the applet (embedded mode).
+ */
+ public void init()
+ {
+ constructSplit();
+
+ /*
+ * Try to make and add dna/protein sequence mappings
+ */
+ final AlignViewport topViewport = topFrame.viewport;
+ final AlignViewport bottomViewport = bottomFrame.viewport;
+ final AlignmentI topAlignment = topViewport.getAlignment();
+ final AlignmentI bottomAlignment = bottomViewport.getAlignment();
+ AlignViewport cdna = topAlignment.isNucleotide() ? topViewport
+ : (bottomAlignment.isNucleotide() ? bottomViewport : null);
+ AlignViewport protein = !topAlignment.isNucleotide() ? topViewport
+ : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
+
+ boolean mapped = AlignmentUtils.mapProteinToCdna(
+ protein.getAlignment(), cdna.getAlignment());
+ if (mapped)
+ {
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(topViewport.applet);
+ ssm.addMappings(protein.getAlignment().getCodonFrames());
+ topViewport.setCodingComplement(bottomViewport);
+ ssm.addCommandListener(cdna);
+ ssm.addCommandListener(protein);
+ }
+
+ adjustLayout();
+ }
+
+ /**
+ *
+ */
+ protected void constructSplit()
+ {
+ setMenuBar(null);
+ outermost = new Panel(new GridLayout(2, 1));
+
+ Panel topPanel = new Panel();
+ Panel bottomPanel = new Panel();
+ outermost.add(topPanel);
+ outermost.add(bottomPanel);
+
+ addAlignFrameComponents(topFrame, topPanel);
+ addAlignFrameComponents(bottomFrame, bottomPanel);
+ }
+
+ /**
+ * Make any adjustments to the layout
+ */
+ protected void adjustLayout()
+ {
+ AlignViewport cdna = topFrame.getAlignViewport().getAlignment()
+ .isNucleotide() ? topFrame.viewport : bottomFrame.viewport;
+ AlignViewport protein = cdna == topFrame.viewport ? bottomFrame.viewport
+ : topFrame.viewport;
+
+ /*
+ * Ensure sequence ids are the same width for good alignment.
+ */
+ // TODO should do this via av.getViewStyle/setViewStyle
+ // however at present av.viewStyle is not set in IdPanel.fontChanged
+ int w1 = topFrame.alignPanel.idPanel.idCanvas.getWidth();
+ int w2 = bottomFrame.alignPanel.idPanel.idCanvas.getWidth();
+ int w3 = Math.max(w1, w2);
+ if (w1 != w3)
+ {
+ Dimension d = topFrame.alignPanel.idPanel.idCanvas.getSize();
+ topFrame.alignPanel.idPanel.idCanvas.setSize(new Dimension(w3,
+ d.height));
+ }
+ if (w2 != w3)
+ {
+ Dimension d = bottomFrame.alignPanel.idPanel.idCanvas.getSize();
+ bottomFrame.alignPanel.idPanel.idCanvas.setSize(new Dimension(w3,
+ d.height));
+ }
+
+ /*
+ * Expand protein to 3 times character width of dna
+ */
+ if (protein != null && cdna != null)
+ {
+ ViewStyleI vs = protein.getViewStyle();
+ vs.setCharWidth(3 * vs.getCharWidth());
+ protein.setViewStyle(vs);
+ }
+ }
+
+ /**
+ * Add the menu bar, alignment panel and status bar from the AlignFrame to the
+ * panel. The menu bar is a panel 'reconstructed' from the AlignFrame's frame
+ * menu bar. This allows each half of the SplitFrame to have its own menu bar.
+ *
+ * @param af
+ * @param panel
+ */
+ private void addAlignFrameComponents(AlignFrame af, Panel panel)
+ {
+ panel.setLayout(new BorderLayout());
+ Panel menuPanel = af
+ .makeEmbeddedPopupMenu(af.getMenuBar(), true, false);
+ panel.add(menuPanel, BorderLayout.NORTH);
+ panel.add(af.statusBar, BorderLayout.SOUTH);
+ panel.add(af.alignPanel, BorderLayout.CENTER);
+ }
+
+ /**
+ * Display the content panel either as a new frame or embedded in the applet.
+ *
+ * @param embedded
+ * @param applet
+ */
+ public void addToDisplay(boolean embedded, JalviewLite applet)
+ {
+ createSplitFrameWindow(embedded, applet);
+ validate();
+ topFrame.alignPanel.adjustAnnotationHeight();
+ topFrame.alignPanel.paintAlignment(true);
+ bottomFrame.alignPanel.adjustAnnotationHeight();
+ bottomFrame.alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Either show the content panel in this frame as a new frame, or (if
+ * embed=true) add it to the applet container instead.
+ *
+ * @param embed
+ * @param applet
+ */
+ protected void createSplitFrameWindow(boolean embed, JalviewLite applet)
+ {
+ if (embed)
+ {
+ applet.add(outermost);
+ applet.validate();
+ }
+ else
+ {
+ this.add(outermost);
+ int width = Math.max(topFrame.DEFAULT_WIDTH,
+ bottomFrame.DEFAULT_WIDTH);
+ int height = topFrame.DEFAULT_HEIGHT + bottomFrame.DEFAULT_HEIGHT;
+ jalview.bin.JalviewLite
+ .addFrame(this, this.getTitle(), width, height);
+ }
+ }
+}
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
+import jalview.util.MappingUtils;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.ScrollPane;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
public class TreeCanvas extends Panel implements MouseListener,
MouseMotionListener
av.setSelectionGroup(null);
av.getAlignment().deleteAllGroups();
av.clearSequenceColours();
+ final AlignViewportI codingComplement = av.getCodingComplement();
+ if (codingComplement != null)
+ {
+ codingComplement.setSelectionGroup(null);
+ codingComplement.getAlignment().deleteAllGroups();
+ codingComplement.clearSequenceColours();
+ }
colourGroups();
if (cs != null)
{
cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.getIgnoreGapsConsensus());
+ av.isIgnoreGapsConsensus());
}
}
// TODO: cs used to be initialized with a sequence collection and
av.getAlignment().addGroup(sg);
+ // TODO this is duplicated with gui TreeCanvas - refactor
+ av.getAlignment().addGroup(sg);
+ final AlignViewportI codingComplement = av.getCodingComplement();
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+ codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ // TODO why does gui require col.brighter() here??
+ codingComplement.setSequenceColour(seq, col);
+ }
+ }
+ }
+
}
ap.updateAnnotation();
-
+ if (av.getCodingComplement() != null)
+ {
+ ((AlignViewport) av.getCodingComplement()).firePropertyChange(
+ "alignment", null, ap.av.getAlignment().getSequences());
+ }
}
public void setShowDistances(boolean state)
{
applyButton_actionPerformed();
if (dialog != null)
+ {
dialog.setVisible(false);
+ }
frame.setVisible(false);
}
UserColourScheme ucs = new UserColourScheme(newColours);
if (ap != null)
{
- ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
if (ap != null)
}
}
if (dialog != null)
+ {
dialog.setVisible(false);
+ }
frame.setVisible(false);
return;
import jalview.appletgui.AlignViewport;
import jalview.appletgui.EmbmenuFrame;
import jalview.appletgui.FeatureSettings;
+import jalview.appletgui.SplitFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
import jalview.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.Hashtable;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
StructureSelectionManagerProvider, JalviewLiteJsApi
{
+ private static final String TRUE = "true";
+
+ private static final String FALSE = "false";
+
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager.getStructureSelectionManager(this);
end = rs.findIndex(end);
if (csel != null)
{
- Vector cs = csel.getSelected();
+ List<Integer> cs = csel.getSelected();
csel.clear();
- for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)
+ for (Integer selectedCol : cs)
{
- csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))
- .intValue()));
+ csel.addElement(rs.findIndex(selectedCol));
}
}
}
{
try
{
- boolean seqlimits = suffix.equalsIgnoreCase("true");
+ boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
if (alf.viewport.getSelectionGroup() != null)
{
// JBPNote: getSelectionAsNewSequence behaviour has changed - this
final String _undoName = undoName;
// TODO: deal with synchronization here: cannot raise any events until after
// this has returned.
- return alf.sortBy(aorder, _undoName) ? "true" : "";
+ return alf.sortBy(aorder, _undoName) ? TRUE : "";
}
/*
*/
public String getAlignment(String format)
{
- return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
+ return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
}
/*
*/
public String getAlignmentFrom(AlignFrame alf, String format)
{
- return getAlignmentFrom(alf, format, "true");
+ return getAlignmentFrom(alf, format, TRUE);
}
/*
{
try
{
- boolean seqlimits = suffix.equalsIgnoreCase("true");
+ boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
String reply = new AppletFormatAdapter().formatSequences(format,
alf.viewport.getAlignment(), seqlimits);
String file = "No file";
- Button launcher = new Button("Start Jalview");
+ String file2 = "No file";
+
+ Button launcher = new Button(
+ MessageManager.getString("label.start_jalview"));
/**
* The currentAlignFrame is static, it will change if and when the user
/**
* turn on extra applet debugging
*/
- String dbg = getParameter("debug");
- if (dbg != null)
- {
- debug = dbg.toLowerCase().equals("true");
- }
+ debug = TRUE.equalsIgnoreCase(getParameter("debug"));
if (debug)
{
if (externalsviewer != null)
{
useXtrnalSviewer = externalsviewer.trim().toLowerCase()
- .equals("true");
+ .equals(TRUE);
}
/**
* if true disable the check for jmol
String chkforJmol = getParameter("nojmol");
if (chkforJmol != null)
{
- checkForJmol = !chkforJmol.equals("true");
+ checkForJmol = !chkforJmol.equals(TRUE);
}
/**
* get the separator parameter if present
file = data.toString();
}
}
+ file2 = getParameter("file2");
- final JalviewLite jvapplet = this;
- if (getParameter("embedded") != null
- && getParameter("embedded").equalsIgnoreCase("true"))
+ embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
+ if (embedded)
{
- // Launch as embedded applet in page
- embedded = true;
- LoadingThread loader = new LoadingThread(file, jvapplet);
+ LoadingThread loader = new LoadingThread(file, file2, this);
loader.start();
}
else if (file != null)
{
- if (getParameter("showbutton") == null
- || !getParameter("showbutton").equalsIgnoreCase("false"))
+ /*
+ * Start the applet immediately or show a button to start it
+ */
+ if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
+ {
+ LoadingThread loader = new LoadingThread(file, file2, this);
+ loader.start();
+ }
+ else
{
- // Add the JalviewLite 'Button' to the page
add(launcher);
launcher.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- LoadingThread loader = new LoadingThread(file, jvapplet);
+ LoadingThread loader = new LoadingThread(file, file2,
+ JalviewLite.this);
loader.start();
}
});
}
- else
- {
- // Open jalviewLite immediately.
- LoadingThread loader = new LoadingThread(file, jvapplet);
- loader.start();
- }
}
else
{
class LoadingThread extends Thread
{
/**
- * State variable: File source
- */
- String file;
-
- /**
* State variable: protocol for access to file source
*/
String protocol;
- /**
- * State variable: format of file source
- */
- String format;
+ String _file; // alignment file or URL spec
- String _file;
+ String _file2; // second alignment file or URL spec
JalviewLite applet;
private void dbgMsg(String msg)
{
- if (applet.debug)
+ if (JalviewLite.debug)
{
System.err.println(msg);
}
return file;
}
- public LoadingThread(String _file, JalviewLite _applet)
+ public LoadingThread(String file, String file2, JalviewLite _applet)
{
- this._file = _file;
+ this._file = file;
+ this._file2 = file2;
applet = _applet;
}
} catch (Exception e)
{
}
- ;
}
startLoading();
// applet.callInitCallback();
}
+ /**
+ * Load the alignment and any related files as specified by applet
+ * parameters
+ */
private void startLoading()
{
- AlignFrame newAlignFrame;
dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
- file = setProtocolState(_file);
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
- dbgMsg("File identified as '" + format + "'");
dbgMsg("Loading started.");
- Alignment al = null;
+
+ AlignFrame newAlignFrame = readAlignment(_file);
+ AlignFrame newAlignFrame2 = readAlignment(_file2);
+ if (newAlignFrame != null)
+ {
+ addToDisplay(newAlignFrame, newAlignFrame2);
+ loadTree(newAlignFrame);
+
+ loadScoreFile(newAlignFrame);
+
+ loadFeatures(newAlignFrame);
+
+ loadAnnotations(newAlignFrame);
+
+ loadJnetFile(newAlignFrame);
+
+ loadPdbFiles(newAlignFrame);
+ }
+ else
+ {
+ fileFound = false;
+ applet.remove(launcher);
+ applet.repaint();
+ }
+ callInitCallback();
+ }
+
+ /**
+ * Add an AlignFrame to the display; or if two are provided, a SplitFrame.
+ *
+ * @param af
+ * @param af2
+ */
+ public void addToDisplay(AlignFrame af, AlignFrame af2)
+ {
+ if (af2 == null)
+ {
+ af.addToDisplay(embedded);
+ }
+ else
+ {
+ SplitFrame sf = new SplitFrame(af, af2);
+ sf.addToDisplay(embedded, JalviewLite.this);
+ }
+ }
+
+ /**
+ * Read the alignment file (from URL, text 'paste', or archive by
+ * classloader).
+ *
+ * @return
+ */
+ protected AlignFrame readAlignment(String fileParam)
+ {
+ if (fileParam == null)
+ {
+ return null;
+ }
+ String resolvedFile = setProtocolState(fileParam);
+ String format = new IdentifyFile().Identify(resolvedFile, protocol);
+ dbgMsg("File identified as '" + format + "'");
+ AlignmentI al = null;
try
{
- al = new AppletFormatAdapter().readFile(file, protocol, format);
+ al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format);
+ if ((al != null) && (al.getHeight() > 0))
+ {
+ dbgMsg("Successfully loaded file.");
+ al.setDataset(null);
+ AlignFrame newAlignFrame = new AlignFrame(al, applet,
+ resolvedFile, embedded, false);
+ newAlignFrame.setTitle(resolvedFile);
+ if (initialAlignFrame == null)
+ {
+ initialAlignFrame = newAlignFrame;
+ }
+ // update the focus.
+ currentAlignFrame = newAlignFrame;
+
+ if (protocol == AppletFormatAdapter.PASTE)
+ {
+ newAlignFrame.setTitle(MessageManager.formatMessage(
+ "label.sequences_from", new Object[]
+ { applet.getDocumentBase().toString() }));
+ }
+
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new Object[]
+ { resolvedFile }));
+
+ return newAlignFrame;
+ }
} catch (java.io.IOException ex)
{
dbgMsg("File load exception.");
{
try
{
- FileParse fp = new FileParse(file, protocol);
+ FileParse fp = new FileParse(resolvedFile, protocol);
String ln = null;
- dbgMsg(">>>Dumping contents of '" + file + "' " + "("
+ dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
+ protocol + ")");
while ((ln = fp.nextLine()) != null)
{
}
}
}
- if ((al != null) && (al.getHeight() > 0))
+ return null;
+ }
+
+ /**
+ * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
+ * else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadPdbFiles(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ /*
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
+ * related to JAL-434
+ */
+
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
+ false));
+ /*
+ * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
+ * PDB|1GAQ|1GAQ|C">
+ *
+ * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
+ *
+ * <param name="PDBfile3" value="1q0o Q45135_9MICO">
+ */
+
+ int pdbFileCount = 0;
+ // Accumulate pdbs here if they are heading for the same view (if
+ // alignPdbStructures is true)
+ Vector pdbs = new Vector();
+ // create a lazy matcher if we're asked to
+ jalview.analysis.SequenceIdMatcher matcher = (applet
+ .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
+ alignFrame.getAlignViewport().getAlignment()
+ .getSequencesArray()) : null;
+
+ String param;
+ do
{
- dbgMsg("Successfully loaded file.");
- newAlignFrame = new AlignFrame(al, applet, file, embedded);
- if (initialAlignFrame == null)
+ if (pdbFileCount > 0)
{
- initialAlignFrame = newAlignFrame;
+ param = applet.getParameter("PDBFILE" + pdbFileCount);
}
- // update the focus.
- currentAlignFrame = newAlignFrame;
-
- if (protocol == jalview.io.AppletFormatAdapter.PASTE)
+ else
{
- newAlignFrame.setTitle(MessageManager.formatMessage(
- "label.sequences_from", new String[]
- { applet.getDocumentBase().toString() }));
+ param = applet.getParameter("PDBFILE");
}
- newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new String[]
- { file }));
-
- String treeFile = applet.getParameter("tree");
- if (treeFile == null)
+ if (param != null)
{
- treeFile = applet.getParameter("treeFile");
- }
+ PDBEntry pdb = new PDBEntry();
- if (treeFile != null)
- {
- try
+ String seqstring;
+ SequenceI[] seqs = null;
+ String[] chains = null;
+
+ StringTokenizer st = new StringTokenizer(param, " ");
+
+ if (st.countTokens() < 2)
{
- treeFile = setProtocolState(treeFile);
- /*
- * if (inArchive(treeFile)) { protocol =
- * AppletFormatAdapter.CLASSLOADER; } else { protocol =
- * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
- */
- jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
- protocol);
-
- fin.parse();
-
- if (fin.getTree() != null)
+ String sequence = applet.getParameter("PDBSEQ");
+ if (sequence != null)
{
- newAlignFrame.loadTree(fin, treeFile);
- dbgMsg("Successfuly imported tree.");
+ seqs = new SequenceI[]
+ { matcher == null ? (Sequence) alignFrame.getAlignViewport()
+ .getAlignment().findName(sequence) : matcher
+ .findIdMatch(sequence) };
}
- else
+
+ }
+ else
+ {
+ param = st.nextToken();
+ Vector tmp = new Vector();
+ Vector tmp2 = new Vector();
+
+ while (st.hasMoreTokens())
{
- dbgMsg("Tree parameter did not resolve to a valid tree.");
+ seqstring = st.nextToken();
+ StringTokenizer st2 = new StringTokenizer(seqstring, "=");
+ if (st2.countTokens() > 1)
+ {
+ // This is the chain
+ tmp2.addElement(st2.nextToken());
+ seqstring = st2.nextToken();
+ }
+ tmp.addElement(matcher == null ? (Sequence) alignFrame
+ .getAlignViewport().getAlignment()
+ .findName(seqstring) : matcher.findIdMatch(seqstring));
+ }
+
+ seqs = new SequenceI[tmp.size()];
+ tmp.copyInto(seqs);
+ if (tmp2.size() == tmp.size())
+ {
+ chains = new String[tmp2.size()];
+ tmp2.copyInto(chains);
}
- } catch (Exception ex)
+ }
+ param = setProtocolState(param);
+
+ if (// !jmolAvailable
+ // &&
+ protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer)
{
- ex.printStackTrace();
+ // Re: JAL-357 : the bug isn't a problem if we are using an
+ // external viewer!
+ // TODO: verify this Re:
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+ // This exception preserves the current behaviour where, even if
+ // the local pdb file was identified in the class loader
+ protocol = AppletFormatAdapter.URL; // this is probably NOT
+ // CORRECT!
+ param = addProtocol(param); //
}
- }
- /*
- * Try to load T-Coffee score file
- */
- String sScoreFile = applet.getParameter("scoreFile");
- if (sScoreFile != null && !"".equals(sScoreFile))
- {
- try
+ pdb.setFile(param);
+
+ if (seqs != null)
{
- if (debug)
+ for (int i = 0; i < seqs.length; i++)
{
- System.err
- .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
+ if (seqs[i] != null)
+ {
+ ((Sequence) seqs[i]).addPDBId(pdb);
+ StructureSelectionManager.getStructureSelectionManager(
+ applet).registerPDBEntry(pdb);
+ }
+ else
+ {
+ if (JalviewLite.debug)
+ {
+ // this may not really be a problem but we give a warning
+ // anyway
+ System.err
+ .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ + i + ")");
+ }
+ }
}
- if (!newAlignFrame.loadScoreFile(sScoreFile))
+
+ if (!alignPdbStructures)
{
- System.err
- .println("Failed to parse T-COFFEE parameter as a valid score file ('"
- + sScoreFile + "')");
+ alignFrame.newStructureView(applet, pdb, seqs, chains,
+ protocol);
+ }
+ else
+ {
+ pdbs.addElement(new Object[]
+ { pdb, seqs, chains, new String(protocol) });
}
- } catch (Exception e)
- {
- System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
- sScoreFile, e.getMessage());
}
}
- // ///////////////////////////
- // modify display of features
- // we do this before any features have been loaded, ensuring any hidden
- // groups are hidden when features first displayed
- //
- // hide specific groups
- //
- String param = applet.getParameter("hidefeaturegroups");
- if (param != null)
- {
- newAlignFrame.setFeatureGroupState(separatorListToArray(param),
- false);
- // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
- }
- // show specific groups
- param = applet.getParameter("showfeaturegroups");
- if (param != null)
- {
- newAlignFrame.setFeatureGroupState(separatorListToArray(param),
- true);
- // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+ pdbFileCount++;
+ } while (param != null || pdbFileCount < 10);
+ if (pdbs.size() > 0)
+ {
+ SequenceI[][] seqs = new SequenceI[pdbs.size()][];
+ PDBEntry[] pdb = new PDBEntry[pdbs.size()];
+ String[][] chains = new String[pdbs.size()][];
+ String[] protocols = new String[pdbs.size()];
+ for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
+ {
+ Object[] o = (Object[]) pdbs.elementAt(pdbsi);
+ pdb[pdbsi] = (PDBEntry) o[0];
+ seqs[pdbsi] = (SequenceI[]) o[1];
+ chains[pdbsi] = (String[]) o[2];
+ protocols[pdbsi] = (String) o[3];
}
- // and now load features
- param = applet.getParameter("features");
- if (param != null)
+ alignFrame.alignedStructureView(applet, pdb, seqs, chains,
+ protocols);
+ result = true;
+ }
+ return result;
+ }
+
+ /**
+ * Load in a Jnetfile if specified by parameter. Returns true if loaded,
+ * else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadJnetFile(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ String param = applet.getParameter("jnetfile");
+ if (param != null)
+ {
+ try
{
param = setProtocolState(param);
-
- newAlignFrame.parseFeaturesFile(param, protocol);
+ JPredFile predictions = new JPredFile(param, protocol);
+ JnetAnnotationMaker.add_annotation(predictions,
+ alignFrame.viewport.getAlignment(), 0, false);
+ // false == do not add sequence profile from concise output
+ SequenceI repseq = alignFrame.viewport.getAlignment()
+ .getSequenceAt(0);
+ alignFrame.viewport.getAlignment().setSeqrep(repseq);
+ ColumnSelection cs = new ColumnSelection();
+ cs.hideInsertionsFor(repseq);
+ alignFrame.viewport.setColumnSelection(cs);
+ alignFrame.alignPanel.fontChanged();
+ alignFrame.alignPanel.setScrollValues(0, 0);
+ result = true;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
+ }
+ return result;
+ }
- param = applet.getParameter("showFeatureSettings");
- if (param != null && param.equalsIgnoreCase("true"))
+ /**
+ * Load annotations if specified by parameter. Returns true if loaded, else
+ * false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadAnnotations(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ String param = applet.getParameter("annotations");
+ if (param != null)
+ {
+ param = setProtocolState(param);
+
+ if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+ param, protocol))
{
- newAlignFrame.viewport.setShowSequenceFeatures(true);
- new FeatureSettings(newAlignFrame.alignPanel);
+ alignFrame.alignPanel.fontChanged();
+ alignFrame.alignPanel.setScrollValues(0, 0);
+ result = true;
}
-
- param = applet.getParameter("annotations");
- if (param != null)
+ else
{
- param = setProtocolState(param);
+ System.err
+ .println("Annotations were not added from annotation file '"
+ + param + "'");
+ }
+ }
+ return result;
+ }
- if (new AnnotationFile().annotateAlignmentView(
- newAlignFrame.viewport, param, protocol))
- {
- newAlignFrame.alignPanel.fontChanged();
- newAlignFrame.alignPanel.setScrollValues(0, 0);
- }
- else
- {
- System.err
- .println("Annotations were not added from annotation file '"
- + param + "'");
- }
+ /**
+ * Load features file and view settings as specified by parameters. Returns
+ * true if features were loaded, else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadFeatures(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ // ///////////////////////////
+ // modify display of features
+ // we do this before any features have been loaded, ensuring any hidden
+ // groups are hidden when features first displayed
+ //
+ // hide specific groups
+ //
+ String param = applet.getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ alignFrame.setFeatureGroupState(separatorListToArray(param), false);
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = applet.getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ alignFrame.setFeatureGroupState(separatorListToArray(param), true);
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+ }
+ // and now load features
+ param = applet.getParameter("features");
+ if (param != null)
+ {
+ param = setProtocolState(param);
- }
+ result = alignFrame.parseFeaturesFile(param, protocol);
+ }
- param = applet.getParameter("jnetfile");
- if (param != null)
+ param = applet.getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase(TRUE))
+ {
+ alignFrame.viewport.setShowSequenceFeatures(true);
+ new FeatureSettings(alignFrame.alignPanel);
+ }
+ return result;
+ }
+
+ /**
+ * Load a score file if specified by parameter. Returns true if file was
+ * loaded, else false.
+ *
+ * @param alignFrame
+ */
+ protected boolean loadScoreFile(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ String sScoreFile = applet.getParameter("scoreFile");
+ if (sScoreFile != null && !"".equals(sScoreFile))
+ {
+ try
{
- try
+ if (debug)
{
- param = setProtocolState(param);
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- param, protocol);
- JnetAnnotationMaker.add_annotation(predictions,
- newAlignFrame.viewport.getAlignment(), 0, false); // false==do
- SequenceI repseq = newAlignFrame.viewport.getAlignment()
- .getSequenceAt(0);
- newAlignFrame.viewport.getAlignment().setSeqrep(repseq);
- ColumnSelection cs = new ColumnSelection();
- cs.hideInsertionsFor(repseq);
- newAlignFrame.viewport.setColumnSelection(cs);
- // not
- // add
- // sequence
- // profile
- // from
- // concise
- // output
- newAlignFrame.alignPanel.fontChanged();
- newAlignFrame.alignPanel.setScrollValues(0, 0);
- } catch (Exception ex)
+ System.err
+ .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
+ }
+ result = alignFrame.loadScoreFile(sScoreFile);
+ if (!result)
{
- ex.printStackTrace();
+ System.err
+ .println("Failed to parse T-COFFEE parameter as a valid score file ('"
+ + sScoreFile + "')");
}
+ } catch (Exception e)
+ {
+ System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
+ sScoreFile, e.getMessage());
}
- /*
- * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
- * - related to JAL-434
- */
- applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
- false));
- /*
- * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
- * PDB|1GAQ|1GAQ|C">
- *
- * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
- *
- * <param name="PDBfile3" value="1q0o Q45135_9MICO">
- */
+ }
+ return result;
+ }
- int pdbFileCount = 0;
- // Accumulate pdbs here if they are heading for the same view (if
- // alignPdbStructures is true)
- Vector pdbs = new Vector();
- // create a lazy matcher if we're asked to
- jalview.analysis.SequenceIdMatcher matcher = (applet
- .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
- newAlignFrame.getAlignViewport().getAlignment()
- .getSequencesArray()) : null;
+ /**
+ * Load a tree for the alignment if specified by parameter. Returns true if
+ * a tree was loaded, else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadTree(AlignFrame alignFrame)
+ {
+ boolean result = false;
+ String treeFile = applet.getParameter("tree");
+ if (treeFile == null)
+ {
+ treeFile = applet.getParameter("treeFile");
+ }
- do
+ if (treeFile != null)
+ {
+ try
{
- if (pdbFileCount > 0)
+ treeFile = setProtocolState(treeFile);
+ NewickFile fin = new NewickFile(treeFile, protocol);
+ fin.parse();
+
+ if (fin.getTree() != null)
{
- param = applet.getParameter("PDBFILE" + pdbFileCount);
+ alignFrame.loadTree(fin, treeFile);
+ result = true;
+ dbgMsg("Successfully imported tree.");
}
else
{
- param = applet.getParameter("PDBFILE");
+ dbgMsg("Tree parameter did not resolve to a valid tree.");
}
-
- if (param != null)
- {
- PDBEntry pdb = new PDBEntry();
-
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
-
- StringTokenizer st = new StringTokenizer(param, " ");
-
- if (st.countTokens() < 2)
- {
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- {
- seqs = new SequenceI[]
- { matcher == null ? (Sequence) newAlignFrame
- .getAlignViewport().getAlignment()
- .findName(sequence) : matcher.findIdMatch(sequence) };
- }
-
- }
- else
- {
- param = st.nextToken();
- Vector tmp = new Vector();
- Vector tmp2 = new Vector();
-
- while (st.hasMoreTokens())
- {
- seqstring = st.nextToken();
- StringTokenizer st2 = new StringTokenizer(seqstring, "=");
- if (st2.countTokens() > 1)
- {
- // This is the chain
- tmp2.addElement(st2.nextToken());
- seqstring = st2.nextToken();
- }
- tmp.addElement(matcher == null ? (Sequence) newAlignFrame
- .getAlignViewport().getAlignment()
- .findName(seqstring) : matcher
- .findIdMatch(seqstring));
- }
-
- seqs = new SequenceI[tmp.size()];
- tmp.copyInto(seqs);
- if (tmp2.size() == tmp.size())
- {
- chains = new String[tmp2.size()];
- tmp2.copyInto(chains);
- }
- }
- param = setProtocolState(param);
-
- if (// !jmolAvailable
- // &&
- protocol == AppletFormatAdapter.CLASSLOADER
- && !useXtrnalSviewer)
- {
- // Re: JAL-357 : the bug isn't a problem if we are using an
- // external viewer!
- // TODO: verify this Re:
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- // This exception preserves the current behaviour where, even if
- // the local pdb file was identified in the class loader
- protocol = AppletFormatAdapter.URL; // this is probably NOT
- // CORRECT!
- param = addProtocol(param); //
- }
-
- pdb.setFile(param);
-
- if (seqs != null)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- ((Sequence) seqs[i]).addPDBId(pdb);
- StructureSelectionManager.getStructureSelectionManager(
- applet).registerPDBEntry(pdb);
- }
- else
- {
- if (JalviewLite.debug)
- {
- // this may not really be a problem but we give a warning
- // anyway
- System.err
- .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
- + i + ")");
- }
- }
- }
-
- if (!alignPdbStructures)
- {
- newAlignFrame.newStructureView(applet, pdb, seqs, chains,
- protocol);
- }
- else
- {
- pdbs.addElement(new Object[]
- { pdb, seqs, chains, new String(protocol) });
- }
- }
- }
-
- pdbFileCount++;
- } while (param != null || pdbFileCount < 10);
- if (pdbs.size() > 0)
+ } catch (Exception ex)
{
- SequenceI[][] seqs = new SequenceI[pdbs.size()][];
- PDBEntry[] pdb = new PDBEntry[pdbs.size()];
- String[][] chains = new String[pdbs.size()][];
- String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
- {
- Object[] o = (Object[]) pdbs.elementAt(pdbsi);
- pdb[pdbsi] = (PDBEntry) o[0];
- seqs[pdbsi] = (SequenceI[]) o[1];
- chains[pdbsi] = (String[]) o[2];
- protocols[pdbsi] = (String) o[3];
- }
- newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
- protocols);
-
+ ex.printStackTrace();
}
}
- else
- {
- fileFound = false;
- applet.remove(launcher);
- applet.repaint();
- }
- callInitCallback();
+ return result;
}
/**
}
}
- String addProtocol(String file)
+ /**
+ * If the file is not already in URL format, tries to locate it by resolving
+ * as a URL.
+ *
+ * @param file
+ * @return
+ */
+ String addProtocol(final String file)
{
if (file.indexOf("://") == -1)
{
- String fl = applet.resolveUrlForLocalOrAbsolute(file,
+ /*
+ * Try relative to document base
+ */
+ String url = applet.resolveUrlForLocalOrAbsolute(file,
getDocumentBase());
- try
+ if (urlExists(url))
{
- if (new java.net.URL(fl).openStream() != null)
+ if (debug)
{
- if (debug)
- {
- System.err.println("Prepended document base for resource: '"
- + file + "'");
- }
- return fl;
+ System.err.println("Prepended document base for resource: '"
+ + file + "'");
}
- } catch (Exception x)
- {
+ return url;
}
- ;
- fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
- try
+
+ /*
+ * Try relative to codebase
+ */
+ url = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
+ if (urlExists(url))
{
- if (new java.net.URL(fl).openStream() != null)
+ if (debug)
{
- if (debug)
- {
- System.err.println("Prepended codebase for resource: '"
- + file + "'");
- }
- return fl;
+ System.err.println("Prepended codebase for resource: '" + file
+ + "'");
}
- } catch (Exception x)
- {
+ return url;
}
- ;
-
}
+ /*
+ * Not resolved, leave unchanged
+ */
return file;
}
+
+ /**
+ * Returns true if an input stream can be opened on the specified URL, else
+ * false.
+ *
+ * @param url
+ * @return
+ */
+ private boolean urlExists(String url)
+ {
+ InputStream is = null;
+ try
+ {
+ is = new URL(url).openStream();
+ if (is != null)
+ {
+ return true;
+ }
+ } catch (Exception x)
+ {
+ // ignore
+ } finally
+ {
+ if (is != null)
+ {
+ try
+ {
+ is.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ return false;
+ }
}
/**
{
return def;
}
- if (stn.toLowerCase().equals("true"))
+ if (stn.toLowerCase().equals(TRUE))
{
return true;
}
*/
package jalview.commands;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
public class ChangeCaseCommand implements CommandI
{
SequenceI[] seqs;
- int[][] regions;
+ List<int[]> regions;
public ChangeCaseCommand(String description, SequenceI[] seqs,
- int[][] regions, int caseChange)
+ List<int[]> regions, int caseChange)
{
this.description = description;
this.seqs = seqs;
String sequence;
int start, end;
char nextChar;
- for (int r = 0; r < regions.length; r++)
+ for (int[] r : regions)
{
- start = regions[r][0];
+ start = r[0];
for (int s = 0; s < seqs.length; s++)
{
sequence = seqs[s].getSequenceAsString();
StringBuffer newSeq = new StringBuffer();
- if (regions[r][1] > sequence.length())
+ if (r[1] > sequence.length())
{
end = sequence.length();
}
else
{
- end = regions[r][1];
+ end = r[1];
}
if (start > 0)
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.ReverseListIterator;
+import jalview.util.StringUtils;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.ListIterator;
+import java.util.Map;
/**
*
{
public enum Action
{
- INSERT_GAP, DELETE_GAP, CUT, PASTE, REPLACE, INSERT_NUC
+ INSERT_GAP
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return DELETE_GAP;
+ }
+ },
+ DELETE_GAP
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return INSERT_GAP;
+ }
+ },
+ CUT
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return PASTE;
+ }
+ },
+ PASTE
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return CUT;
+ }
+ },
+ REPLACE
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return REPLACE;
+ }
+ },
+ INSERT_NUC
+ {
+ @Override
+ public Action getUndoAction()
+ {
+ return null;
+ }
+ };
+ public abstract Action getUndoAction();
};
private List<Edit> edits = new ArrayList<Edit>();
}
/**
- * Add the given edit command to the stored list of commands.
+ * Add the given edit command to the stored list of commands. If simply
+ * expanding the range of the last command added, then modify it instead of
+ * adding a new command.
*
* @param e
*/
- protected void addEdit(Edit e)
+ public void addEdit(Edit e)
{
- edits.add(e);
+ if (!expandEdit(edits, e))
+ {
+ edits.add(e);
+ }
+ }
+
+ /**
+ * Returns true if the new edit is incorporated by updating (expanding the
+ * range of) the last edit on the list, else false. We can 'expand' the last
+ * edit if the new one is the same action, on the same sequences, and acts on
+ * a contiguous range. This is the case where a mouse drag generates a series
+ * of contiguous gap insertions or deletions.
+ *
+ * @param edits
+ * @param e
+ * @return
+ */
+ protected static boolean expandEdit(List<Edit> edits, Edit e)
+ {
+ if (edits == null || edits.isEmpty())
+ {
+ return false;
+ }
+ Edit lastEdit = edits.get(edits.size() - 1);
+ Action action = e.command;
+ if (lastEdit.command != action)
+ {
+ return false;
+ }
+
+ /*
+ * Both commands must act on the same sequences - compare the underlying
+ * dataset sequences, rather than the aligned sequences, which change as
+ * they are edited.
+ */
+ if (lastEdit.seqs.length != e.seqs.length)
+ {
+ return false;
+ }
+ for (int i = 0; i < e.seqs.length; i++)
+ {
+ if (lastEdit.seqs[i].getDatasetSequence() != e.seqs[i]
+ .getDatasetSequence())
+ {
+ return false;
+ }
+ }
+
+ /**
+ * Check a contiguous edit; either
+ * <ul>
+ * <li>a new Insert <n> positions to the right of the last <insert n>, or</li>
+ * <li>a new Delete <n> gaps which is <n> positions to the left of the last
+ * delete.</li>
+ * </ul>
+ */
+ boolean contiguous = (action == Action.INSERT_GAP && e.position == lastEdit.position
+ + lastEdit.number)
+ || (action == Action.DELETE_GAP && e.position + e.number == lastEdit.position);
+ if (contiguous)
+ {
+ /*
+ * We are just expanding the range of the last edit. For delete gap, also
+ * moving the start position left.
+ */
+ lastEdit.number += e.number;
+ lastEdit.seqs = e.seqs;
+ if (action == Action.DELETE_GAP)
+ {
+ lastEdit.position--;
+ }
+ return true;
+ }
+ return false;
}
/**
edit.fullAlignmentHeight = true;
}
- edits.add(edit);
+ addEdit(edit);
+
+ if (performEdit)
+ {
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * Overloaded method that accepts an Edit object with additional parameters.
+ *
+ * @param edit
+ * @param al
+ * @param performEdit
+ * @param views
+ */
+ final public void appendEdit(Edit edit, AlignmentI al,
+ boolean performEdit, AlignmentI[] views)
+ {
+ if (al.getHeight() == edit.seqs.length)
+ {
+ edit.al = al;
+ edit.fullAlignmentHeight = true;
+ }
+
+ addEdit(edit);
if (performEdit)
{
* @param commandIndex
* @param views
*/
- final void performEdit(int commandIndex, AlignmentI[] views)
+ public final void performEdit(int commandIndex, AlignmentI[] views)
{
ListIterator<Edit> iterator = edits.listIterator(commandIndex);
while (iterator.hasNext())
* @param edit
* @param views
*/
- protected void performEdit(Edit edit, AlignmentI[] views)
+ protected static void performEdit(Edit edit, AlignmentI[] views)
{
switch (edit.command)
{
*
* @param command
*/
- final private void insertGap(Edit command)
+ final private static void insertGap(Edit command)
{
for (int s = 0; s < command.seqs.length; s++)
{
- command.seqs[s].insertCharAt(command.position, command.number,
- command.gapChar);
+ command.seqs[s].insertCharAt(command.position,
+ command.number, command.gapChar);
// System.out.println("pos: "+command.position+" number: "+command.number);
}
*
* @param command
*/
- final private void deleteGap(Edit command)
+ final static private void deleteGap(Edit command)
{
for (int s = 0; s < command.seqs.length; s++)
{
* @param command
* @param views
*/
- void cut(Edit command, AlignmentI[] views)
+ static void cut(Edit command, AlignmentI[] views)
{
boolean seqDeleted = false;
command.string = new char[command.seqs.length][];
* @param command
* @param views
*/
- void paste(Edit command, AlignmentI[] views)
+ static void paste(Edit command, AlignmentI[] views)
{
StringBuffer tmp;
boolean newDSNeeded;
if (command.seqs[i].getLength() < 1)
{
// ie this sequence was deleted, we need to
- // read it to the alignment
+ // readd it to the alignment
if (command.alIndex[i] < command.al.getHeight())
{
List<SequenceI> sequences;
command.string = null;
}
- void replace(Edit command)
+ static void replace(Edit command)
{
StringBuffer tmp;
String oldstring;
}
}
- final void adjustAnnotations(Edit command, boolean insert,
+ final static void adjustAnnotations(Edit command, boolean insert,
boolean modifyVisibility, AlignmentI[] views)
{
AlignmentAnnotation[] annotations = null;
}
}
- final void adjustFeatures(Edit command, int index, int i, int j,
+ final static void adjustFeatures(Edit command, int index, int i, int j,
boolean insert)
{
SequenceI seq = command.seqs[index];
}
- class Edit
+ /**
+ * Returns the list of edit commands wrapped by this object.
+ *
+ * @return
+ */
+ public List<Edit> getEdits()
+ {
+ return this.edits;
+ }
+
+ /**
+ * Returns a map whose keys are the dataset sequences, and values their
+ * aligned sequences before the command edit list was applied. The aligned
+ * sequences are copies, which may be updated without affecting the originals.
+ *
+ * The command holds references to the aligned sequences (after editing). If
+ * the command is an 'undo',then the prior state is simply the aligned state.
+ * Otherwise, we have to derive the prior state by working backwards through
+ * the edit list to infer the aligned sequences before editing.
+ *
+ * Note: an alternative solution would be to cache the 'before' state of each
+ * edit, but this would be expensive in space in the common case that the
+ * original is never needed (edits are not mirrored).
+ *
+ * @return
+ * @throws IllegalStateException
+ * on detecting an edit command of a type that can't be unwound
+ */
+ public Map<SequenceI, SequenceI> priorState(boolean forUndo)
+ {
+ Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
+ if (getEdits() == null)
+ {
+ return result;
+ }
+ if (forUndo)
+ {
+ for (Edit e : getEdits())
+ {
+ for (SequenceI seq : e.getSequences())
+ {
+ SequenceI ds = seq.getDatasetSequence();
+ SequenceI preEdit = result.get(ds);
+ if (preEdit == null)
+ {
+ preEdit = new Sequence("", seq.getSequenceAsString());
+ preEdit.setDatasetSequence(ds);
+ result.put(ds, preEdit);
+ }
+ }
+ }
+ return result;
+ }
+
+ /*
+ * Work backwards through the edit list, deriving the sequences before each
+ * was applied. The final result is the sequence set before any edits.
+ */
+ Iterator<Edit> edits = new ReverseListIterator<Edit>(getEdits());
+ while (edits.hasNext())
+ {
+ Edit oldEdit = edits.next();
+ Action action = oldEdit.getAction();
+ int position = oldEdit.getPosition();
+ int number = oldEdit.getNumber();
+ final char gap = oldEdit.getGapCharacter();
+ for (SequenceI seq : oldEdit.getSequences())
+ {
+ SequenceI ds = seq.getDatasetSequence();
+ SequenceI preEdit = result.get(ds);
+ if (preEdit == null)
+ {
+ preEdit = new Sequence("", seq.getSequenceAsString());
+ preEdit.setDatasetSequence(ds);
+ result.put(ds, preEdit);
+ }
+ /*
+ * 'Undo' this edit action on the sequence (updating the value in the
+ * map).
+ */
+ if (ds != null)
+ {
+ if (action == Action.DELETE_GAP)
+ {
+ preEdit.setSequence(new String(StringUtils.insertCharAt(
+ preEdit.getSequence(), position,
+ number, gap)));
+ }
+ else if (action == Action.INSERT_GAP)
+ {
+ preEdit.setSequence(new String(StringUtils.deleteChars(
+ preEdit.getSequence(), position, position + number)));
+ }
+ else
+ {
+ System.err.println("Can't undo edit action " + action);
+ // throw new IllegalStateException("Can't undo edit action " +
+ // action);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ public class Edit
{
public SequenceI[] oldds;
char gapChar;
- Edit(Action command, SequenceI[] seqs, int position, int number,
+ public Edit(Action command, SequenceI[] seqs, int position, int number,
char gapChar)
{
this.command = command;
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
+
+ public SequenceI[] getSequences()
+ {
+ return seqs;
+ }
+
+ public int getPosition()
+ {
+ return position;
+ }
+
+ public Action getAction()
+ {
+ return command;
+ }
+
+ public int getNumber()
+ {
+ return number;
+ }
+
+ public char getGapCharacter()
+ {
+ return gapChar;
+ }
+ }
+
+ /**
+ * Returns an iterator over the list of edit commands which traverses the list
+ * either forwards or backwards.
+ *
+ * @param forwards
+ * @return
+ */
+ public Iterator<Edit> getEditIterator(boolean forwards)
+ {
+ if (forwards)
+ {
+ return getEdits().iterator();
+ }
+ else
+ {
+ return new ReverseListIterator<Edit>(getEdits());
+ }
}
}
*/
package jalview.commands;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+/**
+ * An undoable command to reorder the sequences in an alignment.
+ *
+ * @author gmcarstairs
+ *
+ */
public class OrderCommand implements CommandI
{
String description;
+ /*
+ * The sequence order before sorting (target order for an undo)
+ */
SequenceI[] seqs;
+ /*
+ * The sequence order specified by this command
+ */
SequenceI[] seqs2;
+ /*
+ * The alignment the command acts on
+ */
AlignmentI al;
+ /**
+ * Constructor given the 'undo' sequence order, and the (already) sorted
+ * alignment.
+ *
+ * @param description
+ * a text label for the 'undo' menu option
+ * @param seqs
+ * the sequence order for undo
+ * @param al
+ * the alignment as ordered by this command
+ */
public OrderCommand(String description, SequenceI[] seqs, AlignmentI al)
{
this.description = description;
{
AlignmentSorter.setOrder(al, seqs);
}
+
+ /**
+ * Returns the sequence order used to sort, or before sorting if undo=true.
+ *
+ * @param undo
+ * @return
+ */
+ public SequenceI[] getSequenceOrder(boolean undo)
+ {
+ return undo ? seqs : seqs2;
+ }
}
int tfeat = 0;
if (sq != null)
{
- SequenceI dsq = sq.getDatasetSequence();
- while (dsq.getDatasetSequence() != null)
- {
- dsq = dsq.getDatasetSequence();
- }
- ;
- SequenceFeature[] sf = dsq.getSequenceFeatures();
+ SequenceFeature[] sf = sq.getSequenceFeatures();
if (sf != null)
{
int ist = sq.findIndex(sq.getStart());
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * Holds the aligned column positions (base 0) for one codon in a nucleotide
+ * sequence, and (optionally) its peptide translation. The object is immutable
+ * once created.
+ *
+ * Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8).
+ *
+ * @author gmcarstairs
+ *
+ */
+public final class AlignedCodon
+{
+ public final int pos1;
+
+ public final int pos2;
+
+ public final int pos3;
+
+ public final String product;
+
+ public AlignedCodon(int i, int j, int k)
+ {
+ this(i, j, k, null);
+ }
+
+ public AlignedCodon(int i, int j, int k, String prod)
+ {
+ pos1 = i;
+ pos2 = j;
+ pos3 = k;
+ product = prod;
+ }
+
+ /**
+ * Returns the column position for the given base (1, 2, 3).
+ *
+ * @param base
+ * @return
+ * @throws IllegalArgumentException
+ * if an argument value other than 1, 2 or 3 is supplied
+ */
+ public int getBaseColumn(int base)
+ {
+ if (base < 1 || base > 3)
+ {
+ throw new IllegalArgumentException(Integer.toString(base));
+ }
+ return base == 1 ? pos1 : (base == 2 ? pos2 : pos3);
+ }
+
+ /**
+ * Two aligned codons are equal if all their base positions are the same. We
+ * don't care about the protein product. This test is required for correct
+ * alignment of translated gapped dna alignments (the same codon positions in
+ * different sequences occupy the same column in the translated alignment).
+ */
+ @Override
+ public boolean equals(Object o)
+ {
+ /*
+ * Equality with null value required for consistency with
+ * Dna.compareCodonPos
+ */
+ if (o == null)
+ {
+ return true;
+ }
+ if (!(o instanceof AlignedCodon))
+ {
+ return false;
+ }
+ AlignedCodon ac = (AlignedCodon) o;
+ return (pos1 == ac.pos1 && pos2 == ac.pos2 && pos3 == ac.pos3);
+ }
+
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("[").append(pos1).append(", ").append(pos2).append(", ")
+ .append(pos3).append("]");
+ return sb.toString();
+ }
+}
*/
package jalview.datamodel;
-import java.util.Enumeration;
-import java.util.Vector;
-
import jalview.util.MapList;
+import jalview.util.MappingUtils;
/**
* Stores mapping between the columns of a protein alignment and a DNA alignment
* and a list of individual codon to amino acid mappings between sequences.
*/
-
public class AlignedCodonFrame
{
- /**
- * array of nucleotide positions for aligned codons at column of aligned
- * proteins.
- */
- public int[][] codons = null;
-
- /**
- * width of protein sequence alignement implicit assertion that codons.length
- * >= aaWidth
- */
- public int aaWidth = 0;
- /**
- * initialise codon frame with a nominal alignment width
- *
- * @param aWidth
+ /*
+ * tied array of na Sequence objects.
*/
- public AlignedCodonFrame(int aWidth)
- {
- if (aWidth <= 0)
- {
- codons = null;
- return;
- }
- codons = new int[aWidth][];
- for (int res = 0; res < aWidth; res++)
- codons[res] = null;
- }
+ private SequenceI[] dnaSeqs = null;
- /**
- * ensure that codons array is at least as wide as aslen residues
- *
- * @param aslen
- * @return (possibly newly expanded) codon array
+ /*
+ * tied array of Mappings to protein sequence Objects and SequenceI[]
+ * aaSeqs=null; MapLists where each maps from the corresponding dnaSeqs
+ * element to corresponding aaSeqs element
*/
- public int[][] checkCodonFrameWidth(int aslen)
- {
- if (codons.length <= aslen + 1)
- {
- // probably never have to do this ?
- int[][] c = new int[codons.length + 10][];
- for (int i = 0; i < codons.length; i++)
- {
- c[i] = codons[i];
- codons[i] = null;
- }
- codons = c;
- }
- return codons;
- }
+ private Mapping[] dnaToProt = null;
/**
- * @return width of aligned translated amino acid residues
+ * Constructor
*/
- public int getaaWidth()
+ public AlignedCodonFrame()
{
- return aaWidth;
}
/**
- * TODO: not an ideal solution - we reference the aligned amino acid sequences
- * in order to make insertions on them Better would be dnaAlignment and
- * aaAlignment reference....
- */
- Vector a_aaSeqs = new Vector();
-
- /**
- * increase aaWidth by one and insert a new aligned codon position space at
- * aspos.
- *
- * @param aspos
- */
- public void insertAAGap(int aspos, char gapCharacter)
- {
- // this aa appears before the aligned codons at aspos - so shift them in
- // each pair of mapped sequences
- aaWidth++;
- if (a_aaSeqs != null)
- {
- // we actually have to modify the aligned sequences here, so use the
- // a_aaSeqs vector
- Enumeration sq = a_aaSeqs.elements();
- while (sq.hasMoreElements())
- {
- ((SequenceI) sq.nextElement()).insertCharAt(aspos, gapCharacter);
- }
- }
- checkCodonFrameWidth(aspos);
- if (aspos < aaWidth)
- {
- aaWidth++;
- System.arraycopy(codons, aspos, codons, aspos + 1, codons.length
- - aspos - 1);
- codons[aspos] = null; // clear so new codon position can be marked.
- }
- }
-
- public void setAaWidth(int aapos)
- {
- aaWidth = aapos;
- }
-
- /**
- * tied array of na Sequence objects.
- */
- SequenceI[] dnaSeqs = null;
-
- /**
- * tied array of Mappings to protein sequence Objects and SequenceI[]
- * aaSeqs=null; MapLists where eac maps from the corresponding dnaSeqs element
- * to corresponding aaSeqs element
- */
- Mapping[] dnaToProt = null;
-
- /**
- * add a mapping between the dataset sequences for the associated dna and
+ * Adds a mapping between the dataset sequences for the associated dna and
* protein sequence objects
*
* @param dnaseq
// aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
mp.to = (aaseq.getDatasetSequence() == null) ? aaseq : aaseq
.getDatasetSequence();
- a_aaSeqs.addElement(aaseq);
dnaToProt[nlen] = mp;
}
public SequenceI[] getAaSeqs()
{
if (dnaToProt == null)
+ {
return null;
+ }
SequenceI[] sqs = new SequenceI[dnaToProt.length];
for (int sz = 0; sz < dnaToProt.length; sz++)
{
public MapList[] getdnaToProt()
{
if (dnaToProt == null)
+ {
return null;
+ }
MapList[] sqs = new MapList[dnaToProt.length];
for (int sz = 0; sz < dnaToProt.length; sz++)
{
}
/**
+ * Returns the first mapping found which is to or from the given sequence, or
+ * null.
+ *
+ * @param seq
+ * @return
+ */
+ public Mapping getMappingForSequence(SequenceI seq)
+ {
+ if (dnaSeqs == null)
+ {
+ return null;
+ }
+ SequenceI seqDs = seq.getDatasetSequence();
+ seqDs = seqDs != null ? seqDs : seq;
+
+ for (int ds = 0; ds < dnaSeqs.length; ds++)
+ {
+ if (dnaSeqs[ds] == seqDs || dnaToProt[ds].to == seqDs)
+ {
+ return dnaToProt[ds];
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Return the corresponding aligned or dataset aa sequence for given dna
+ * sequence, null if not found.
*
* @param sequenceRef
- * @return null or corresponding aaSeq entry for dnaSeq entry
+ * @return
*/
public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)
{
for (int ds = 0; ds < dnaSeqs.length; ds++)
{
if (dnaSeqs[ds] == dnaSeqRef || dnaSeqs[ds] == dnads)
+ {
return dnaToProt[ds].to;
+ }
}
return null;
}
for (int as = 0; as < dnaToProt.length; as++)
{
if (dnaToProt[as].to == aaSeqRef || dnaToProt[as].to == aads)
+ {
return dnaSeqs[as];
+ }
}
return null;
}
}
}
}
+
+ /**
+ * Returns the DNA codon positions (base 1) for the given position (base 1) in
+ * a mapped protein sequence, or null if no mapping is found.
+ *
+ * Intended for use in aligning cDNA to match aligned protein. Only the first
+ * mapping found is returned, so not suitable for use if multiple protein
+ * sequences are mapped to the same cDNA (but aligning cDNA as protein is
+ * ill-defined for this case anyway).
+ *
+ * @param seq
+ * the DNA dataset sequence
+ * @param aaPos
+ * residue position (base 1) in a protein sequence
+ * @return
+ */
+ public int[] getDnaPosition(SequenceI seq, int aaPos)
+ {
+ /*
+ * Adapted from markMappedRegion().
+ */
+ MapList ml = null;
+ for (int i = 0; i < dnaToProt.length; i++)
+ {
+ if (dnaSeqs[i] == seq)
+ {
+ ml = getdnaToProt()[i];
+ break;
+ }
+ }
+ return ml == null ? null : ml.locateInFrom(aaPos, aaPos);
+ }
+
+ /**
+ * Convenience method to return the first aligned sequence in the given
+ * alignment whose dataset has a mapping with the given dataset sequence.
+ *
+ * @param seq
+ *
+ * @param al
+ * @return
+ */
+ public SequenceI findAlignedSequence(SequenceI seq, AlignmentI al)
+ {
+ /*
+ * Search mapped protein ('to') sequences first.
+ */
+ if (this.dnaToProt != null)
+ {
+ for (int i = 0; i < dnaToProt.length; i++)
+ {
+ if (this.dnaSeqs[i] == seq)
+ {
+ for (SequenceI sourceAligned : al.getSequences())
+ {
+ if (this.dnaToProt[i].to == sourceAligned.getDatasetSequence())
+ {
+ return sourceAligned;
+ }
+ }
+ }
+ }
+ }
+
+ /*
+ * Then try mapped dna sequences.
+ */
+ if (this.dnaToProt != null)
+ {
+ for (int i = 0; i < dnaToProt.length; i++)
+ {
+ if (this.dnaToProt[i].to == seq)
+ {
+ for (SequenceI sourceAligned : al.getSequences())
+ {
+ if (this.dnaSeqs[i] == sourceAligned.getDatasetSequence())
+ {
+ return sourceAligned;
+ }
+ }
+ }
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * Returns the region in the 'mappedFrom' sequence's dataset that is mapped to
+ * position 'pos' (base 1) in the 'mappedTo' sequence's dataset. The region is
+ * a set of start/end position pairs.
+ *
+ * @param mappedFrom
+ * @param mappedTo
+ * @param pos
+ * @return
+ */
+ public int[] getMappedRegion(SequenceI mappedFrom, SequenceI mappedTo,
+ int pos)
+ {
+ SequenceI targetDs = mappedFrom.getDatasetSequence() == null ? mappedFrom
+ : mappedFrom.getDatasetSequence();
+ SequenceI sourceDs = mappedTo.getDatasetSequence() == null ? mappedTo
+ : mappedTo.getDatasetSequence();
+ if (targetDs == null || sourceDs == null || dnaToProt == null)
+ {
+ return null;
+ }
+ for (int mi = 0; mi < dnaToProt.length; mi++)
+ {
+ if (dnaSeqs[mi] == targetDs && dnaToProt[mi].to == sourceDs)
+ {
+ int[] codon = dnaToProt[mi].map.locateInFrom(pos, pos);
+ if (codon != null) {
+ return codon;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns the DNA codon for the given position (base 1) in a mapped protein
+ * sequence, or null if no mapping is found.
+ *
+ * @param protein
+ * the peptide dataset sequence
+ * @param aaPos
+ * residue position (base 1) in the peptide sequence
+ * @return
+ */
+ public char[] getMappedCodon(SequenceI protein, int aaPos)
+ {
+ if (dnaToProt == null)
+ {
+ return null;
+ }
+ MapList ml = null;
+ char[] dnaSeq = null;
+ for (int i = 0; i < dnaToProt.length; i++)
+ {
+ if (dnaToProt[i].to == protein)
+ {
+ ml = getdnaToProt()[i];
+ dnaSeq = dnaSeqs[i].getSequence();
+ break;
+ }
+ }
+ if (ml == null)
+ {
+ return null;
+ }
+ int[] codonPos = ml.locateInFrom(aaPos, aaPos);
+ if (codonPos == null)
+ {
+ return null;
+ }
+
+ /*
+ * Read off the mapped nucleotides (converting to position base 0)
+ */
+ codonPos = MappingUtils.flattenRanges(codonPos);
+ return new char[]
+ { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
+ dnaSeq[codonPos[2] - 1] };
+ }
}
*/
package jalview.datamodel;
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
import jalview.util.MessageManager;
import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.HashSet;
import java.util.Hashtable;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.Vector;
/**
public Hashtable alignmentProperties;
+ private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+
private void initAlignment(SequenceI[] seqs)
{
int i = 0;
}
/**
+ * Make a 'copy' alignment - sequences have new copies of features and
+ * annotations, but share the original dataset sequences.
+ */
+ public Alignment(AlignmentI al)
+ {
+ SequenceI[] seqs = al.getSequencesArray();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = new Sequence(seqs[i]);
+ }
+
+ /*
+ * Share the same dataset sequence mappings (if any). TODO: find a better
+ * place for these to live (alignment dataset?).
+ */
+ this.codonFrameList = ((Alignment) al).codonFrameList;
+
+ initAlignment(seqs);
+ }
+
+ /**
* Make an alignment from an array of Sequences.
*
* @param sequences
// this(compactAlignment.refCigars);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
public List<SequenceI> getSequences()
{
}
/**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ @Override
+ public Map<String, List<SequenceI>> getSequencesByName()
+ {
+ return AlignmentUtils.getSequencesByName(this);
+ }
+
+ /**
* DOCUMENT ME!
*
* @param i
@Override
public void setSequenceAt(int i, SequenceI snew)
{
- SequenceI oldseq = getSequenceAt(i);
- deleteSequence(i);
synchronized (sequences)
{
+ deleteSequence(i);
sequences.set(i, snew);
}
}
synchronized (sequences)
{
sequences.remove(i);
+ hiddenSequences.adjustHeightSequenceDeleted(i);
}
- hiddenSequences.adjustHeightSequenceDeleted(i);
}
}
for (int i = 0; i < gSize; i++)
{
SequenceGroup sg = groups.get(i);
- if (sg == null || sg.getSequences(null) == null)
+ if (sg == null || sg.getSequences() == null)
{
this.deleteGroup(sg);
gSize--;
continue;
}
- if (sg.getSequences(null).contains(s))
+ if (sg.getSequences().contains(s))
{
temp.add(sg);
}
return true;
}
+ /**
+ * Delete all annotations, including auto-calculated if the flag is set true.
+ * Returns true if at least one annotation was deleted, else false.
+ *
+ * @param includingAutoCalculated
+ * @return
+ */
+ @Override
+ public boolean deleteAllAnnotations(boolean includingAutoCalculated)
+ {
+ boolean result = false;
+ for (AlignmentAnnotation alan : getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated || includingAutoCalculated)
+ {
+ deleteAnnotation(alan);
+ result = true;
+ }
+ }
+ return result;
+ }
+
/*
* (non-Javadoc)
*
return alignmentProperties;
}
- AlignedCodonFrame[] codonFrameList = null;
-
/*
* (non-Javadoc)
*
@Override
public void addCodonFrame(AlignedCodonFrame codons)
{
- if (codons == null)
+ if (codons != null)
{
- return;
- }
- if (codonFrameList == null)
- {
- codonFrameList = new AlignedCodonFrame[]
- { codons };
- return;
+ codonFrameList.add(codons);
}
- AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
- System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
- t[codonFrameList.length] = codons;
- codonFrameList = t;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
- */
- @Override
- public AlignedCodonFrame getCodonFrame(int index)
- {
- return codonFrameList[index];
}
/*
* jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
@Override
- public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+ public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
{
- if (seq == null || codonFrameList == null)
+ if (seq == null)
{
return null;
}
- Vector cframes = new Vector();
- for (int f = 0; f < codonFrameList.length; f++)
+ List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+ for (AlignedCodonFrame acf : codonFrameList)
{
- if (codonFrameList[f].involvesSequence(seq))
+ if (acf.involvesSequence(seq))
{
- cframes.addElement(codonFrameList[f]);
+ cframes.add(acf);
}
}
- if (cframes.size() == 0)
- {
- return null;
- }
- AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
- cframes.copyInto(cfr);
- return cfr;
+ return cframes;
}
- /*
- * (non-Javadoc)
+ /**
+ * Sets the codon frame mappings (replacing any existing mappings).
+ *
+ * @see jalview.datamodel.AlignmentI#setCodonFrames()
+ */
+ @Override
+ public void setCodonFrames(Set<AlignedCodonFrame> acfs)
+ {
+ this.codonFrameList = acfs;
+ }
+
+ /**
+ * Returns the set of codon frame mappings. Any changes to the returned set
+ * will affect the alignment.
*
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
@Override
- public AlignedCodonFrame[] getCodonFrames()
+ public Set<AlignedCodonFrame> getCodonFrames()
{
return codonFrameList;
}
{
return false;
}
- boolean removed = false;
- int i = 0, iSize = codonFrameList.length;
- while (i < iSize)
- {
- if (codonFrameList[i] == codons)
- {
- removed = true;
- if (i + 1 < iSize)
- {
- System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
- - i - 1);
- }
- iSize--;
- }
- else
- {
- i++;
- }
- }
- return removed;
+ return codonFrameList.remove(codons);
}
@Override
{
addAnnotation(alan[a]);
}
- AlignedCodonFrame[] acod = toappend.getCodonFrames();
- for (int a = 0; acod != null && a < acod.length; a++)
- {
- this.addCodonFrame(acod[a]);
- }
+
+ this.codonFrameList.addAll(toappend.getCodonFrames());
+
List<SequenceGroup> sg = toappend.getGroups();
if (sg != null)
{
{
return dataset;
}
+
+ /**
+ * Align this alignment like the given (mapped) one.
+ */
+ @Override
+ public int alignAs(AlignmentI al)
+ {
+ /*
+ * Currently retains unmapped gaps (in introns), regaps mapped regions
+ * (exons)
+ */
+ return alignAs(al, false, true);
+ }
+
+ /**
+ * Align this alignment 'the same as' the given one. Mapped sequences only are
+ * realigned. If both of the same type (nucleotide/protein) then align both
+ * identically. If this is nucleotide and the other is protein, make 3 gaps
+ * for each gap in the protein sequences. If this is protein and the other is
+ * nucleotide, insert a gap for each 3 gaps (or part thereof) between
+ * nucleotide bases. Does nothing if alignment of protein from cDNA is
+ * requested (not yet implemented).
+ *
+ * Parameters control whether gaps in exon (mapped) and intron (unmapped)
+ * regions are preserved. Gaps that connect introns to exons are treated
+ * conservatively, i.e. only preserved if both intron and exon gaps are
+ * preserved.
+ *
+ * @param al
+ * @param preserveMappedGaps
+ * if true, gaps within and between mapped codons are preserved
+ * @param preserveUnmappedGaps
+ * if true, gaps within and between unmapped codons are preserved
+ */
+// @Override
+ public int alignAs(AlignmentI al, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
+ {
+ // TODO should this method signature be the one in the interface?
+ int count = 0;
+ boolean thisIsNucleotide = this.isNucleotide();
+ boolean thatIsProtein = !al.isNucleotide();
+ if (!thatIsProtein && !thisIsNucleotide)
+ {
+ return AlignmentUtils.alignProteinAsDna(this, al);
+ }
+
+ char thisGapChar = this.getGapCharacter();
+ String gap = thisIsNucleotide && thatIsProtein ? String
+ .valueOf(new char[]
+ { thisGapChar, thisGapChar, thisGapChar }) : String
+ .valueOf(thisGapChar);
+
+ /*
+ * Get mappings from 'that' alignment's sequences to this.
+ */
+ for (SequenceI alignTo : getSequences())
+ {
+ count += AlignmentUtils.alignSequenceAs(alignTo, al, gap, preserveMappedGaps,
+ preserveUnmappedGaps) ? 1 : 0;
+ }
+ return count;
+ }
+
+ /**
+ * Returns the alignment in Fasta format. Behaviour of this method is not
+ * guaranteed between versions.
+ */
+ @Override
+ public String toString()
+ {
+ return new FastaFile().print(getSequencesArray());
+ }
+
+ /**
+ * Returns the set of distinct sequence names. No ordering is guaranteed.
+ */
+ @Override
+ public Set<String> getSequenceNames()
+ {
+ Set<String> names = new HashSet<String>();
+ for (SequenceI seq : getSequences())
+ {
+ names.add(seq.getName());
+ }
+ return names;
+ }
}
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
-import java.util.Enumeration;
import java.util.HashMap;
-import java.util.Hashtable;
+import java.util.Iterator;
import java.util.Map;
import java.util.Map.Entry;
*/
public class AlignmentAnnotation
{
+ /*
+ * Identifers for different types of profile data
+ */
+ public static final int SEQUENCE_PROFILE = 0;
+
+ public static final int STRUCTURE_PROFILE = 1;
+
+ public static final int CDNA_PROFILE = 2;
+
/**
* If true, this annotations is calculated every edit, eg consensus, quality
* or conservation graphs
/**
* map of positions in the associated annotation
*/
- public java.util.Hashtable<Integer, Annotation> sequenceMapping;
+ private Map<Integer, Annotation> sequenceMapping;
/** DOCUMENT ME!! */
public float graphMin;
: annotations[index + offset].secondaryStructure);
}
+ @Override
public String toString()
{
char[] string = new char[max - offset];
if (annotation.sequenceMapping != null)
{
Integer p = null;
- sequenceMapping = new Hashtable();
- Enumeration pos = annotation.sequenceMapping.keys();
- while (pos.hasMoreElements())
+ sequenceMapping = new HashMap<Integer, Annotation>();
+ Iterator<Integer> pos = annotation.sequenceMapping.keySet()
+ .iterator();
+ while (pos.hasNext())
{
// could optimise this!
- p = (Integer) pos.nextElement();
+ p = pos.next();
Annotation a = annotation.sequenceMapping.get(p);
if (a == null)
{
int epos = sequenceRef.findPosition(endRes);
if (sequenceMapping != null)
{
- Hashtable newmapping = new Hashtable();
- Enumeration e = sequenceMapping.keys();
- while (e.hasMoreElements())
+ Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+ Iterator<Integer> e = sequenceMapping.keySet().iterator();
+ while (e.hasNext())
{
- Integer pos = (Integer) e.nextElement();
+ Integer pos = e.next();
if (pos.intValue() >= spos && pos.intValue() <= epos)
{
newmapping.put(pos, sequenceMapping.get(pos));
*
* @return DOCUMENT ME!
*/
+ @Override
public String toString()
{
- StringBuffer buffer = new StringBuffer();
+ StringBuilder buffer = new StringBuilder(256);
for (int i = 0; i < annotations.length; i++)
{
{
return;
}
- sequenceMapping = new java.util.Hashtable();
+ sequenceMapping = new HashMap<Integer, Annotation>();
int seqPos;
.getTo() == sq.getDatasetSequence()) : false;
// TODO build a better annotation element map and get rid of annotations[]
- Hashtable<Integer, Annotation> mapForsq = new Hashtable();
+ Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
if (sequenceMapping != null)
{
if (sp2sq != null)
{
if (mapping != null)
{
- Hashtable<Integer, Annotation> old = sequenceMapping, remap = new Hashtable<Integer, Annotation>();
+ Map<Integer, Annotation> old = sequenceMapping;
+ Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
int index = -1;
for (int mp[] : mapping)
{
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview 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.
+ * PURPOSE. See the GNU General License for more details.
*
- * You should have received a copy of the GNU General Public License
+ * You should have received a copy of the GNU General License
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
+import java.util.Set;
/**
* Data structure to hold and manipulate a multiple sequence alignment
*
* @return Number of sequences in alignment
*/
- public int getHeight();
+ int getHeight();
/**
+ *
* Calculates the maximum width of the alignment, including gaps.
*
* @return Greatest sequence length within alignment.
*/
@Override
- public int getWidth();
+ int getWidth();
/**
* Calculates if this set of sequences (visible and invisible) are all the
*
* @return true if all sequences in alignment are the same length
*/
- public boolean isAligned();
+ boolean isAligned();
/**
* Calculates if this set of sequences is all the same length
* optionally exclude hidden sequences from test
* @return true if all (or just visible) sequences are the same length
*/
- public boolean isAligned(boolean includeHidden);
+ boolean isAligned(boolean includeHidden);
/**
* Gets sequences as a Synchronized collection
* @return All sequences in alignment.
*/
@Override
- public List<SequenceI> getSequences();
+ List<SequenceI> getSequences();
/**
* Gets sequences as a SequenceI[]
*
* @return All sequences in alignment.
*/
- public SequenceI[] getSequencesArray();
+ SequenceI[] getSequencesArray();
/**
* Find a specific sequence in this alignment.
*
* @return SequenceI at given index.
*/
- public SequenceI getSequenceAt(int i);
+ SequenceI getSequenceAt(int i);
+
+ /**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ Map<String, List<SequenceI>> getSequencesByName();
/**
* Add a new sequence to this alignment.
* @param seq
* New sequence will be added at end of alignment.
*/
- public void addSequence(SequenceI seq);
+ void addSequence(SequenceI seq);
/**
* Used to set a particular index of the alignment with the given sequence.
* @param seq
* New sequence to be inserted.
*/
- public void setSequenceAt(int i, SequenceI seq);
+ void setSequenceAt(int i, SequenceI seq);
/**
* Deletes a sequence from the alignment
* @param s
* Sequence to be deleted.
*/
- public void deleteSequence(SequenceI s);
+ void deleteSequence(SequenceI s);
/**
* Deletes a sequence from the alignment.
* @param i
* Index of sequence to be deleted.
*/
- public void deleteSequence(int i);
+ void deleteSequence(int i);
/**
* Finds sequence in alignment using sequence name as query.
*
* @return Sequence matching query, if found. If not found returns null.
*/
- public SequenceI findName(String name);
+ SequenceI findName(String name);
- public SequenceI[] findSequenceMatch(String name);
+ SequenceI[] findSequenceMatch(String name);
/**
* Finds index of a given sequence in the alignment.
*
* @return Index of sequence within the alignment or -1 if not found
*/
- public int findIndex(SequenceI s);
+ int findIndex(SequenceI s);
/**
* Finds group that given sequence is part of.
* @return First group found for sequence. WARNING : Sequences may be members
* of several groups. This method is incomplete.
*/
- public SequenceGroup findGroup(SequenceI s);
+ SequenceGroup findGroup(SequenceI s);
/**
* Finds all groups that a given sequence is part of.
*
* @return All groups containing given sequence.
*/
- public SequenceGroup[] findAllGroups(SequenceI s);
+ SequenceGroup[] findAllGroups(SequenceI s);
/**
* Adds a new SequenceGroup to this alignment.
* @param sg
* New group to be added.
*/
- public void addGroup(SequenceGroup sg);
+ void addGroup(SequenceGroup sg);
/**
* Deletes a specific SequenceGroup
* @param g
* Group will be deleted from alignment.
*/
- public void deleteGroup(SequenceGroup g);
+ void deleteGroup(SequenceGroup g);
/**
* Get all the groups associated with this alignment.
*
* @return All groups as a list.
*/
- public List<SequenceGroup> getGroups();
+ List<SequenceGroup> getGroups();
/**
* Deletes all groups from this alignment.
*/
- public void deleteAllGroups();
+ void deleteAllGroups();
/**
* Adds a new AlignmentAnnotation to this alignment
* @note Care should be taken to ensure that annotation is at least as wide as
* the longest sequence in the alignment for rendering purposes.
*/
- public void addAnnotation(AlignmentAnnotation aa);
+ void addAnnotation(AlignmentAnnotation aa);
/**
* moves annotation to a specified index in alignment annotation display stack
* @param index
* the destination position
*/
- public void setAnnotationIndex(AlignmentAnnotation aa, int index);
+ void setAnnotationIndex(AlignmentAnnotation aa, int index);
+
+ /**
+ * Delete all annotations, including auto-calculated if the flag is set true.
+ * Returns true if at least one annotation was deleted, else false.
+ *
+ * @param includingAutoCalculated
+ * @return
+ */
+ boolean deleteAllAnnotations(boolean includingAutoCalculated);
/**
* Deletes a specific AlignmentAnnotation from the alignment, and removes its
* the annotation to delete
* @return true if annotation was deleted from this alignment.
*/
- public boolean deleteAnnotation(AlignmentAnnotation aa);
+ boolean deleteAnnotation(AlignmentAnnotation aa);
/**
* Deletes a specific AlignmentAnnotation from the alignment, and optionally
* into the alignment
* @return true if annotation was deleted from this alignment.
*/
- public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
+ boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
/**
* Get the annotation associated with this alignment (this can be null if no
* @return array of AlignmentAnnotation objects
*/
@Override
- public AlignmentAnnotation[] getAlignmentAnnotation();
+ AlignmentAnnotation[] getAlignmentAnnotation();
/**
* Change the gap character used in this alignment to 'gc'
* @param gc
* the new gap character.
*/
- public void setGapCharacter(char gc);
+ void setGapCharacter(char gc);
/**
* Get the gap character used in this alignment
*
* @return gap character
*/
- public char getGapCharacter();
+ char getGapCharacter();
/**
* Test for all nucleotide alignment
*
* @return true if alignment is nucleotide sequence
*/
- public boolean isNucleotide();
+ boolean isNucleotide();
/**
* Test if alignment contains RNA structure
*
* @return true if RNA structure AligmnentAnnotation was added to alignment
*/
- public boolean hasRNAStructure();
+ boolean hasRNAStructure();
/**
* Set alignment to be a nucleotide sequence
*
*/
- public void setNucleotide(boolean b);
+ void setNucleotide(boolean b);
/**
* Get the associated dataset for the alignment.
* @return Alignment containing dataset sequences or null of this is a
* dataset.
*/
- public Alignment getDataset();
+ Alignment getDataset();
/**
* Set the associated dataset for the alignment, or create one.
* @param dataset
* The dataset alignment or null to construct one.
*/
- public void setDataset(Alignment dataset);
+ void setDataset(Alignment dataset);
/**
* pads sequences with gaps (to ensure the set looks like an alignment)
*
* @return boolean true if alignment was modified
*/
- public boolean padGaps();
+ boolean padGaps();
- public HiddenSequences getHiddenSequences();
+ HiddenSequences getHiddenSequences();
/**
* Compact representation of alignment
*
* @return CigarArray
*/
- public CigarArray getCompactAlignment();
+ CigarArray getCompactAlignment();
/**
* Set an arbitrary key value pair for an alignment. Note: both key and value
* @param key
* @param value
*/
- public void setProperty(Object key, Object value);
+ void setProperty(Object key, Object value);
/**
* Get a named property from the alignment.
* @param key
* @return value of property
*/
- public Object getProperty(Object key);
+ Object getProperty(Object key);
/**
* Get the property hashtable.
*
* @return hashtable of alignment properties (or null if none are defined)
*/
- public Hashtable getProperties();
+ Hashtable getProperties();
/**
* add a reference to a frame of aligned codons for this alignment
*
* @param codons
*/
- public void addCodonFrame(AlignedCodonFrame codons);
+ void addCodonFrame(AlignedCodonFrame codons);
/**
* remove a particular codon frame reference from this alignment
* @param codons
* @return true if codon frame was removed.
*/
- public boolean removeCodonFrame(AlignedCodonFrame codons);
+ boolean removeCodonFrame(AlignedCodonFrame codons);
/**
* get all codon frames associated with this alignment
*
* @return
*/
- public AlignedCodonFrame[] getCodonFrames();
+ Set<AlignedCodonFrame> getCodonFrames();
/**
- * get a particular codon frame
- *
- * @param index
- * @return
+ * Set the codon frame mappings (replacing any existing set).
*/
- public AlignedCodonFrame getCodonFrame(int index);
+ void setCodonFrames(Set<AlignedCodonFrame> acfs);
/**
* get codon frames involving sequenceI
*/
- public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+ List<AlignedCodonFrame> getCodonFrame(SequenceI seq);
/**
* find sequence with given name in alignment
* tried
* @return matched sequence or null
*/
- public SequenceI findName(String token, boolean b);
+ SequenceI findName(String token, boolean b);
/**
* find next sequence with given name in alignment starting after a given
* tried
* @return matched sequence or null
*/
- public SequenceI findName(SequenceI startAfter, String token, boolean b);
+ SequenceI findName(SequenceI startAfter, String token, boolean b);
/**
* find first sequence in alignment which is involved in the given search
* @param results
* @return -1 or index of sequence in alignment
*/
- public int findIndex(SearchResults results);
+ int findIndex(SearchResults results);
/**
* append sequences and annotation from another alignment object to this one.
* @param toappend
* - the alignment to be appended.
*/
- public void append(AlignmentI toappend);
+ void append(AlignmentI toappend);
/**
* Justify the sequences to the left or right by deleting and inserting gaps
* true if alignment padded to right, false to justify to left
* @return true if alignment was changed TODO: return undo object
*/
- public boolean justify(boolean right);
+ boolean justify(boolean right);
/**
* add given annotation row at given position (0 is start, -1 is end)
* @param consensus
* @param i
*/
- public void addAnnotation(AlignmentAnnotation consensus, int i);
+ void addAnnotation(AlignmentAnnotation consensus, int i);
/**
* search for or create a specific annotation row on the alignment
*
* @return existing annotation matching the given attributes
*/
- public AlignmentAnnotation findOrCreateAnnotation(String name,
+ AlignmentAnnotation findOrCreateAnnotation(String name,
String calcId, boolean autoCalc, SequenceI seqRef,
SequenceGroup groupRef);
* @param up
* @param i
*/
- public void moveSelectedSequencesByOne(SequenceGroup sg,
+ void moveSelectedSequencesByOne(SequenceGroup sg,
Map<SequenceI, SequenceCollectionI> map, boolean up);
/**
*
* @param alignmentAnnotation
*/
- public void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
+ void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
+
+ /**
+ * Align this alignment the same as the given one. If both of the same type
+ * (nucleotide/protein) then align both identically. If this is nucleotide and
+ * the other is protein, make 3 gaps for each gap in the protein sequences. If
+ * this is protein and the other is nucleotide, insert a gap for each 3 gaps
+ * (or part thereof) between nucleotide bases. Returns the number of mapped
+ * sequences that were realigned .
+ *
+ * @param al
+ * @return
+ */
+ int alignAs(AlignmentI al);
+
+ /**
+ * Returns the set of distinct sequence names in the alignment.
+ *
+ * @return
+ */
+ Set<String> getSequenceNames();
}
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
public class AlignmentOrder
{
private String Name;
- private Vector Order = null;
+ private List<SequenceI> Order = null;
/**
* Creates a new AlignmentOrder object.
* AlignmentOrder
*
* @param anOrder
- * Vector
*/
- public AlignmentOrder(Vector anOrder)
+ public AlignmentOrder(List<SequenceI> anOrder)
{
Order = anOrder;
}
*/
public AlignmentOrder(AlignmentI orderFrom)
{
- Order = new Vector();
+ Order = new ArrayList<SequenceI>();
- for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
+ for (SequenceI seq : orderFrom.getSequences())
{
- Order.addElement(orderFrom.getSequenceAt(i));
+ Order.add(seq);
}
}
*/
public AlignmentOrder(SequenceI[] orderFrom)
{
- Order = new Vector();
-
- for (int i = 0, ns = orderFrom.length; i < ns; i++)
- {
- Order.addElement(orderFrom[i]);
- }
+ Order = new ArrayList<SequenceI>(Arrays.asList(orderFrom));
}
/**
* @param Order
* DOCUMENT ME!
*/
- public void setOrder(Vector Order)
+ public void setOrder(List<SequenceI> Order)
{
this.Order = Order;
}
*
* @return DOCUMENT ME!
*/
- public Vector getOrder()
+ public List<SequenceI> getOrder()
{
return Order;
}
int found = Order.indexOf(oldref);
if (found > -1)
{
- Order.setElementAt(newref, found);
+ Order.set(found, newref);
}
return found > -1;
}
* @param o
* @return true if o orders the same sequenceI objects in the same way
*/
- public boolean equals(AlignmentOrder o)
+ @Override
+ public boolean equals(Object o)
{
- return equals(o, true);
+ if (o == null || !(o instanceof AlignmentOrder))
+ {
+ return false;
+ }
+ return equals((AlignmentOrder) o, true);
}
/**
{
for (int i = 0, j = o.Order.size(); i < j; i++)
{
- if (Order.elementAt(i) != o.Order.elementAt(i))
+ if (Order.get(i) != o.Order.get(i))
{
return false;
}
}
if (Order != null && o.Order != null)
{
- Vector c, s;
+ List<SequenceI> c, s;
if (o.Order.size() > Order.size())
{
c = o.Order;
int last = -1;
for (int i = 0, j = s.size(); i < j; i++)
{
- int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by
+ int pos = c.indexOf(s.get(i)); // JBPNote - optimize by
// incremental position search
if (pos > last)
{
sgrps[g] = new ScGroup();
sgrps[g].sg = new SequenceGroup(sg);
addedgps[g] = false;
- seqsets.set(g, sg.getSequences(null));
+ // can't set entry 0 in an empty list
+ // seqsets.set(g, sg.getSequences(null));
+ seqsets.add(sg.getSequences());
}
// seqsets now contains vectors (should be sets) for each group, so we can
// track when we've done with the group
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
+import java.util.Collections;
import java.util.List;
import java.util.Vector;
*/
public class ColumnSelection
{
- Vector selected = new Vector();
+ Vector<Integer> selected = new Vector<Integer>();
// Vector of int [] {startCol, endCol}
Vector<int[]> hiddenColumns;
}
/**
- * removes col from selection
+ * Removes value 'col' from the selection (not the col'th item)
*
* @param col
* index of column to be removed
if (selected.contains(colInt))
{
+ // if this ever changes to List.remove(), ensure Integer not int argument
+ // as List.remove(int i) removes the i'th item which is wrong
selected.removeElement(colInt);
}
}
*/
public int columnAt(int i)
{
- return ((Integer) selected.elementAt(i)).intValue();
+ return selected.elementAt(i).intValue();
}
/**
if (temp >= start)
{
+ // if this ever changes to List.set(), swap parameter order!!
selected.setElementAt(new Integer(temp - change), i);
}
}
if (temp >= start)
{
+ // if this ever changes to List.set(), swap parameter order!!
selected.setElementAt(new Integer(temp - change), i);
}
}
{
if (shiftrecord != null)
{
- Vector shifts = shiftrecord.shifts;
+ final List<int[]> shifts = shiftrecord.getShifts();
if (shifts != null && shifts.size() > 0)
{
int shifted = 0;
for (int i = 0, j = shifts.size(); i < j; i++)
{
- int[] sh = (int[]) shifts.elementAt(i);
+ int[] sh = shifts.get(i);
// compensateForEdit(shifted+sh[0], sh[1]);
compensateForDelEdits(shifted + sh[0], sh[1]);
shifted -= sh[1];
* removes intersection of position,length ranges in deletions from the
* start,end regions marked in intervals.
*
- * @param deletions
+ * @param shifts
* @param intervals
* @return
*/
- private boolean pruneIntervalVector(Vector deletions, Vector intervals)
+ private boolean pruneIntervalVector(final List<int[]> shifts,
+ Vector<int[]> intervals)
{
boolean pruned = false;
- int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;
- int hr[] = (int[]) intervals.elementAt(i);
- int sr[] = (int[]) deletions.elementAt(s);
+ int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
+ int hr[] = intervals.elementAt(i);
+ int sr[] = shifts.get(s);
while (i <= j && s <= t)
{
boolean trailinghn = hr[1] >= sr[0];
{
if (i < j)
{
- hr = (int[]) intervals.elementAt(++i);
+ hr = intervals.elementAt(++i);
}
else
{
{ // leadinghc disjoint or not a deletion
if (s < t)
{
- sr = (int[]) deletions.elementAt(++s);
+ sr = shifts.get(++s);
}
else
{
j--;
if (i <= j)
{
- hr = (int[]) intervals.elementAt(i);
+ hr = intervals.elementAt(i);
}
continue;
}
// sr contained in hr
if (s < t)
{
- sr = (int[]) deletions.elementAt(++s);
+ sr = shifts.get(++s);
}
else
{
// operations.
}
- private boolean pruneColumnList(Vector deletion, Vector list)
+ private boolean pruneColumnList(final List<int[]> shifts,
+ Vector<Integer> list)
{
- int s = 0, t = deletion.size();
- int[] sr = (int[]) list.elementAt(s++);
+ int s = 0, t = shifts.size();
+ int[] sr = shifts.get(s++);
boolean pruned = false;
int i = 0, j = list.size();
while (i < j && s <= t)
{
- int c = ((Integer) list.elementAt(i++)).intValue();
+ int c = list.elementAt(i++).intValue();
if (sr[0] <= c)
{
if (sr[1] + sr[0] >= c)
{
if (s < t)
{
- sr = (int[]) deletion.elementAt(s);
+ sr = shifts.get(s);
}
s++;
}
{
if (deletions != null)
{
- Vector shifts = deletions.shifts;
+ final List<int[]> shifts = deletions.getShifts();
if (shifts != null && shifts.size() > 0)
{
// delete any intervals intersecting.
*/
public List<int[]> getHiddenColumns()
{
- return hiddenColumns == null ? Arrays.asList(new int[]
- {}) : hiddenColumns;
+ return hiddenColumns == null ? Collections.<int[]> emptyList()
+ : hiddenColumns;
}
/**
{
if (hiddenColumns == null)
{
- hiddenColumns = new Vector();
+ hiddenColumns = new Vector<int[]>();
}
boolean added = false;
{
if (copy.selected != null)
{
- selected = new Vector();
+ selected = new Vector<Integer>();
for (int i = 0, j = copy.selected.size(); i < j; i++)
{
selected.addElement(copy.selected.elementAt(i));
}
if (copy.hiddenColumns != null)
{
- hiddenColumns = new Vector(copy.hiddenColumns.size());
+ hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
{
int[] rh, cp;
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- Vector visiblecontigs = new Vector();
+ List<int[]> visiblecontigs = new ArrayList<int[]>();
List<int[]> regions = getHiddenColumns();
int vstart = start;
}
if (hideStart > vstart)
{
- visiblecontigs.addElement(new int[]
+ visiblecontigs.add(new int[]
{ vstart, hideStart - 1 });
}
vstart = hideEnd + 1;
if (vstart < end)
{
- visiblecontigs.addElement(new int[]
+ visiblecontigs.add(new int[]
{ vstart, end - 1 });
}
int[] vcontigs = new int[visiblecontigs.size() * 2];
for (int i = 0, j = visiblecontigs.size(); i < j; i++)
{
- int[] vc = (int[]) visiblecontigs.elementAt(i);
- visiblecontigs.setElementAt(null, i);
+ int[] vc = visiblecontigs.get(i);
+ visiblecontigs.set(i, null);
vcontigs[i * 2] = vc[0];
vcontigs[i * 2 + 1] = vc[1];
}
- visiblecontigs.removeAllElements();
+ visiblecontigs.clear();
return vcontigs;
}
else
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
- Vector annels = new Vector();
+ Vector<Annotation []> annels = new Vector<Annotation []>();
Annotation[] els = null;
List<int[]> regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
{
return;
}
- Enumeration e = annels.elements();
+
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
- while (e.hasMoreElements())
+
+ for (Annotation [] chnk : annels)
{
- Annotation[] chnk = (Annotation[]) e.nextElement();
System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
chnk.length);
w += chnk.length;
{
if (colsel != null && colsel.size() > 0)
{
- Enumeration e = colsel.getSelected().elements();
- while (e.hasMoreElements())
+ for (Integer col : colsel.getSelected())
{
- Object eo = e.nextElement();
- if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+ if (hiddenColumns != null && isVisible(col.intValue()))
{
- if (!selected.contains(eo))
+ if (!selected.contains(col))
{
- selected.addElement(eo);
+ selected.addElement(col);
}
}
}
*/
public void setElementsFrom(ColumnSelection colsel)
{
- selected = new Vector();
+ selected = new Vector<Integer>();
if (colsel.selected != null && colsel.selected.size() > 0)
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// only select visible columns in this columns selection
- selected = new Vector();
addElementsFrom(colsel);
}
else
{
// add everything regardless
- Enumeration en = colsel.selected.elements();
- while (en.hasMoreElements())
+ for (Integer col : colsel.getSelected())
{
- selected.addElement(en.nextElement());
+ addElement(col);
}
}
}
(entry.map == null ? null : new Mapping(entry.map)));
}
- public boolean equals(DBRefEntry entry)
+ @Override
+ public boolean equals(Object o)
{
+ // TODO should also override hashCode to ensure equal objects have equal
+ // hashcodes
+ if (o == null || !(o instanceof DBRefEntry))
+ {
+ return false;
+ }
+ DBRefEntry entry = (DBRefEntry) o;
if (entry == this)
+ {
return true;
- if (entry == null)
- return false;
+ }
if (equalRef(entry)
&& ((map == null && entry.map == null) || (map != null
&& entry.map != null && map.equals(entry.map))))
return false;
}
if (entry == this)
+ {
return true;
+ }
if ((source != null && entry.source != null && source
.equalsIgnoreCase(entry.source))
&& (accessionId != null && entry.accessionId != null && accessionId
return ((source != null) ? source : "") + ":"
+ ((accessionId != null) ? accessionId : "");
}
+
+ public String toString()
+ {
+ return getSrcAccString();
+ }
}
/**
* UNIPROT Entry Name
*/
- public static String UP_NAME = "UNIPROT_NAME";
+ public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
- public static final String UNIPROTKB = "UniProtKB/TrEMBL";
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+
+ public static final String EMBLCDSProduct = "EMBLCDSProtein"
+ .toUpperCase();
/**
* PDB Entry Code
/**
* GeneDB ID
*/
- public static final String GENEDB = "GeneDB";
+ public static final String GENEDB = "GeneDB".toUpperCase();
/**
* List of databases whose sequences might have coding regions annotated
{ EMBLCDS, GENEDB };
public static final String[] PROTEINDBS =
- { UNIPROT, PDB, UNIPROTKB };
+ { UNIPROT, PDB, UNIPROTKB, EMBLCDSProduct };
public static final String[] PROTEINSEQ =
- { UNIPROT, UNIPROTKB };
+ { UNIPROT, UNIPROTKB, EMBLCDSProduct };
public static final String[] PROTEINSTR =
{ PDB };
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * An exception to indicate that less than 3 nucleotide bases are available when
+ * trying to form a codon.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class IncompleteCodonException extends RuntimeException
+{
+
+}
*/
package jalview.datamodel;
-import java.util.Vector;
-
import jalview.util.MapList;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.Vector;
+
public class Mapping
{
/**
+ * An iterator that serves the aligned codon positions (with their protein
+ * products).
+ *
+ * @author gmcarstairs
+ *
+ */
+ public class AlignedCodonIterator implements Iterator<AlignedCodon>
+ {
+ /*
+ * The gap character used in the aligned sequence
+ */
+ private final char gap;
+
+ /*
+ * The characters of the aligned sequence e.g. "-cGT-ACgTG-"
+ */
+ private final char[] alignedSeq;
+
+ /*
+ * Next position (base 0) in the aligned sequence
+ */
+ private int alignedColumn = 0;
+
+ /*
+ * Count of bases up to and including alignedColumn position
+ */
+ private int alignedBases = 0;
+
+ /*
+ * [start, end] from ranges (base 1)
+ */
+ private Iterator<int[]> fromRanges;
+
+ /*
+ * [start, end] to ranges (base 1)
+ */
+ private Iterator<int[]> toRanges;
+
+ /*
+ * The current [start, end] (base 1) from range
+ */
+ private int[] currentFromRange = null;
+
+ /*
+ * The current [start, end] (base 1) to range
+ */
+ private int[] currentToRange = null;
+
+ /*
+ * The next 'from' position (base 1) to process
+ */
+ private int fromPosition = 0;
+
+ /*
+ * The next 'to' position (base 1) to process
+ */
+ private int toPosition = 0;
+
+ /**
+ * Constructor
+ *
+ * @param cs
+ * the aligned sequence characters
+ * @param gapChar
+ */
+ public AlignedCodonIterator(char[] cs, char gapChar)
+ {
+ this.alignedSeq = cs;
+ this.gap = gapChar;
+ fromRanges = map.getFromRanges().iterator();
+ toRanges = map.getToRanges().iterator();
+ if (fromRanges.hasNext())
+ {
+ currentFromRange = fromRanges.next();
+ fromPosition = currentFromRange[0];
+ }
+ if (toRanges.hasNext())
+ {
+ currentToRange = toRanges.next();
+ toPosition = currentToRange[0];
+ }
+ }
+
+ /**
+ * Returns true unless we have already traversed the whole mapping.
+ */
+ @Override
+ public boolean hasNext()
+ {
+ if (fromRanges.hasNext())
+ {
+ return true;
+ }
+ if (currentFromRange == null || fromPosition >= currentFromRange[1])
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the next codon's aligned positions, and translated value.
+ *
+ * @throws NoSuchElementException
+ * if hasNext() would have returned false
+ * @throws IncompleteCodonException
+ * if not enough mapped bases are left to make up a codon
+ */
+ @Override
+ public AlignedCodon next() throws IncompleteCodonException
+ {
+ if (!hasNext())
+ {
+ throw new NoSuchElementException();
+ }
+
+ int[] codon = getNextCodon();
+ int[] alignedCodon = getAlignedCodon(codon);
+
+ String peptide = getPeptide();
+ return new AlignedCodon(alignedCodon[0], alignedCodon[1],
+ alignedCodon[2], peptide);
+ }
+
+ /**
+ * Retrieve the translation as the 'mapped to' position in the mapped to
+ * sequence.
+ *
+ * @return
+ */
+ private String getPeptide()
+ {
+ // TODO should ideally handle toRatio other than 1 as well...
+ // i.e. code like getNextCodon()
+ if (toPosition <= currentToRange[1]) {
+ char pep = Mapping.this.to.getSequence()[toPosition - 1];
+ toPosition++;
+ return String.valueOf(pep);
+ }
+ if (!toRanges.hasNext())
+ {
+ throw new NoSuchElementException("Ran out of peptide at position "
+ + toPosition);
+ }
+ currentToRange = toRanges.next();
+ toPosition = currentToRange[0];
+ return getPeptide();
+ }
+
+ /**
+ * Get the (base 1) dataset positions for the next codon in the mapping.
+ *
+ * @throws IncompleteCodonException
+ * if less than 3 remaining bases are mapped
+ */
+ private int[] getNextCodon()
+ {
+ int[] codon = new int[3];
+ int codonbase = 0;
+
+ while (codonbase < 3)
+ {
+ if (fromPosition <= currentFromRange[1])
+ {
+ /*
+ * Add next position from the current start-end range
+ */
+ codon[codonbase++] = fromPosition++;
+ }
+ else
+ {
+ /*
+ * Move to the next range - if there is one
+ */
+ if (!fromRanges.hasNext())
+ {
+ throw new IncompleteCodonException();
+ }
+ currentFromRange = fromRanges.next();
+ fromPosition = currentFromRange[0];
+ }
+ }
+ return codon;
+ }
+
+ /**
+ * Get the aligned column positions (base 0) for the given sequence
+ * positions (base 1), by counting ungapped characters in the aligned
+ * sequence.
+ *
+ * @param codon
+ * @return
+ */
+ private int[] getAlignedCodon(int[] codon)
+ {
+ int[] aligned = new int[codon.length];
+ for (int i = 0; i < codon.length; i++)
+ {
+ aligned[i] = getAlignedColumn(codon[i]);
+ }
+ return aligned;
+ }
+
+ /**
+ * Get the aligned column position (base 0) for the given sequence position
+ * (base 1).
+ *
+ * @param sequencePos
+ * @return
+ */
+ private int getAlignedColumn(int sequencePos)
+ {
+ while (alignedBases < sequencePos
+ && alignedColumn < alignedSeq.length)
+ {
+ if (alignedSeq[alignedColumn++] != gap)
+ {
+ alignedBases++;
+ }
+ }
+ return alignedColumn - 1;
+ }
+
+ @Override
+ public void remove()
+ {
+ // ignore
+ }
+
+ }
+
+ /**
* Contains the start-end pairs mapping from the associated sequence to the
- * sequence in the database coordinate system it also takes care of step
- * difference between coordinate systems
+ * sequence in the database coordinate system. It also takes care of step
+ * difference between coordinate systems.
*/
MapList map = null;
/**
- * The seuqence that map maps the associated seuqence to (if any).
+ * The sequence that map maps the associated sequence to (if any).
*/
SequenceI to = null;
* @param other
* @return
*/
- public boolean equals(Mapping other)
+ @Override
+ public boolean equals(Object o)
{
- if (other == null)
+ // TODO should override Object.hashCode() to ensure that equal objects have
+ // equal hashcodes
+ if (o == null || !(o instanceof Mapping))
+ {
return false;
+ }
+ Mapping other = (Mapping) o;
if (other == this)
+ {
return true;
+ }
if (other.to != to)
+ {
return false;
+ }
if ((map != null && other.map == null)
|| (map == null && other.map != null))
+ {
return false;
- if (map.equals(other.map))
+ }
+ if ((map == null && other.map == null) || map.equals(other.map))
+ {
return true;
+ }
return false;
}
vf[v].setBegin(frange[i]);
vf[v].setEnd(frange[i + 1]);
if (frange.length > 2)
+ {
vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
+ }
}
return vf;
}
from = (map.getToLowest() < from) ? from : map.getToLowest();
to = (map.getToHighest() > to) ? to : map.getToHighest();
if (from > to)
+ {
return null;
+ }
}
else
{
from = (map.getToHighest() > from) ? from : map.getToHighest();
to = (map.getToLowest() < to) ? to : map.getToLowest();
if (from < to)
+ {
return null;
+ }
}
return map.locateInFrom(from, to);
}
from = (map.getFromLowest() < from) ? from : map.getFromLowest();
to = (map.getFromHighest() > to) ? to : map.getFromHighest();
if (from > to)
+ {
return null;
+ }
}
else
{
from = (map.getFromHighest() > from) ? from : map.getFromHighest();
to = (map.getFromLowest() < to) ? to : map.getFromLowest();
if (from < to)
+ {
return null;
+ }
}
return map.locateInTo(from, to);
}
super.finalize();
}
+ public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
+ {
+ return new AlignedCodonIterator(seq.getSequence(), gapChar);
+ }
+
}
*/
package jalview.datamodel;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Holds a list of search result matches, where each match is a contiguous
+ * stretch of a single sequence.
+ *
+ * @author gmcarstairs
+ *
+ */
public class SearchResults
{
- Match[] matches;
+ private List<Match> matches = new ArrayList<Match>();
+
+ public class Match
+ {
+ SequenceI sequence;
+
+ /**
+ * Start position of match in sequence (base 1)
+ */
+ int start;
+
+ /**
+ * End position (inclusive) (base 1)
+ */
+ int end;
+
+ /**
+ * Constructor
+ *
+ * @param seq
+ * a sequence
+ * @param start
+ * start position of matched range (base 1)
+ * @param end
+ * end of matched range (inclusive, base 1)
+ */
+ public Match(SequenceI seq, int start, int end)
+ {
+ sequence = seq;
+ this.start = start;
+ this.end = end;
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ public int getStart()
+ {
+ return start;
+ }
+
+ public int getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Returns the string of characters in the matched region.
+ */
+ @Override
+ public String toString()
+ {
+ char[] chars = sequence.getSequence();
+ // convert start/end to base 0 (with bounds check)
+ final int from = Math.max(start - 1, 0);
+ final int to = Math.min(end, chars.length + 1);
+ return String.valueOf(Arrays.copyOfRange(chars, from, to));
+ }
+ }
/**
* This method replaces the old search results which merely held an alignment
*/
public void addResult(SequenceI seq, int start, int end)
{
- if (matches == null)
- {
- matches = new Match[]
- { new Match(seq, start, end) };
- return;
- }
-
- int mSize = matches.length;
-
- Match[] tmp = new Match[mSize + 1];
- int m;
- for (m = 0; m < mSize; m++)
- {
- tmp[m] = matches[m];
- }
-
- tmp[m] = new Match(seq, start, end);
-
- matches = tmp;
+ matches.add(new Match(seq, start, end));
}
/**
*/
public boolean involvesSequence(SequenceI sequence)
{
- if (matches == null || matches.length == 0)
- {
- return false;
- }
SequenceI ds = sequence.getDatasetSequence();
- for (int m = 0; m < matches.length; m++)
+ for (Match m : matches)
{
- if (matches[m].sequence != null
- && (matches[m].sequence == sequence || matches[m].sequence == ds))
+ if (m.sequence != null
+ && (m.sequence == sequence || m.sequence == ds))
{
return true;
}
*/
public int[] getResults(SequenceI sequence, int start, int end)
{
- if (matches == null)
+ if (matches.isEmpty())
{
return null;
}
int[] tmp = null;
int resultLength, matchStart = 0, matchEnd = 0;
boolean mfound;
- for (int m = 0; m < matches.length; m++)
+ for (Match m : matches)
{
mfound = false;
- if (matches[m].sequence == sequence)
+ if (m.sequence == sequence)
{
mfound = true;
// locate aligned position
- matchStart = sequence.findIndex(matches[m].start) - 1;
- matchEnd = sequence.findIndex(matches[m].end) - 1;
+ matchStart = sequence.findIndex(m.start) - 1;
+ matchEnd = sequence.findIndex(m.end) - 1;
}
- else if (matches[m].sequence == sequence.getDatasetSequence())
+ else if (m.sequence == sequence.getDatasetSequence())
{
mfound = true;
// locate region in local context
- matchStart = sequence.findIndex(matches[m].start) - 1;
- matchEnd = sequence.findIndex(matches[m].end) - 1;
+ matchStart = sequence.findIndex(m.start) - 1;
+ matchEnd = sequence.findIndex(m.end) - 1;
}
if (mfound)
{
public int getSize()
{
- return matches == null ? 0 : matches.length;
+ return matches.size();
}
public SequenceI getResultSequence(int index)
{
- return matches[index].sequence;
+ return matches.get(index).sequence;
}
- public int getResultStart(int index)
+ /**
+ * Returns the start position of the i'th match in the search results.
+ *
+ * @param i
+ * @return
+ */
+ public int getResultStart(int i)
{
- return matches[index].start;
+ return matches.get(i).start;
}
- public int getResultEnd(int index)
+ /**
+ * Returns the end position of the i'th match in the search results.
+ *
+ * @param i
+ * @return
+ */
+ public int getResultEnd(int i)
{
- return matches[index].end;
+ return matches.get(i).end;
}
- class Match
+ /**
+ * Returns true if no search result matches are held.
+ *
+ * @return
+ */
+ public boolean isEmpty()
{
- SequenceI sequence;
-
- int start;
+ return matches.isEmpty();
+ }
- int end;
+ /**
+ * Returns the list of matches.
+ *
+ * @return
+ */
+ public List<Match> getResults()
+ {
+ return matches;
+ }
- public Match(SequenceI seq, int start, int end)
+ /**
+ * Return the results as a string of characters. Meant for use when the
+ * context ensures that all matches are to regions of the same sequence
+ * (otherwise the result is meaningless).
+ *
+ * @return
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder result = new StringBuilder(256);
+ for (Match m : matches)
{
- sequence = seq;
- this.start = start;
- this.end = end;
+ result.append(m.toString());
}
+ return result.toString();
}
}
package jalview.datamodel;
import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
import java.util.ArrayList;
import java.util.Enumeration;
}
/**
- * DOCUMENT ME!
+ * Returns the sequence features (if any), looking first on the sequence, then
+ * on its dataset sequence, and so on until a non-null value is found (or
+ * none). This supports retrieval of sequence features stored on the sequence
+ * (as in the applet) or on the dataset sequence (as in the Desktop version).
*
- * @return DOCUMENT ME!
+ * @return
*/
public SequenceFeature[] getSequenceFeatures()
{
- return sequenceFeatures;
+ SequenceFeature[] features = sequenceFeatures;
+
+ SequenceI seq = this;
+ int count = 0; // failsafe against loop in sequence.datasetsequence...
+ while (features == null && seq.getDatasetSequence() != null
+ && count++ < 10)
+ {
+ seq = seq.getDatasetSequence();
+ features = ((Sequence) seq).sequenceFeatures;
+ }
+ return features;
}
public void addPDBId(PDBEntry entry)
return;
}
- char[] tmp;
-
- if (j >= sequence.length)
- {
- tmp = new char[i];
- System.arraycopy(sequence, 0, tmp, 0, i);
- j = sequence.length;
- }
- else
- {
- tmp = new char[sequence.length - j + i];
- System.arraycopy(sequence, 0, tmp, 0, i);
- System.arraycopy(sequence, j, tmp, i, sequence.length - j);
- }
+ char[] tmp = StringUtils.deleteChars(sequence, i, j);
boolean createNewDs = false;
- // TODO: take a look at the new dataset creation validation method below -
- // this could become time comsuming for large sequences - consider making it
- // more efficient
+ // TODO: take a (second look) at the dataset creation validation method for
+ // the very large sequence case
+ int eindex = -1, sindex = -1;
+ boolean ecalc = false, scalc = false;
for (int s = i; s < j; s++)
{
if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
}
else
{
- int sindex = findIndex(start) - 1;
+ if (!scalc)
+ {
+ sindex = findIndex(start) - 1;
+ scalc = true;
+ }
if (sindex == s)
{
// delete characters including start of sequence
else
{
// delete characters after start.
- int eindex = findIndex(end) - 1;
+ if (!ecalc)
+ {
+ eindex = findIndex(end) - 1;
+ ecalc = true;
+ }
if (eindex < j)
{
// delete characters at end of sequence
AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
_aa.sequenceRef = datasetSequence;
_aa.adjustForAlignment(); // uses annotation's own record of
- // sequence-column mapping
+ // sequence-column mapping
datasetSequence.addAlignmentAnnotation(_aa);
}
}
String label)
{
List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
- if (this.annotation != null) {
- for (AlignmentAnnotation ann : annotation) {
+ if (this.annotation != null)
+ {
+ for (AlignmentAnnotation ann : annotation)
+ {
if (ann.calcId != null && ann.calcId.equals(calcId)
&& ann.label != null && ann.label.equals(label))
{
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* DOCUMENT ME!
public Hashtable otherDetails;
- public java.util.Vector links;
+ public Vector<String> links;
// Feature group can be set from a features file
// as a group of features between STARTGROUP and ENDGROUP markers
}
if (cpy.links != null && cpy.links.size() > 0)
{
- links = new Vector();
+ links = new Vector<String>();
for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
{
links.addElement(cpy.links.elementAt(i));
{
if (links == null)
{
- links = new java.util.Vector();
+ links = new Vector<String>();
}
links.insertElementAt(labelLink, 0);
{
String stat = (String) otherDetails.get("status");
if (stat != null)
+ {
return new String(stat);
+ }
}
return null;
}
return false;
}
+ /**
+ * Remove all sequences from the group (leaving other properties unchanged).
+ */
public void clear()
{
synchronized (sequences)
public String getDescription();
/**
- * Return the alignment column for a sequence position * Return the alignment
- * position for a sequence position
+ * Return the alignment column for a sequence position
*
* @param pos
* lying from start to end
* if necessary and adjusting start and end positions accordingly.
*
* @param i
- * first column in range to delete
+ * first column in range to delete (inclusive)
* @param j
- * last column in range to delete
+ * last column in range to delete (exclusive)
*/
public void deleteChars(int i, int j);
/**
* DOCUMENT ME!
- *
- * @param i
+ * @param position
* DOCUMENT ME!
- * @param c
+ * @param ch
* DOCUMENT ME!
*/
- public void insertCharAt(int i, int length, char c);
+ public void insertCharAt(int position, int count, char ch);
/**
* DOCUMENT ME!
{ 1, dna.getLength() }, 1, 1));
// TODO: transform EMBL Database refs to canonical form
if (dbRefs != null)
+ {
for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
.addDBRef((DBRefEntry) i.next()))
+ {
;
+ }
+ }
}
try
{
{
for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
.addDBRef((DBRefEntry) dbr.next()))
+ {
;
+ }
}
}
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
.addDBRef((DBRefEntry) dbr.next()))
+ {
;
+ }
}
}
}
}
}
Sequence product = null;
+ DBRefEntry protEMBLCDS = null;
exon = adjustForPrStart(prstart, exon);
-
+ boolean noProteinDbref=true;
+
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
// { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
pcdnaref.setMap(new Mapping(mp));
if (product != null)
+ {
product.addDBRef(pcdnaref);
-
+ protEMBLCDS = new DBRefEntry(pcdnaref);
+ protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+ product.addDBRef(protEMBLCDS);
+
+ }
+
}
}
// add cds feature to dna seq - this may include the stop codon
sf.setEnd(exon[xint + 1]);
sf.setType(feature.getName());
sf.setFeatureGroup(sourceDb);
- sf.setDescription("Exon " + (1 + (int) (xint / 2))
+ sf.setDescription("Exon " + (1 + xint / 2)
+ " for protein '" + prname + "' EMBLCDS:" + prid);
sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
sf.setValue(FeatureProperties.EXONPRODUCT, prname);
if (vals != null && vals.size() > 0)
{
- Enumeration kv = vals.elements();
+ Enumeration kv = vals.keys();
while (kv.hasMoreElements())
{
Object key = kv.nextElement();
if (key != null)
+ {
sf.setValue(key.toString(), vals.get(key));
+ }
}
}
dna.addSequenceFeature(sf);
+ ref.getAccessionId());
}
}
+ noProteinDbref = false;
}
if (product != null)
{
}
dna.addDBRef(ref);
}
+ if (noProteinDbref && product != null)
+ {
+ // add protein coding reference to dna sequence so xref matches
+ if (protEMBLCDS == null)
+ {
+ protEMBLCDS = new DBRefEntry();
+ protEMBLCDS.setAccessionId(prid);
+ protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+ protEMBLCDS.setVersion(getVersion());
+ protEMBLCDS
+ .setMap(new Mapping(product, map.getMap().getInverse()));
+ }
+ product.addDBRef(protEMBLCDS);
+
+ // Add converse mapping reference
+ if (map != null)
+ {
+ Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
+ .getInverse());
+ DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
+ ncMap.setMap(pmap);
+ if (map.getTo() != null)
+ {
+ dna.addDBRef(ncMap);
+ }
+ }
+ }
}
}
import java.io.File;
import java.net.URL;
import java.security.AccessControlException;
-import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
return;
}
- String res;
int index;
Color col;
jmolHistory(false);
// TODO: Switch between nucleotide or aa selection expressions
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
+ StringBuilder command = new StringBuilder(128);
+ command.append("select *;color white;");
+ for (String res : ResidueProperties.aa3Hash.keySet())
{
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
+ index = ResidueProperties.aa3Hash.get(res).intValue();
if (index > 20)
{
continue;
import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
+import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.net.URL;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import org.apache.http.message.BasicNameValuePair;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
-import org.json.simple.JSONStreamAware;
import org.json.simple.parser.ContentHandler;
import org.json.simple.parser.ParseException;
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
ArrayList<Reader> readers = new ArrayList<Reader>();
- readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+ final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+ readers.add(postResponse);
return readers.iterator();
}
*/
package jalview.ext.rbvi.chimera;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*
final Map<String, List<int[]>> modelData = colourData.get(model);
for (String chain : modelData.keySet())
{
+ boolean hasChain = !"".equals(chain.trim());
for (int[] range : modelData.get(chain))
{
if (!firstPositionForModel)
{
sb.append(range[0]).append("-").append(range[1]);
}
- sb.append(".").append(chain);
+ if (hasChain)
+ {
+ sb.append(".").append(chain);
+ }
firstPositionForModel = false;
}
}
import java.awt.Color;
import java.util.ArrayList;
-import java.util.Enumeration;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
private Map<String, String> chainFile;
- private StringBuffer eval = new StringBuffer();
-
public String fileLoadingError;
/*
private boolean loadedInline;
/**
+ * current set of model filenames loaded
+ */
+ String[] modelFileNames = null;
+
+ String lastMousedOverAtomSpec;
+
+ private List<String> lastReply;
+
+ /**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
* We check if the PDB model id is already loaded in Chimera, if so don't
}
/**
- * current set of model filenames loaded
- */
- String[] modelFileNames = null;
-
-
- StringBuffer resetLastRes = new StringBuffer();
-
- private List<String> lastReply;
-
- /**
* Constructor
*
* @param ssm
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ files, sr, fr, alignment))
{
for (String command : cpdbbyseq.commands)
{
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- return ChimeraCommands
- .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
- fr,
- alignment);
+ return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, fr, alignment);
}
/**
}
}
-
+
// End StructureListener
// //////////////////////////
public abstract SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment);
- // jmol/ssm only
+ /**
+ * Construct and send a command to highlight an atom.
+ *
+ * <pre>
+ * Done by generating a command like (to 'highlight' position 44)
+ * ~select #0:43.C;select #0:44.C
+ * Note this removes the selection from the previous position.
+ * </pre>
+ */
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
if (cms != null)
{
- int mdlNum = cms.get(0).getModelNumber();
-
- viewerCommandHistory(false);
- // viewer.stopListening();
- if (resetLastRes.length() > 0)
+ StringBuilder sb = new StringBuilder();
+ sb.append(" #" + cms.get(0).getModelNumber());
+ sb.append(":" + pdbResNum);
+ if (!chain.equals(" "))
{
- eval.setLength(0);
- eval.append(resetLastRes.toString() + ";");
+ sb.append("." + chain);
}
+ String atomSpec = sb.toString();
- eval.append("display "); // +modelNum
-
- resetLastRes.setLength(0);
- resetLastRes.append("~display ");
+ StringBuilder command = new StringBuilder(32);
+ if (lastMousedOverAtomSpec != null)
{
- eval.append(" #" + (mdlNum));
- resetLastRes.append(" #" + (mdlNum));
+ command.append("~show " + lastMousedOverAtomSpec + ";");
}
- // complete select string
-
- eval.append(":" + pdbResNum);
- resetLastRes.append(":" + pdbResNum);
- if (!chain.equals(" "))
+ viewerCommandHistory(false);
+ command.append("show ").append(atomSpec);
+ String cmd = command.toString();
+ if (cmd.length() > 0)
{
- eval.append("." + chain);
- resetLastRes.append("." + chain);
+ viewer.sendChimeraCommand(cmd, false);
}
-
- viewer.sendChimeraCommand(eval.toString(), false);
viewerCommandHistory(true);
- // viewer.startListening();
+ this.lastMousedOverAtomSpec = atomSpec;
}
}
return;
}
- String res;
int index;
Color col;
// Chimera expects RBG values in the range 0-1
final double normalise = 255D;
viewerCommandHistory(false);
// TODO: Switch between nucleotide or aa selection expressions
- Enumeration en = ResidueProperties.aa3Hash.keys();
StringBuilder command = new StringBuilder(128);
command.append("color white;");
- while (en.hasMoreElements())
+ for (String res : ResidueProperties.aa3Hash.keySet())
{
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
+ index = ResidueProperties.aa3Hash.get(res).intValue();
if (index > 20)
{
continue;
*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.analysis.CrossRef;
-import jalview.analysis.NJTree;
+import jalview.analysis.Dna;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.GridLayout;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
/**
* DOCUMENT ME!
*
IProgressIndicator, AlignViewControllerGuiI
{
- /** DOCUMENT ME!! */
public static final int DEFAULT_WIDTH = 700;
- /** DOCUMENT ME!! */
public static final int DEFAULT_HEIGHT = 500;
+ /*
+ * The currently displayed panel (selected tabbed view if more than one)
+ */
public AlignmentPanel alignPanel;
AlignViewport viewport;
public AlignViewControllerI avc;
- Vector alignPanels = new Vector();
+ List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
/**
* Last format used to load or save alignments in this window
buildSortByAnnotationScoresMenu();
buildTreeMenu();
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
wrapMenuItem_actionPerformed(null);
}
addKeyListener();
+ final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
+ final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
+ ViewSelectionMenu vsel = new ViewSelectionMenu("Transfer colours from",
+ new ViewSetProvider()
+ {
+
+ @Override
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ origview.clear();
+ origview.add(alignPanel);
+ return Desktop.getAlignmentPanels(null);
+ }
+ }, selviews, new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (origview.size() > 0)
+ {
+ ViewStyleI vs = selviews.get(0).getAlignViewport()
+ .getViewStyle();
+ origview.get(0).getAlignViewport().setViewStyle(vs);
+ AlignViewportI complement = origview.get(0)
+ .getAlignViewport().getCodingComplement();
+ if (complement != null)
+ {
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ if (complement.isNucleotide())
+ {
+ complement.setViewStyle(vs);
+ vs.setCharWidth(vs.getCharWidth() / 3);
+ }
+ else
+ {
+ int rw = vs.getCharWidth();
+ vs.setCharWidth(rw * 3);
+ complement.setViewStyle(vs);
+ vs.setCharWidth(rw);
+ }
+ af.alignPanel.updateLayout();
+ af.setMenusForViewport();
+ }
+ origview.get(0).updateLayout();
+ origview.get(0).setSelected(true);
+ origview.get(0).alignFrame.setMenusForViewport();
+
+ }
+ }
+ });
+ formatMenu.add(vsel);
+
}
/**
public void setFileName(String file, String format)
{
fileName = file;
- currentFileFormat = format;
+ setFileFormat(format);
reload.setEnabled(true);
}
+ /**
+ * Add a KeyListener with handlers for various KeyPressed and KeyReleased
+ * events
+ */
void addKeyListener()
{
addKeyListener(new KeyAdapter()
break;
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(true);
}
}
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(false);
}
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
- alignPanels.addElement(ap);
+ alignPanels.add(ap);
PaintRefresher.Register(ap, ap.av.getSequenceSetId());
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
- AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+ AlignmentPanel first = alignPanels.get(0);
tabbedPane.addTab(first.av.viewName, first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
}).start();
}
+ /**
+ * Configure menu items that vary according to whether the alignment is
+ * nucleotide or protein
+ *
+ * @param nucleotide
+ */
public void setGUINucleotide(boolean nucleotide)
{
showTranslation.setVisible(nucleotide);
showGroupConservation.setEnabled(!nucleotide);
rnahelicesColour.setEnabled(nucleotide);
purinePyrimidineColour.setEnabled(nucleotide);
- // Remember AlignFrame always starts as protein
- // if (!nucleotide)
- // {
- // showTr
- // calculateMenu.remove(calculateMenu.getItemCount() - 2);
- // }
+ showComplementMenuItem.setText(MessageManager
+ .getString(nucleotide ? "label.protein" : "label.nucleotide"));
+ setColourSelected(jalview.bin.Cache.getDefault(
+ nucleotide ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT, "None"));
}
/**
- * set up menus for the currently viewport. This may be called after any
+ * set up menus for the current viewport. This may be called after any
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
- colourTextMenuItem.setSelected(av.showColourText);
+ colourTextMenuItem.setSelected(av.isShowColourText());
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
conservationMenuItem.setSelected(av.getConservationSelected());
seqLimits.setSelected(av.getShowJVSuffix());
idRightAlign.setSelected(av.isRightAlignIds());
- centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
- renderGapsMenuItem.setSelected(av.renderGaps);
- wrapMenuItem.setSelected(av.wrapAlignment);
- scaleAbove.setVisible(av.wrapAlignment);
- scaleLeft.setVisible(av.wrapAlignment);
- scaleRight.setVisible(av.wrapAlignment);
+ centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
+ renderGapsMenuItem.setSelected(av.isRenderGaps());
+ wrapMenuItem.setSelected(av.getWrapAlignment());
+ scaleAbove.setVisible(av.getWrapAlignment());
+ scaleLeft.setVisible(av.getWrapAlignment());
+ scaleRight.setVisible(av.getWrapAlignment());
annotationPanelMenuItem.setState(av.isShowAnnotation());
/*
* Show/hide annotations only enabled if annotation panel is shown
hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
- viewBoxesMenuItem.setSelected(av.showBoxes);
- viewTextMenuItem.setSelected(av.showText);
+ viewBoxesMenuItem.setSelected(av.getShowBoxes());
+ viewTextMenuItem.setSelected(av.getShowText());
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
showGroupConsensus.setSelected(av.isShowGroupConsensus());
showGroupConservation.setSelected(av.isShowGroupConservation());
.getGlobalColourScheme()));
showSeqFeatures.setSelected(av.isShowSequenceFeatures());
- hiddenMarkers.setState(av.showHiddenMarkers);
+ hiddenMarkers.setState(av.getShowHiddenMarkers());
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
- showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
- showDbRefsMenuitem.setSelected(av.isShowDbRefs());
+ showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
+ showDbRefsMenuitem.setSelected(av.isShowDBRefs());
autoCalculate.setSelected(av.autoCalculateConsensus);
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new Object[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
currentFileFormat = chooser.getSelectedFormat();
- if (currentFileFormat == null)
+ while (currentFileFormat == null)
{
JOptionPane
.showInternalMessageDialog(
MessageManager
.getString("label.file_format_not_specified"),
JOptionPane.WARNING_MESSAGE);
+ currentFileFormat = chooser.getSelectedFormat();
value = chooser.showSaveDialog(this);
- return;
+ if (value != JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
}
fileName = chooser.getSelectedFile().getPath();
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
- new String[]
+ new Object[]
{ fileName, format }));
} catch (Exception ex)
{
if (!success)
{
JOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new String[]
+ .formatMessage("label.couldnt_save_file", new Object[]
{ fileName }), MessageManager
.getString("label.error_saving_file"),
JOptionPane.WARNING_MESSAGE);
viewport.getAlignment(), omitHidden,
viewport.getColumnSelection()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new String[]
+ "label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
// setClosed(true) is called
for (int i = 0; i < alignPanels.size(); i++)
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ AlignmentPanel ap = alignPanels.get(i);
ap.closePanel();
}
}
}
/**
- * close alignPanel2 and shuffle tabs appropriately.
+ * Close the specified panel and close up tabs appropriately.
*
- * @param alignPanel2
+ * @param panelToClose
*/
- public void closeView(AlignmentPanel alignPanel2)
+ public void closeView(AlignmentPanel panelToClose)
{
int index = tabbedPane.getSelectedIndex();
- int closedindex = tabbedPane.indexOfComponent(alignPanel2);
- alignPanels.removeElement(alignPanel2);
- // Unnecessary
- // if (viewport == alignPanel2.av)
- // {
- // viewport = null;
- // }
- alignPanel2.closePanel();
- alignPanel2 = null;
+ int closedindex = tabbedPane.indexOfComponent(panelToClose);
+ alignPanels.remove(panelToClose);
+ panelToClose.closePanel();
+ panelToClose = null;
tabbedPane.removeTabAt(closedindex);
tabbedPane.validate();
void updateEditMenuBar()
{
- if (viewport.historyList.size() > 0)
+ if (viewport.getHistoryList().size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = viewport.historyList.peek();
+ CommandI command = viewport.getHistoryList().peek();
undoMenuItem.setText(MessageManager.formatMessage(
- "label.undo_command", new String[]
+ "label.undo_command", new Object[]
{ command.getDescription() }));
}
else
undoMenuItem.setText(MessageManager.getString("action.undo"));
}
- if (viewport.redoList.size() > 0)
+ if (viewport.getRedoList().size() > 0)
{
redoMenuItem.setEnabled(true);
- CommandI command = viewport.redoList.peek();
+ CommandI command = viewport.getRedoList().peek();
redoMenuItem.setText(MessageManager.formatMessage(
- "label.redo_command", new String[]
+ "label.redo_command", new Object[]
{ command.getDescription() }));
}
else
{
if (command.getSize() > 0)
{
- viewport.historyList.push(command);
- viewport.redoList.clear();
+ viewport.addToHistoryList(command);
+ viewport.clearRedoList();
updateEditMenuBar();
viewport.updateHiddenColumns();
// viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
{
if (alignPanels != null)
{
- Enumeration e = alignPanels.elements();
AlignmentI[] als = new AlignmentI[alignPanels.size()];
- for (int i = 0; e.hasMoreElements(); i++)
+ int i = 0;
+ for (AlignmentPanel ap : alignPanels)
{
- als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
+ als[i++] = ap.av.getAlignment();
}
return als;
}
@Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.historyList.empty())
+ if (viewport.getHistoryList().isEmpty())
{
return;
}
- CommandI command = viewport.historyList.pop();
- viewport.redoList.push(command);
+ CommandI command = viewport.getHistoryList().pop();
+ viewport.addToRedoList(command);
command.undoCommand(getViewAlignments());
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
if (originalSource != null)
@Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.redoList.size() < 1)
+ if (viewport.getRedoList().size() < 1)
{
return;
}
- CommandI command = viewport.redoList.pop();
- viewport.historyList.push(command);
+ CommandI command = viewport.getRedoList().pop();
+ viewport.addToHistoryList(command);
command.doCommand(getViewAlignments());
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
if (originalSource != null)
}
}
- AlignViewport getOriginatingSource(CommandI command)
+ AlignmentViewport getOriginatingSource(CommandI command)
{
- AlignViewport originalSource = null;
+ AlignmentViewport originalSource = null;
// For sequence removal and addition, we need to fire
// the property change event FROM the viewport where the
// original alignment was altered
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+ List<Component> comps = PaintRefresher.components.get(viewport
.getSequenceSetId());
- for (int i = 0; i < comps.size(); i++)
+ for (Component comp : comps)
{
- if (comps.elementAt(i) instanceof AlignmentPanel)
+ if (comp instanceof AlignmentPanel)
{
- if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
+ if (al == ((AlignmentPanel) comp).av.getAlignment())
{
- originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
+ originalSource = ((AlignmentPanel) comp).av;
break;
}
}
synchronized void slideSequences(boolean right, int size)
{
- List<SequenceI> sg = new Vector();
+ List<SequenceI> sg = new ArrayList<SequenceI>();
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
return;
}
- Vector invertGroup = new Vector();
+ List<SequenceI> invertGroup = new ArrayList<SequenceI>();
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
+ for (SequenceI seq : viewport.getAlignment().getSequences())
{
- if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ if (!sg.contains(seq))
{
- invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+ invertGroup.add(seq);
}
}
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
{
- seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+ seqs2[i] = invertGroup.get(i);
}
SlideSequencesCommand ssc;
}
boolean appendHistoryItem = false;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ Deque<CommandI> historyList = viewport.getHistoryList();
+ if (historyList != null
+ && historyList.size() > 0
+ && historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .appendSlideCommand((SlideSequencesCommand) historyList
.peek());
}
Desktop.jalviewClipboard = new Object[]
{ seqs, viewport.getAlignment().getDataset(), hiddenColumns };
statusBar.setText(MessageManager.formatMessage(
- "label.copied_sequences_to_clipboard", new String[]
+ "label.copied_sequences_to_clipboard", new Object[]
{ Integer.valueOf(seqs.length).toString() }));
}
alignment.getSequences());
if (alignPanels != null)
{
- for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+ for (AlignmentPanel ap : alignPanels)
{
ap.validateAnnotationDimensions(false);
}
return;
}
- List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
- SequenceI seq;
- for (int i = 0; i < sg.getSize(); i++)
- {
- seq = sg.getSequenceAt(i);
- seqs.add(seq);
- }
-
- // If the cut affects all sequences, warn, remove highlighted columns
+ /*
+ * If the cut affects all sequences, warn, remove highlighted columns
+ */
if (sg.getSize() == viewport.getAlignment().getHeight())
{
int confirm = JOptionPane.showConfirmDialog(this,
sg.getEndRes() + 1);
}
- SequenceI[] cut = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- cut[i] = seqs.get(i);
- }
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
- /*
- * //ADD HISTORY ITEM
- */
addHistoryItem(new EditCommand(
MessageManager.getString("label.cut_sequences"), Action.CUT,
cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
addHistoryItem(removeGapCols);
statusBar.setText(MessageManager.formatMessage(
- "label.removed_empty_columns", new String[]
+ "label.removed_empty_columns", new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
.getSequences());
}
- // else
- {
- // if (justifySeqs>0)
- {
- // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
- }
- }
-
- // }
-
/**
* DOCUMENT ME!
*
new Finder();
}
- @Override
- public void newView_actionPerformed(ActionEvent e)
- {
- newView(true);
- }
-
- /**
- *
- * @param copyAnnotation
- * if true then duplicate all annnotation, groups and settings
- * @return new alignment panel, already displayed.
- */
- public AlignmentPanel newView(boolean copyAnnotation)
- {
- return newView(null, copyAnnotation);
- }
-
/**
- *
- * @param viewTitle
- * title of newly created view
- * @return new alignment panel, already displayed.
+ * Create a new view of the current alignment.
*/
- public AlignmentPanel newView(String viewTitle)
+ @Override
+ public void newView_actionPerformed(ActionEvent e)
{
- return newView(viewTitle, true);
+ newView(null, true);
}
/**
+ * Creates and shows a new view of the current alignment.
*
* @param viewTitle
- * title of newly created view
+ * title of newly created view; if null, one will be generated
* @param copyAnnotation
* if true then duplicate all annnotation, groups and settings
* @return new alignment panel, already displayed.
*/
public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
{
+ /*
+ * Create a new AlignmentPanel (with its own, new Viewport)
+ */
AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
true);
if (!copyAnnotation)
{
- // just remove all the current annotation except for the automatic stuff
+ /*
+ * remove all groups and annotation except for the automatic stuff
+ */
newap.av.getAlignment().deleteAllGroups();
- for (AlignmentAnnotation alan : newap.av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (!alan.autoCalculated)
- {
- newap.av.getAlignment().deleteAnnotation(alan);
- }
- ;
- }
+ newap.av.getAlignment().deleteAllAnnotations(false);
}
- newap.av.gatherViewsHere = false;
+ newap.av.setGatherViewsHere(false);
if (viewport.viewName == null)
{
- viewport.viewName = "Original";
+ viewport.viewName = MessageManager
+ .getString("label.view_name_original");
}
- newap.av.historyList = viewport.historyList;
- newap.av.redoList = viewport.redoList;
+ /*
+ * Views share the same edits, undo and redo stacks, mappings.
+ */
+ newap.av.setHistoryList(viewport.getHistoryList());
+ newap.av.setRedoList(viewport.getRedoList());
+ newap.av.getAlignment().setCodonFrames(
+ viewport.getAlignment().getCodonFrames());
+
+ newap.av.viewName = getNewViewName(viewTitle);
+ addAlignmentPanel(newap, true);
+ newap.alignmentChanged();
+
+ if (alignPanels.size() == 2)
+ {
+ viewport.setGatherViewsHere(true);
+ }
+ tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newap;
+ }
+
+ /**
+ * Make a new name for the view, ensuring it is unique within the current
+ * sequenceSetId. (This used to be essential for Jalview Project archives, but
+ * these now use viewId. Unique view names are still desirable for usability.)
+ *
+ * @param viewTitle
+ * @return
+ */
+ protected String getNewViewName(String viewTitle)
+ {
int index = Desktop.getViewCount(viewport.getSequenceSetId());
- // make sure the new view has a unique name - this is essential for Jalview
- // 2 archives
boolean addFirstIndex = false;
if (viewTitle == null || viewTitle.trim().length() == 0)
{
index = 1;// we count from 1 if given a specific name
}
String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+
+ List<Component> comps = PaintRefresher.components.get(viewport
.getSequenceSetId());
- Vector existingNames = new Vector();
- for (int i = 0; i < comps.size(); i++)
- {
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
- if (!existingNames.contains(ap.av.viewName))
- {
- existingNames.addElement(ap.av.viewName);
- }
- }
- }
+
+ List<String> existingNames = getExistingViewNames(comps);
while (existingNames.contains(newViewName))
{
newViewName = viewTitle + " " + (++index);
}
+ return newViewName;
+ }
- newap.av.viewName = newViewName;
-
- addAlignmentPanel(newap, true);
- newap.alignmentChanged();
-
- if (alignPanels.size() == 2)
+ /**
+ * Returns a list of distinct view names found in the given list of
+ * components. View names are held on the viewport of an AlignmentPanel.
+ *
+ * @param comps
+ * @return
+ */
+ protected List<String> getExistingViewNames(List<Component> comps)
+ {
+ List<String> existingNames = new ArrayList<String>();
+ for (Component comp : comps)
{
- viewport.gatherViewsHere = true;
+ if (comp instanceof AlignmentPanel)
+ {
+ AlignmentPanel ap = (AlignmentPanel) comp;
+ if (!existingNames.contains(ap.av.viewName))
+ {
+ existingNames.add(ap.av.viewName);
+ }
+ }
}
- tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
- return newap;
+ return existingNames;
}
+ /**
+ * Explode tabbed views into separate windows.
+ */
@Override
public void expandViews_actionPerformed(ActionEvent e)
{
Desktop.instance.explodeViews(this);
}
+ /**
+ * Gather views in separate windows back into a tabbed presentation.
+ */
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
@Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
- viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+ viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
alignPanel.paintAlignment(true);
}
@Override
protected void followHighlight_actionPerformed()
{
+ /*
+ * Set the 'follow' flag on the Viewport (and scroll to position if now
+ * true).
+ */
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
{
alignPanel.scrollToPosition(
scaleLeft.setVisible(wrapMenuItem.isSelected());
scaleRight.setVisible(wrapMenuItem.isSelected());
viewport.setWrapAlignment(wrapMenuItem.isSelected());
- alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.updateLayout();
}
@Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
+// alignPanel.paintAlignment(true);
}
/**
{
final boolean setVisible = annotationPanelMenuItem.isSelected();
viewport.setShowAnnotation(setVisible);
- alignPanel.setAnnotationVisible(setVisible);
this.showAllSeqAnnotations.setEnabled(setVisible);
this.hideAllSeqAnnotations.setEnabled(setVisible);
this.showAllAlAnnotations.setEnabled(setVisible);
this.hideAllAlAnnotations.setEnabled(setVisible);
+ alignPanel.updateLayout();
}
@Override
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
editPane.setText(MessageManager.formatMessage("label.html_content",
- new String[]
+ new Object[]
{ contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
- Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
- "label.alignment_properties", new String[]
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new Object[]
{ getTitle() }), 500, 400);
}
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, MessageManager.formatMessage(
- "label.overview_params", new String[]
+ "label.overview_params", new Object[]
{ this.getTitle() }), frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+ cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
}
else
{
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
}
if (viewport.getConservationSelected())
|| cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(viewport.getHiddenRepSequences()),
}
else
{
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
}
if (viewport.getConservationSelected())
{
Component[] menuItems = colourMenu.getMenuComponents();
- int i, iSize = menuItems.length;
- for (i = 0; i < iSize; i++)
+ int iSize = menuItems.length;
+ for (int i = 0; i < iSize; i++)
{
if (menuItems[i].getName() != null
&& menuItems[i].getName().equals("USER_DEFINED"))
@Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ newTreePanel("AV", "PID", "Average distance tree using PID");
}
/**
@Override
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
}
/**
@Override
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
}
/**
@Override
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
}
/**
* @param title
* DOCUMENT ME!
*/
- void NewTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String pwType, String title)
{
TreePanel tp;
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
- final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
+ final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
{
String treecalcnm = MessageManager.getString("label.tree_calc_"
+ type.toLowerCase());
- for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
+ for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
{
JMenuItem tm = new JMenuItem();
ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
@Override
public void actionPerformed(ActionEvent e)
{
- NewTreePanel(type, (String) pwtype, title);
+ newTreePanel(type, pwtype, title);
}
});
calculateTree.add(tm);
}
sortByTreeMenu.removeAll();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+ List<Component> comps = PaintRefresher.components.get(viewport
.getSequenceSetId());
- Vector treePanels = new Vector();
- int i, iSize = comps.size();
- for (i = 0; i < iSize; i++)
+ List<TreePanel> treePanels = new ArrayList<TreePanel>();
+ for (Component comp : comps)
{
- if (comps.elementAt(i) instanceof TreePanel)
+ if (comp instanceof TreePanel)
{
- treePanels.add(comps.elementAt(i));
+ treePanels.add((TreePanel) comp);
}
}
- iSize = treePanels.size();
-
- if (iSize < 1)
+ if (treePanels.size() < 1)
{
sortByTreeMenu.setVisible(false);
return;
sortByTreeMenu.setVisible(true);
- for (i = 0; i < treePanels.size(); i++)
+ for (final TreePanel tp : treePanels)
{
- final TreePanel tp = (TreePanel) treePanels.elementAt(i);
final JMenuItem item = new JMenuItem(tp.getTitle());
- final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- tp.sortByTree_actionPerformed(null);
+ tp.sortByTree_actionPerformed();
addHistoryItem(tp.sortAlignmentIn(alignPanel));
}
* DOCUMENT ME!
*/
@Override
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
} catch (Exception e)
{
}
- ;
}
final AlignFrame me = this;
buildingMenu = true;
.debug("Exception during web service menu building process.",
e);
}
- ;
}
});
} catch (Exception e)
{
}
- ;
-
buildingMenu = false;
}
}).start();
public void actionPerformed(ActionEvent e)
{
// TODO: new thread for this call with vis-delay
- af.showProductsFor(af.viewport.getSequenceSelection(), ds,
+ af.showProductsFor(af.viewport.getSequenceSelection(),
isRegSel, dna, source);
}
return showp;
}
- protected void showProductsFor(SequenceI[] sel, Alignment ds,
- boolean isRegSel, boolean dna, String source)
+ protected void showProductsFor(final SequenceI[] sel,
+ final boolean isRegSel, final boolean dna, final String source)
{
- final boolean fisRegSel = isRegSel;
- final boolean fdna = dna;
- final String fsrc = source;
- final AlignFrame ths = this;
- final SequenceI[] fsel = sel;
Runnable foo = new Runnable()
{
public void run()
{
final long sttime = System.currentTimeMillis();
- ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
+ AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+ "status.searching_for_sequences_from", new Object[]
+ { source }), sttime);
try
{
- Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
- // our local
- // dataset
- // reference
+ // update our local dataset reference
+ Alignment ds = AlignFrame.this.getViewport().getAlignment()
+ .getDataset();
Alignment prods = CrossRef
- .findXrefSequences(fsel, fdna, fsrc, ds);
+ .findXrefSequences(sel, dna, source, ds);
if (prods != null)
{
SequenceI[] sprods = new SequenceI[prods.getHeight()];
sprods[s].updatePDBIds();
}
Alignment al = new Alignment(sprods);
- AlignedCodonFrame[] cf = prods.getCodonFrames();
+ Set<AlignedCodonFrame> cf = prods.getCodonFrames();
al.setDataset(ds);
- for (int s = 0; cf != null && s < cf.length; s++)
+ for (AlignedCodonFrame acf : cf)
{
- al.addCodonFrame(cf[s]);
- cf[s] = null;
+ al.addCodonFrame(acf);
}
AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
- String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
- + " for " + ((fisRegSel) ? "selected region of " : "")
+ String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
+ + " for " + ((isRegSel) ? "selected region of " : "")
+ getTitle();
- Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ naf.setTitle(newtitle);
+
+ // remove this flag once confirmed we want a split view
+ boolean asSplitFrame = true;
+ if (asSplitFrame)
+ {
+ final Alignment copyAlignment = new Alignment(new Alignment(
+ AlignFrame.this.viewport.getSequenceSelection()));
+ AlignFrame copyThis = new AlignFrame(copyAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyThis.setTitle(AlignFrame.this.getTitle());
+ // SplitFrame with dna above, protein below
+ SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
+ dna ? naf : copyThis);
+ naf.setVisible(true);
+ copyThis.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+ }
+ else
+ {
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
}
else
{
System.err.println("No Sequences generated for xRef type "
- + fsrc);
+ + source);
}
} catch (Exception e)
{
jalview.bin.Cache.log.error("Error when finding crossreferences",
e);
}
- ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
+ AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+ "status.finished_searching_for_sequences_from",
+ new Object[]
+ { source }),
sttime);
}
}
}
- @Override
- public void showProducts_actionPerformed(ActionEvent e)
- {
- // /////////////////////////////
- // Collect Data to be translated/transferred
-
- SequenceI[] selection = viewport.getSequenceSelection();
- AlignmentI al = null;
- try
- {
- al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
- .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
- viewport.getAlignment().getDataset());
- } catch (Exception ex)
- {
- al = null;
- jalview.bin.Cache.log.debug("Exception during translation.", ex);
- }
- if (al == null)
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
- MessageManager.getString("label.translation_failed"),
- JOptionPane.WARNING_MESSAGE);
- }
- else
- {
- AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.translation_of_params", new String[]
- { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
- }
- }
-
+ /**
+ * Construct and display a new frame containing the translation of this
+ * frame's DNA sequences to their aligned protein (amino acid) equivalents.
+ */
@Override
public void showTranslation_actionPerformed(ActionEvent e)
{
- // /////////////////////////////
- // Collect Data to be translated/transferred
-
- SequenceI[] selection = viewport.getSequenceSelection();
- String[] seqstring = viewport.getViewAsString(true);
AlignmentI al = null;
try
{
- al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
- viewport.getViewAsVisibleContigs(true), viewport
- .getGapCharacter(), viewport.getAlignment()
- .getAlignmentAnnotation(), viewport.getAlignment()
- .getWidth(), viewport.getAlignment().getDataset());
+ Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+ al = dna.translateCdna();
} catch (Exception ex)
{
- al = null;
jalview.bin.Cache.log.error(
"Exception during translation. Please report this !", ex);
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.error_when_translating_sequences_submit_bug_report"),
- MessageManager
- .getString("label.implementation_error")
- + MessageManager
- .getString("translation_failed"),
- JOptionPane.ERROR_MESSAGE);
+ final String msg = MessageManager
+ .getString("label.error_when_translating_sequences_submit_bug_report");
+ final String title = MessageManager
+ .getString("label.implementation_error")
+ + MessageManager.getString("translation_failed");
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.ERROR_MESSAGE);
return;
}
- if (al == null)
+ if (al == null || al.getHeight() == 0)
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
- MessageManager.getString("label.translation_failed"),
- JOptionPane.WARNING_MESSAGE);
+ final String msg = MessageManager
+ .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
+ final String title = MessageManager
+ .getString("label.translation_failed");
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.WARNING_MESSAGE);
}
else
{
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.translation_of_params", new String[]
- { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ af.setFileFormat(this.currentFileFormat);
+ final String newTitle = MessageManager.formatMessage(
+ "label.translation_of_params", new Object[]
+ { this.getTitle() });
+ af.setTitle(newTitle);
+ final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
+ viewport.openSplitFrame(af, new Alignment(seqs), al.getCodonFrames());
+ // Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
/**
+ * Set the file format
+ *
+ * @param fileFormat
+ */
+ public void setFileFormat(String fileFormat)
+ {
+ this.currentFileFormat = fileFormat;
+ }
+
+ /**
* Try to load a features file onto the alignment.
*
* @param file
MessageManager
.formatMessage(
"label.automatically_associate_pdb_files_with_sequences_same_name",
- new String[]
+ new Object[]
{ Integer.valueOf(
filesmatched
.size())
"<html>"+MessageManager
.formatMessage(
"label.ignore_unmatched_dropped_files_info",
- new String[]
+ new Object[]
{ Integer.valueOf(
filesnotmatched
.size())
{
jalview.io.JPredFile predictions = new jalview.io.JPredFile(
file, protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
+ new JnetAnnotationMaker();
+ JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
viewport.getAlignment().setSeqrep(repseq);
}
}
+ /**
+ * Method invoked by the ChangeListener on the tabbed pane, in other words
+ * when a different tabbed pane is selected by the user or programmatically.
+ */
@Override
public void tabSelectionChanged(int index)
{
if (index > -1)
{
- alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+ alignPanel = alignPanels.get(index);
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
}
+
+ /*
+ * If there is a frame linked to this one in a SplitPane, switch it to the
+ * same view tab index. No infinite recursion of calls should happen, since
+ * tabSelectionChanged() should not get invoked on setting the selected
+ * index to an unchanged value. Guard against setting an invalid index
+ * before the new view peer tab has been created.
+ */
+ final AlignViewportI peer = viewport.getCodingComplement();
+ if (peer != null)
+ {
+ AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
+ if (linkedAlignFrame.tabbedPane.getTabCount() > index)
+ {
+ linkedAlignFrame.tabbedPane.setSelectedIndex(index);
+ }
+ }
}
+ /**
+ * On right mouse click on view tab, prompt for and set new view name.
+ */
@Override
public void tabbedPane_mousePressed(MouseEvent e)
{
if (SwingUtilities.isRightMouseButton(e))
{
- String reply = JOptionPane.showInternalInputDialog(this,
- MessageManager.getString("label.enter_view_name"),
- MessageManager.getString("label.enter_view_name"),
+ String msg = MessageManager.getString("label.enter_view_name");
+ String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
JOptionPane.QUESTION_MESSAGE);
if (reply != null)
{
viewport.viewName = reply;
+ // TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
}
@Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
- viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
+ viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
}
/*
@Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
- viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
+ viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
}
/**
*
* @param av
*/
- public boolean closeView(AlignViewport av)
+ public boolean closeView(AlignViewportI av)
{
if (viewport == av)
{
}
});
- fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
dfetch.add(fetchr);
comp++;
}
// fetch all entry
DbSourceProxy src = otherdb.get(0);
fetchr = new JMenuItem(MessageManager.formatMessage(
- "label.fetch_all_param", new String[]
+ "label.fetch_all_param", new Object[]
{ src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
}
});
- fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
dfetch.add(fetchr);
comp++;
// and then build the rest of the individual menus
- ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
+ ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
icomp = 0;
String imname = null;
int i = 0;
0, 10) + "..." : dbname;
if (imname == null)
{
- imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
+ imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
}
fetchr = new JMenuItem(msname);
final DbSourceProxy[] dassrc =
});
fetchr.setToolTipText("<html>"
- + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
+ + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
ifetch.add(fetchr);
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
}
if (tabbedPane != null
- & alignPanels.indexOf(alignmentPanel) != tabbedPane
+ && tabbedPane.getTabCount() > 0
+ && alignPanels.indexOf(alignmentPanel) != tabbedPane
.getSelectedIndex())
{
tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
/**
*
- * @return alignment panels in this alignemnt frame
+ * @return alignment panels in this alignment frame
+ */
+ public List<? extends AlignmentViewPanel> getAlignPanels()
+ {
+ return alignPanels == null ? Arrays.asList(alignPanel)
+ : alignPanels;
+ }
+
+ /**
+ * Open a new alignment window, with the cDNA associated with this (protein)
+ * alignment, aligned as is the protein.
+ */
+ protected void viewAsCdna_actionPerformed()
+ {
+ // TODO no longer a menu action - refactor as required
+ final AlignmentI alignment = getViewport().getAlignment();
+ Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+ if (mappings == null)
+ {
+ return;
+ }
+ List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
+ for (SequenceI aaSeq : alignment.getSequences()) {
+ for (AlignedCodonFrame acf : mappings) {
+ SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
+ if (dnaSeq != null)
+ {
+ /*
+ * There is a cDNA mapping for this protein sequence - add to new
+ * alignment. It will share the same dataset sequence as other mapped
+ * cDNA (no new mappings need to be created).
+ */
+ final Sequence newSeq = new Sequence(dnaSeq);
+ newSeq.setDatasetSequence(dnaSeq);
+ cdnaSeqs.add(newSeq);
+ }
+ }
+ }
+ if (cdnaSeqs.size() == 0)
+ {
+ // show a warning dialog no mapped cDNA
+ return;
+ }
+ AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
+ .size()]));
+ AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ cdna.alignAs(alignment);
+ String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
+ + this.title;
+ Desktop.addInternalFrame(alignFrame, newtitle,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /**
+ * Set visibility of dna/protein complement view (available when shown in a
+ * split frame).
+ *
+ * @param show
*/
- public List<AlignmentViewPanel> getAlignPanels()
+ @Override
+ protected void showComplement_actionPerformed(boolean show)
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ SplitContainerI sf = getSplitViewContainer();
+ if (sf != null) {
+ sf.setComplementVisible(this, show);
+ }
}
}
*/
package jalview.gui;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
+import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
-import java.awt.Color;
-import java.awt.Container;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Stack;
-import java.util.Vector;
-
/**
* DOCUMENT ME!
*
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, VamsasSource, AlignViewportI
+ SelectionSource, AlignViewportI, CommandListener
{
int startRes;
int endSeq;
- boolean showJVSuffix = true;
-
- boolean showText = true;
-
- boolean showColourText = false;
-
- boolean showBoxes = true;
-
- boolean wrapAlignment = false;
-
- boolean renderGaps = true;
-
- SequenceAnnotationOrder sortAnnotationsBy = null;
-
- int charHeight;
-
- int charWidth;
-
- boolean validCharWidth;
-
- int wrappedWidth;
-
Font font;
- boolean seqNameItalics;
-
NJTree currentTree = null;
- boolean scaleAboveWrapped = false;
-
- boolean scaleLeftWrapped = true;
-
- boolean scaleRightWrapped = true;
-
- boolean showHiddenMarkers = true;
-
boolean cursorMode = false;
boolean antiAlias = false;
- Rectangle explodedPosition;
+ private Rectangle explodedGeometry;
String viewName;
- boolean gatherViewsHere = false;
-
- Stack<CommandI> historyList = new Stack<CommandI>();
-
- Stack<CommandI> redoList = new Stack<CommandI>();
-
- int thresholdTextColour = 0;
-
- Color textColour = Color.black;
-
- Color textColour2 = Color.white;
+ /*
+ * Flag set true on the view that should 'gather' multiple views of the same
+ * sequence set id when a project is reloaded. Set false on all views when
+ * they are 'exploded' into separate windows. Set true on the current view
+ * when 'Gather' is performed, and also on the first tab when the first new
+ * view is created.
+ */
+ private boolean gatherViewsHere = false;
private AnnotationColumnChooser annotationColumnSelectionState;
/**
init();
}
- void init()
+ private void applyViewProperties()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
-
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
- showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+ viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
- centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
+ setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
setPadGaps(Cache.getDefault("PAD_GAPS", true));
- shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
- showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+ setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+ viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+ viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+ viewStyle.setShowUnconserved(Cache
+ .getDefault("SHOW_UNCONSERVED", false));
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+ Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
+
+ }
+
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+ applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
String fontSize = Cache.getDefault("FONT_SIZE", "10");
- seqNameItalics = Cache.getDefault("ID_ITALICS", true);
-
int style = 0;
if (fontStyle.equals("bold"))
style = 2;
}
- setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
alignment
.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
}
initAutoAnnotation();
- if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+ String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT;
+ String propertyValue = Cache.getProperty(colourProperty);
+ if (propertyValue == null)
+ {
+ // fall back on this property for backwards compatibility
+ propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ }
+ if (propertyValue != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment,
- jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+ propertyValue);
if (globalColourScheme instanceof UserColourScheme)
{
globalColourScheme = UserDefinedColours.loadDefaultColours();
((UserColourScheme) globalColourScheme).setThreshold(0,
- getIgnoreGapsConsensus());
+ isIgnoreGapsConsensus());
}
if (globalColourScheme != null)
globalColourScheme.setConsensus(hconsensus);
}
}
-
- wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
- sortByTree = Cache.getDefault("SORT_BY_TREE", false);
- followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
- sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
- Preferences.SORT_ANNOTATIONS,
- SequenceAnnotationOrder.NONE.name()));
- showAutocalculatedAbove = Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false);
}
/**
- * centre columnar annotation labels in displayed alignment annotation TODO:
- * add to jalviewXML and annotation display settings
- */
- boolean centreColumnLabels = false;
-
- private boolean showdbrefs;
-
- private boolean shownpfeats;
-
- // --------END Structure Conservation
-
- /**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
*
return endSeq;
}
+ boolean validCharWidth;
+
/**
- * DOCUMENT ME!
+ * update view settings with the given font. You may need to call
+ * alignPanel.fontChanged to update the layout geometry
*
- * @param f
- * DOCUMENT ME!
+ * @param setGrid
+ * when true, charWidth/height is set according to font mentrics
*/
- public void setFont(Font f)
+ public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
java.awt.FontMetrics fm = c.getFontMetrics(font);
- setCharHeight(fm.getHeight());
- setCharWidth(fm.charWidth('M'));
- validCharWidth = true;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Font getFont()
- {
- return font;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param w
- * DOCUMENT ME!
- */
- public void setCharWidth(int w)
- {
- this.charWidth = w;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharWidth()
- {
- return charWidth;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param h
- * DOCUMENT ME!
- */
- public void setCharHeight(int h)
- {
- this.charHeight = h;
- }
+ int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
+ .getCharHeight();
+ if (setGrid)
+ {
+ setCharHeight(fm.getHeight());
+ setCharWidth(ww);
+ }
+ viewStyle.setFontName(font.getName());
+ viewStyle.setFontStyle(font.getStyle());
+ viewStyle.setFontSize(font.getSize());
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharHeight()
- {
- return charHeight;
+ validCharWidth = true;
}
- /**
- * DOCUMENT ME!
- *
- * @param w
- * DOCUMENT ME!
- */
- public void setWrappedWidth(int w)
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
{
- this.wrappedWidth = w;
- }
+ super.setViewStyle(settingsForView);
+ setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
+ viewStyle.getFontSize()), false);
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWrappedWidth()
- {
- return wrappedWidth;
}
-
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public AlignmentI getAlignment()
+ public Font getFont()
{
- return alignment;
+ return font;
}
/**
/**
* DOCUMENT ME!
*
- * @param state
- * DOCUMENT ME!
- */
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourText()
- {
- return showColourText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowText()
- {
- return showText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
-
- /**
- * DOCUMENT ME!
- *
* @return DOCUMENT ME!
*/
public char getGapCharacter()
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- public void setDataset(boolean b)
- {
- isDataset = b;
- }
-
- public boolean isDataset()
- {
- return isDataset;
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
- /**
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
return false;
}
- public boolean getCentreColumnLabels()
- {
- return centreColumnLabels;
- }
-
- public void setCentreColumnLabels(boolean centrecolumnlabels)
- {
- centreColumnLabels = centrecolumnlabels;
- }
-
- /**
- * enable or disable the display of Database Cross References in the sequence
- * ID tooltip
- */
- public void setShowDbRefs(boolean show)
- {
- showdbrefs = show;
- }
-
- /**
- *
- * @return true if Database References are to be displayed on tooltips.
- */
- public boolean isShowDbRefs()
- {
- return showdbrefs;
- }
-
- /**
- *
- * @return true if Non-positional features are to be displayed on tooltips.
- */
- public boolean isShowNpFeats()
- {
- return shownpfeats;
- }
-
- /**
- * enable or disable the display of Non-Positional sequence features in the
- * sequence ID tooltip
- *
- * @param show
- */
- public void setShowNpFeats(boolean show)
- {
- shownpfeats = show;
- }
-
-
/**
* when set, view will scroll to show the highlighted position
*/
return followSelection;
}
+ /**
+ * Send the current selection to be broadcast to any selection listeners.
+ */
public void sendSelection()
{
jalview.structure.StructureSelectionManager
{
AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
.getSequenceSetId());
- AlignmentPanel ap = null;
for (int p = 0; aps != null && p < aps.length; p++)
{
if (aps[p].av == this)
}
}
+ /**
+ * Returns the (Desktop) instance of the StructureSelectionManager
+ */
+ @Override
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
- private boolean showAutocalculatedAbove;
-
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);
}
}
- protected SequenceAnnotationOrder getSortAnnotationsBy()
- {
- return sortAnnotationsBy;
+ /**
+ * Method called when another alignment's edit (or possibly other) command is
+ * broadcast to here.
+ *
+ * To allow for sequence mappings (e.g. protein to cDNA), we have to first
+ * 'unwind' the command on the source sequences (in simulation, not in fact),
+ * and then for each edit in turn:
+ * <ul>
+ * <li>compute the equivalent edit on the mapped sequences</li>
+ * <li>apply the mapped edit</li>
+ * <li>'apply' the source edit to the working copy of the source sequences</li>
+ * </ul>
+ *
+ * @param command
+ * @param undo
+ * @param ssm
+ */
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
+ {
+ /*
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
+ */
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
+ {
+ // ok to continue;
+ }
+ else
+ {
+ return;
+ }
+
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
+ {
+ AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
+ mappedCommand.doCommand(views);
+ getAlignPanel().alignmentChanged();
+ }
}
- protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ /**
+ * Add the sequences from the given alignment to this viewport. Optionally,
+ * may give the user the option to open a new frame, or split panel, with cDNA
+ * and protein linked.
+ *
+ * @param al
+ * @param title
+ */
+ public void addAlignment(AlignmentI al, String title)
{
- this.sortAnnotationsBy = sortAnnotationsBy;
+ // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
+
+ // JBPComment: title is a largely redundant parameter at the moment
+ // JBPComment: this really should be an 'insert/pre/append' controller
+ // JBPComment: but the DNA/Protein check makes it a bit more complex
+
+ // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+ // this comment:
+ // TODO: create undo object for this JAL-1101
+
+ /*
+ * If one alignment is protein and one nucleotide, with at least one
+ * sequence name in common, offer to open a linked alignment.
+ */
+ if (AlignmentUtils.isMappable(al, getAlignment()))
+ {
+ if (openLinkedAlignment(al, title))
+ {
+ return;
+ }
+ }
+ // TODO: JAL-407 regardless of above - identical sequences (based on ID and
+ // provenance) should share the same dataset sequence
+
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ getAlignment().addSequence(al.getSequenceAt(i));
+ }
+ // TODO this call was done by SequenceFetcher but not FileLoader or
+ // CutAndPasteTransfer. Is it needed?
+ // JBPComment: this repositions the view to show the new sequences
+ // JBPComment: so it is needed for UX
+ setEndSeq(getAlignment().getHeight());
+ firePropertyChange("alignment", null, getAlignment().getSequences());
}
- protected boolean isShowAutocalculatedAbove()
- {
- return showAutocalculatedAbove;
+ /**
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment. Returns true if the new alignment was opened, false if not,
+ * because the user declined the offer.
+ *
+ * @param title
+ */
+ protected boolean openLinkedAlignment(AlignmentI al, String title)
+ {
+ String[] options = new String[]
+ { MessageManager.getString("action.no"),
+ MessageManager.getString("label.split_window"),
+ MessageManager.getString("label.new_window"), };
+ final String question = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.open_split_window?"));
+ int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ MessageManager.getString("label.open_split_window"),
+ JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+
+ if (response != 1 && response != 2)
+ {
+ return false;
+ }
+ final boolean openSplitPane = (response == 1);
+ final boolean openInNewWindow = (response == 2);
+
+ /*
+ * Create the AlignFrame first (which creates the new alignment's datasets),
+ * before attempting sequence mapping.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(title);
+
+ /*
+ * Identify protein and dna alignments. Make a copy of this one if opening
+ * in a new split pane.
+ */
+ AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ : getAlignment();
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new Object[]
+ { title }));
+
+ // TODO if we want this (e.g. to enable reload of the alignment from file),
+ // we will need to add parameters to the stack.
+ // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
+
+ if (openInNewWindow)
+ {
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /*
+ * Map sequences. At least one should get mapped as we have already passed
+ * the test for 'mappability'. Any mappings made will be added to the
+ * protein alignment.
+ */
+ AlignmentUtils.mapProteinToCdna(protein, cdna);
+
+ try
+ {
+ newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN",
+ false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+
+ if (openSplitPane)
+ {
+ protein = openSplitFrame(newAlignFrame, thisAlignment,
+ protein.getCodonFrames());
+ }
+
+ /*
+ * Register the mappings (held on the protein alignment) with the
+ * StructureSelectionManager (for mouseover linking).
+ */
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addMappings(protein.getCodonFrames());
+
+ return true;
}
- protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
- {
- this.showAutocalculatedAbove = showAutocalculatedAbove;
+ /**
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
+ *
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param complement
+ * cdna/protein complement alignment to show in the other split half
+ * @param mappings
+ * @return the protein alignment in the split frame
+ */
+ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+ AlignmentI complement, Set<AlignedCodonFrame> mappings)
+ {
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ AlignFrame copyMe = new AlignFrame(complement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
+ : copyMe;
+ AlignmentI protein = proteinFrame.viewport.getAlignment();
+ protein.setCodonFrames(mappings);
+
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ return protein;
}
public AnnotationColumnChooser getAnnotationColumnSelectionState()
{
this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
}
+
+ @Override
+ public void setIdWidth(int i)
+ {
+ super.setIdWidth(i);
+ AlignmentPanel ap = getAlignPanel();
+ if (ap != null)
+ {
+ // modify GUI elements to reflect geometry change
+ Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
+ .getPreferredSize();
+ idw.width = i;
+ getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+ }
+ }
+
+ public Rectangle getExplodedGeometry()
+ {
+ return explodedGeometry;
+ }
+
+ public void setExplodedGeometry(Rectangle explodedPosition)
+ {
+ this.explodedGeometry = explodedPosition;
+ }
+
+ public boolean isGatherViewsHere()
+ {
+ return gatherViewsHere;
+ }
+
+ public void setGatherViewsHere(boolean gatherViewsHere)
+ {
+ this.gatherViewsHere = gatherViewsHere;
+ }
}
package jalview.gui;
import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
* Creates a new AlignmentPanel object.
*
* @param af
- * DOCUMENT ME!
* @param av
- * DOCUMENT ME!
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
setScrollValues(0, 0);
- setAnnotationVisible(av.isShowAnnotation());
-
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
});
fontChanged();
adjustAnnotationHeight();
-
+ updateLayout();
}
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
public void alignmentChanged()
{
av.alignmentChanged(this);
// to prevent drawing old image
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
+ scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
+ .getCharHeight()
+ fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getAnnotationPanel().adjustPanelHeight();
Dimension d = calculateIdWidth();
+
d.setSize(d.width + 4, d.height);
getIdPanel().getIdCanvas().setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(d);
{
overviewPanel.setBoxPosition();
}
+ if (this.alignFrame.getSplitViewContainer() != null)
+ {
+ ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
+ }
repaint();
}
public Dimension calculateIdWidth()
{
// calculate sensible default width when no preference is available
-
- int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
- int maxwidth = Math.max(20,
- Math.min(afwidth - 200, 2 * afwidth / 3));
- return calculateIdWidth(maxwidth);
+ Dimension r = null;
+ if (av.getIdWidth() < 0)
+ {
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
+ r = calculateIdWidth(maxwidth);
+ av.setIdWidth(r.width);
+ }
+ else
+ {
+ r = new Dimension();
+ r.width = av.getIdWidth();
+ r.height = 0;
+ }
+ return r;
}
/**
}
}
}
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
if ((startv = av.getStartRes()) >= start)
{
*/
public void setAnnotationVisible(boolean b)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
annotationSpaceFillerHolder.setVisible(b);
annotationScroller.setVisible(b);
}
/**
- * DOCUMENT ME!
+ * update alignment layout for viewport settings
*
* @param wrap
* DOCUMENT ME!
*/
- public void setWrapAlignment(boolean wrap)
+ public void updateLayout()
{
+ fontChanged();
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
av.startSeq = 0;
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.charWidth)) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
- hextent = getSeqPanel().seqCanvas.getWidth() / av.charWidth;
- vextent = getSeqPanel().seqCanvas.getHeight() / av.charHeight;
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
if (hextent > width)
{
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
-
int oldX = av.getStartRes();
int oldY = av.getStartSeq();
{
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
pg.setColor(Color.white);
pg.fillRect(0, 0, pwidth, pheight);
}
pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
av.getCharHeight());
pg.setColor(currentTextColor);
pg.drawString(
seq.getDisplayId(av.getShowJVSuffix()),
xPos,
- (((i - startSeq) * av.charHeight) + av.getCharHeight())
+ (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
// draw annotation - need to offset for current scroll position
int offset = -getAlabels().getScrollOffset();
pg.translate(0, offset);
- pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
+ pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight()
+ + 3);
getAlabels().drawComponent(pg, idWidth);
pg.translate(idWidth + 3, 0);
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
int pi) throws PrinterException
{
-
int annotationHeight = 0;
AnnotationLabels labels = null;
if (av.isShowAnnotation())
labels = new AnnotationLabels(av);
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ annotationHeight;
int idWidth = getVisibleIdWidth(false);
xPos = idWidth - fm.stringWidth(string) - 4;
}
pg.drawString(string, xPos,
- ((i * av.charHeight) + ypos + av.charHeight)
- - (av.charHeight / 5));
+ ((i * av.getCharHeight()) + ypos + av.getCharHeight())
+ - (av.getCharHeight() / 5));
}
if (labels != null)
{
pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.charHeight));
+ + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
pg.translate(+3, -ypos
- - (av.getAlignment().getHeight() * av.charHeight));
+ - (av.getAlignment().getHeight() * av
+ .getCharHeight()));
}
ypos += cHeight;
if (alignFrame != null && !headless)
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file",
- new String[]
+ "status.saving_file", new Object[]
{ type.getLabel() }), progress);
}
try
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
}
- int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
+ int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ getScalePanel().getHeight();
- int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
+ int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
if (av.getWrapAlignment())
{
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
// Gen image map
// ////////////////////////////////
for (s = 0; s < sSize; s++)
{
- sy = s * av.charHeight + scaleHeight;
+ sy = s * av.getCharHeight() + scaleHeight;
SequenceI seq = av.getAlignment().getSequenceAt(s);
- SequenceFeature[] features = seq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature[] features = seq.getSequenceFeatures();
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
text = new StringBuffer();
- Object obj = null;
+ String triplet = null;
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+ triplet = ResidueProperties.nucleotideName.get(seq
+ .getCharAt(res)
+ "");
}
else
{
- obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ "");
}
- if (obj == null)
+ if (triplet == null)
{
continue;
}
- String triplet = obj.toString();
int alIndex = seq.findPosition(res);
gSize = groups.length;
for (g = 0; g < gSize; g++)
if (text.length() < 1)
{
text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
+ + (idWidth + res * av.getCharWidth()) + "," + sy
+ + "," + (idWidth + (res + 1) * av.getCharWidth())
+ + ","
+ + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
if (text.length() < 1)
{
text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
+ + (idWidth + res * av.getCharWidth()) + "," + sy
+ + "," + (idWidth + (res + 1) * av.getCharWidth())
+ + ","
+ + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
int chunkWidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(seqPanelWidth);
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
int annotationHeight = 0;
annotationHeight = getAnnotationPanel().adjustPanelHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ annotationHeight;
int maxwidth = av.getAlignment().getWidth();
.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
+ ssm.removeCommandListener(av);
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
av.setAlignment(null);
av = null;
}
{
text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
.getDataset().getSequencesArray(), ap.getFeatureRenderer()
- .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
+ .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats());// ap.av.featuresDisplayed//);
}
else
{
text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
.getDataset().getSequencesArray(), ap.getFeatureRenderer()
- .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
+ .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
}
}
else
*/
package jalview.gui;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.util.MessageManager;
-
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.image.BufferedImage;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+
String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
String ADDNEW = MessageManager.getString("label.add_new_row");
Dimension d = ap.annotationScroller.getPreferredSize();
int dif = evt.getY() - oldY;
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
if ((d.height - dif) > 20)
{
|| (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
{
// clean the description ready for embedding in html
- desc = new StringBuffer(Pattern.compile("<").matcher(desc)
+ desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
.replaceAll("<"));
desc.insert(0, "<html>");
}
item.addActionListener(this);
pop.add(item);
// JAL-1264 hide all sequence-specific annotations of this type
- final String label = aa[selectedRow].label;
if (selectedRow < aa.length)
{
if (aa[selectedRow].sequenceRef != null)
{
+ final String label = aa[selectedRow].label;
JMenuItem hideType = new JMenuItem();
String text = MessageManager.getString("label.hide_all") + " " + label;
hideType.setText(text);
@Override
public void actionPerformed(ActionEvent e)
{
- for (AlignmentAnnotation ann : ap.av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (ann.sequenceRef != null && ann.label != null
- && ann.label.equals(label))
- {
- ann.visible = false;
- }
- }
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ ap.av.getAlignment(), Collections.singleton(label),
+ null, false, false);
+ // for (AlignmentAnnotation ann : ap.av.getAlignment()
+ // .getAlignmentAnnotation())
+ // {
+ // if (ann.sequenceRef != null && ann.label != null
+ // && ann.label.equals(label))
+ // {
+ // ann.visible = false;
+ // }
+ // }
refresh();
}
});
// property methods
if (selectedRow < aa.length)
{
+ final String label = aa[selectedRow].label;
if (!aa[selectedRow].autoCalculated)
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
+ MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
- .getIgnoreGapsConsensus());
+ .isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
if (aaa.groupRef != null)
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
+ MessageManager.getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
});
pop.add(chist);
final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_logo"),
+ MessageManager.getString("label.show_group_logo"),
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addActionListener(new ActionListener()
{
});
pop.add(cprofl);
final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
+ MessageManager.getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(cprof);
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
cprofnorm.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
dragEvent.getY() - getScrollOffset());
}
- if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
int y1)
{
- int pady = av.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
if (av.validCharWidth)
{
char s = seq.getCharAt(res);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ (y1 + av.getCharHeight()) - pady);
}
}
return;
}
}
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+ imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
if (imgWidth < 1)
{
return;
return;
}
long stime = System.currentTimeMillis();
- gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
+ gg.copyArea(0, 0, imgWidth, getHeight(),
+ -horizontal * av.getCharWidth(), 0);
long mtime = System.currentTimeMillis();
int sr = av.startRes;
int er = av.endRes + 1;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * av.getCharWidth();
sr = er - horizontal;
}
else if (horizontal < 0)
}
g.setColor(Color.white);
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
g.setFont(av.getFont());
if (fm == null)
*/
package jalview.gui;
+import jalview.structure.AtomSpec;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
public void onWarningEmitted(String s)
{
- // TODO Auto-generated method stub
-
}
public void mouseClicked(MouseEvent e)
public void mouseEntered(MouseEvent arg0)
{
- // TODO Auto-generated method stub
-
}
public void mouseExited(MouseEvent arg0)
{
- // TODO Auto-generated method stub
-
}
public void mousePressed(MouseEvent arg0)
{
- // TODO Auto-generated method stub
-
}
public void mouseReleased(MouseEvent arg0)
{
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbId)
- {
- // TODO Auto-generated method stub
- return null;
}
@Override
public String[] getPdbFile()
{
- // TODO Auto-generated method stub
return null;
}
@Override
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbId)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
public void releaseReferences(Object svl)
{
- // TODO Auto-generated method stub
-
}
@Override
public void updateColours(Object source)
{
- // TODO Auto-generated method stub
-
}
@Override
public void componentHidden(ComponentEvent e)
{
- // TODO Auto-generated method stub
-
}
@Override
public void componentMoved(ComponentEvent e)
{
- // TODO Auto-generated method stub
-
}
@Override
public void componentResized(ComponentEvent e)
{
- // TODO Auto-generated method stub
-
}
@Override
public void componentShown(ComponentEvent e)
{
- // TODO Auto-generated method stub
-
}
@Override
public void onStructureRedrawn()
{
- // TODO Auto-generated method stub
-
}
@Override
public void onZoomLevelChanged()
{
- // TODO Auto-generated method stub
-
}
@Override
public void onTranslationChanged()
{
- // TODO Auto-generated method stub
+ }
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
}
}
-
-/*
- * public static void main(String[] args) { JTextField str = new
- * JTextField("ATGC");
- *
- * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
- * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- * vab.varnagui.pack(); vab.varnagui.setVisible(true); } }
- */
import jalview.io.*;
import jalview.jbgui.*;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
/**
* Cut'n'paste files into the desktop See JAL-1105
public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
{
- AlignViewport viewport;
+ AlignmentViewport viewport;
public CutAndPasteHtmlTransfer()
{
/**
* DOCUMENT ME!
*/
- public void setForInput(AlignViewport viewport)
+ public void setForInput(AlignmentViewport viewport)
{
this.viewport = viewport;
if (viewport != null)
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
+import jalview.datamodel.Alignment;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteTransfer;
import jalview.util.MessageManager;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+
/**
* Cut'n'paste files into the desktop See JAL-1105
*
if (al != null)
{
+ String title = MessageManager.formatMessage(
+ "label.input_cut_paste_params", new String[]
+ { format });
if (viewport != null)
{
- for (int i = 0; i < al.getHeight(); i++)
- {
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
- }
-
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.addAlignment(al, title);
}
else
{
AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.currentFileFormat = format;
- Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.input_cut_paste_params", new String[]
- { format }), AlignFrame.DEFAULT_WIDTH,
+ Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.statusBar.setText(MessageManager
.getString("label.successfully_pasted_alignment_file"));
*/
package jalview.gui;
-import jalview.jbgui.GDasSourceBrowser;
-import jalview.util.MessageManager;
-import jalview.util.TableSorter;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import org.biodas.jdas.schema.sources.PROP;
import org.biodas.jdas.schema.sources.VERSION;
+import jalview.jbgui.GDasSourceBrowser;
+import jalview.util.MessageManager;
+import jalview.util.TableSorter;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+
public class DasSourceBrowser extends GDasSourceBrowser implements
Runnable, ListSelectionListener
{
seqs.setSelected(seqsrc);
JPanel panel = new JPanel(new BorderLayout());
JPanel pane12 = new JPanel(new BorderLayout());
- pane12.add(
- new JLabel(MessageManager.getString("label.structure_manager")),
+ pane12.add(new JLabel(MessageManager.getString("label.name")),
BorderLayout.CENTER);
pane12.add(nametf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.NORTH);
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import java.awt.BorderLayout;
String group;
for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- if (af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures() == null)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
+ .getSequenceFeatures();
+ if (tmpfeatures == null)
{
continue;
}
- tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
-
int index = 0;
while (index < tmpfeatures.length)
{
{
tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
+ .getSequenceFeatures();
if (tmpfeatures == null)
{
continue;
{
SequenceI[] dataset, seqs;
int iSize;
- AlignViewport vp = af.getViewport();
+ AlignmentViewport vp = af.getViewport();
if (vp.getSelectionGroup() != null
&& vp.getSelectionGroup().getSize() > 0)
{
import jalview.datamodel.SequenceI;
import jalview.jbgui.GFinder;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.event.ActionEvent;
import java.util.Vector;
private static final int WIDTH = 340;
- AlignViewport av;
+ AlignmentViewport av;
AlignmentPanel ap;
* @param viewport
* @param alignPanel
*/
- public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+ public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
{
av = viewport;
ap = alignPanel;
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.jbgui.*;
+import jalview.bin.Cache;
+import jalview.jbgui.GFontChooser;
import jalview.util.MessageManager;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.event.ActionEvent;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
{
if (ap != null)
{
- ap.av.setFont(oldFont);
+ ap.av.setFont(oldFont, true);
ap.paintAlignment(true);
}
else if (tp != null)
}
else if (ap != null)
{
- ap.av.setFont(newFont);
+ ap.av.setFont(newFont, true);
ap.fontChanged();
}
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.image.*;
+import jalview.datamodel.SequenceI;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
import java.util.List;
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import javax.swing.JPanel;
/**
* DOCUMENT ME!
{
int xPos = 0;
int panelWidth = getWidth();
- int charHeight = av.charHeight;
+ int charHeight = av.getCharHeight();
if ((searchResults != null) && searchResults.contains(s))
{
gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
- if (av.hasHiddenRows() && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.getShowHiddenMarkers())
{
drawMarker(i, starty, ypos);
}
return;
}
- gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0,
+ -vertical * av.getCharHeight());
int ss = av.startSeq;
int es = av.endSeq;
}
else
{
- transY = imgHeight - (vertical * av.charHeight);
+ transY = imgHeight - (vertical * av.getCharHeight());
}
}
else if (vertical < 0)
int oldHeight = imgHeight;
imgHeight = getHeight();
- imgHeight -= (imgHeight % av.charHeight);
+ imgHeight -= (imgHeight % av.getCharHeight());
if (imgHeight < 1)
{
*/
void drawIds(int starty, int endy)
{
- if (av.seqNameItalics)
+ if (av.isSeqNameItalics())
{
setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
.getSize()));
}
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+ int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
int rowSize = av.getEndRes() - av.getStartRes();
if (labels != null && av.isShowAnnotation())
{
- gg.translate(0, ypos + (alheight * av.charHeight));
+ gg.translate(0, ypos + (alheight * av.getCharHeight()));
labels.drawComponent(gg, getWidth());
- gg.translate(0, -ypos - (alheight * av.charHeight));
+ gg.translate(0, -ypos - (alheight * av.getCharHeight()));
}
}
}
gg.setColor(currentColor);
- gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
- av.charHeight);
+ gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
+ av.getCharHeight());
gg.setColor(currentTextColor);
}
gg.drawString(string, xPos,
- (((i - starty) * av.charHeight) + av.charHeight)
- - (av.charHeight / 5));
+ (((i - starty) * av.getCharHeight()) + av.getCharHeight())
+ - (av.getCharHeight() / 5));
- if (av.hasHiddenRows() && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.getShowHiddenMarkers())
{
drawMarker(i, starty, 0);
}
{
gg.fillPolygon(
new int[]
- { getWidth() - av.charHeight, getWidth() - av.charHeight,
+ { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(),
getWidth() }, new int[]
{
- (i - starty) * av.charHeight + yoffset,
- (i - starty) * av.charHeight + yoffset + av.charHeight
- / 4, (i - starty) * av.charHeight + yoffset }, 3);
+ (i - starty) * av.getCharHeight() + yoffset,
+ (i - starty) * av.getCharHeight() + yoffset
+ + av.getCharHeight() / 4,
+ (i - starty) * av.getCharHeight() + yoffset }, 3);
}
if (above)
{
gg.fillPolygon(
new int[]
- { getWidth() - av.charHeight, getWidth() - av.charHeight,
+ { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(),
getWidth() }, new int[]
{
- (i - starty + 1) * av.charHeight + yoffset,
- (i - starty + 1) * av.charHeight + yoffset
- - av.charHeight / 4,
- (i - starty + 1) * av.charHeight + yoffset }, 3);
+ (i - starty + 1) * av.getCharHeight() + yoffset,
+ (i - starty + 1) * av.getCharHeight() + yoffset
+ - av.getCharHeight() / 4,
+ (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
}
}
StringBuffer tip = new StringBuffer(64);
seqAnnotReport
.createSequenceAnnotationReport(tip, sequence,
- av.isShowDbRefs(), av.isShowNpFeats(),
+ av.isShowDBRefs(), av.isShowNPFeats(),
sp.seqCanvas.fr.getMinMax());
setToolTipText("<html>" + sequence.getDisplayId(true) + " "
+ tip.toString() + "</html>");
// build a new links menu based on the current links + any non-positional
// features
Vector nlinks = new Vector(Preferences.sequenceURLLinks);
- SequenceFeature sf[] = sq == null ? null : sq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
for (int sl = 0; sf != null && sl < sf.length; sl++)
{
if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
{
selectSeq(seq);
}
+ // TODO is this addition ok here?
+ av.isSelectionGroupChanged(true);
+
alignPanel.paintAlignment(true);
}
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+import javax.swing.JPanel;
/**
* DOCUMENT ME!
{
active = true;
- Dimension d = ap.getIdPanel().getIdCanvas().getPreferredSize();
+ int curwidth = ap.getAlignViewport().getIdWidth();
int dif = evt.getX() - oldX;
- if (((d.width + dif) > 20) || (dif > 0))
+ if (((curwidth + dif) > 20) || (dif > 0))
{
- ap.getIdPanel().getIdCanvas().setPreferredSize(new Dimension(d.width + dif,
- d.height));
+ ap.getAlignViewport().setIdWidth(curwidth + dif);
+
ap.paintAlignment(true);
}
*/
package jalview.gui;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import org.exolab.castor.xml.Unmarshaller;
+
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.StructureViewerModel;
import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.schemabinding.version2.AlcodMap;
-import jalview.schemabinding.version2.Alcodon;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
import jalview.schemabinding.version2.AnnotationColours;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.StringTokenizer;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
-import org.exolab.castor.xml.Unmarshaller;
-
/**
* Write out the current jalview desktop state as a Jalview XML stream.
*
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+ /*
+ * Map of reconstructed AlignFrame objects that appear to have come from
+ * SplitFrame objects (have a dna/protein complement view).
+ */
+ private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
+
/**
* create/return unique hash string for sq
*
}
/**
- * This maintains a list of viewports, the key being the seqSetId. Important
- * to set historyItem and redoList for multiple views
+ * This maintains a map of viewports, the key being the seqSetId. Important to
+ * set historyItem and redoList for multiple views
*/
- Hashtable viewportsAdded;
+ Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
- Hashtable annotationIds = new Hashtable();
+ Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
String uniqueSetSuffix = "";
*/
public void saveState(JarOutputStream jout)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ AlignFrame[] frames = Desktop.getAlignFrames(); // Desktop.desktop.getAllFrames();
if (frames == null)
{
// REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
- if (frames[i] instanceof AlignFrame)
+ AlignFrame af = frames[i];
+ // skip ?
+ if (skipList != null
+ && skipList
+ .containsKey(af.getViewport().getSequenceSetId()))
{
- AlignFrame af = (AlignFrame) frames[i];
- // skip ?
- if (skipList != null
- && skipList.containsKey(af.getViewport()
- .getSequenceSetId()))
- {
- continue;
- }
+ continue;
+ }
+
+ String shortName = af.getTitle();
+
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName
+ .lastIndexOf(File.separatorChar) + 1);
+ }
- String shortName = af.getTitle();
+ int count = 1;
- if (shortName.indexOf(File.separatorChar) > -1)
+ while (shortNames.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
{
- shortName = shortName.substring(shortName
- .lastIndexOf(File.separatorChar) + 1);
+ shortName = shortName.substring(0, shortName.lastIndexOf("_"));
}
- int count = 1;
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
- while (shortNames.contains(shortName))
- {
- if (shortName.endsWith("_" + (count - 1)))
- {
- shortName = shortName
- .substring(0, shortName.lastIndexOf("_"));
- }
+ shortNames.addElement(shortName);
- shortName = shortName.concat("_" + count);
- count++;
- }
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
- shortNames.addElement(shortName);
+ int ap, apSize = af.alignPanels.size();
- if (!shortName.endsWith(".xml"))
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = af.alignPanels.get(ap);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
{
- shortName = shortName + ".xml";
+ fileName = fileName + ".xml";
}
- int ap, apSize = af.alignPanels.size();
+ saveState(apanel, fileName, jout);
- for (ap = 0; ap < apSize; ap++)
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
{
- AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
- .elementAt(ap);
- String fileName = apSize == 1 ? shortName : ap + shortName;
- if (!fileName.endsWith(".xml"))
- {
- fileName = fileName + ".xml";
- }
-
- saveState(apanel, fileName, jout);
-
- String dssid = getDatasetIdRef(af.getViewport().getAlignment()
- .getDataset());
- if (!dsses.containsKey(dssid))
- {
- dsses.put(dssid, af);
- }
-
+ dsses.put(dssid, af);
}
}
}
{
try
{
- int ap, apSize = af.alignPanels.size();
+ int ap = 0;
+ int apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
- for (ap = 0; ap < apSize; ap++)
+ for (AlignmentPanel apanel : af.alignPanels)
{
- AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
- .elementAt(ap);
String jfileName = apSize == 1 ? fileName : fileName + ap;
+ ap++;
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
}
}
- if (jdatasq.getSequenceFeatures() != null)
+ if (jds.getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf = jdatasq
+ jalview.datamodel.SequenceFeature[] sf = jds
.getSequenceFeatures();
int index = 0;
while (index < sf.length)
{
byte[] data = new byte[(int) file.length()];
jout.putNextEntry(new JarEntry(entry.getId()));
- dis = new DataInputStream(
- new FileInputStream(file));
+ dis = new DataInputStream(new FileInputStream(file));
dis.readFully(data);
DataOutputStream dout = new DataOutputStream(jout);
jal = av.getAlignment();
}
// SAVE MAPPINGS
- if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
+ if (jal.getCodonFrames() != null)
{
- jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
- for (int i = 0; i < jac.length; i++)
+ Set<AlignedCodonFrame> jac = jal.getCodonFrames();
+ for (AlignedCodonFrame acf : jac)
{
AlcodonFrame alc = new AlcodonFrame();
vamsasSet.addAlcodonFrame(alc);
- for (int p = 0; p < jac[i].aaWidth; p++)
+ if (acf.getProtMappings() != null
+ && acf.getProtMappings().length > 0)
{
- Alcodon cmap = new Alcodon();
- if (jac[i].codons[p] != null)
- {
- // Null codons indicate a gapped column in the translated peptide
- // alignment.
- cmap.setPos1(jac[i].codons[p][0]);
- cmap.setPos2(jac[i].codons[p][1]);
- cmap.setPos3(jac[i].codons[p][2]);
- }
- alc.addAlcodon(cmap);
- }
- if (jac[i].getProtMappings() != null
- && jac[i].getProtMappings().length > 0)
- {
- SequenceI[] dnas = jac[i].getdnaSeqs();
- jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
+ SequenceI[] dnas = acf.getdnaSeqs();
+ jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
for (int m = 0; m < pmaps.length; m++)
{
AlcodMap alcmap = new AlcodMap();
alc.addAlcodMap(alcmap);
}
}
+
+// {
+// AlcodonFrame alc = new AlcodonFrame();
+// vamsasSet.addAlcodonFrame(alc);
+// for (int p = 0; p < acf.aaWidth; p++)
+// {
+// Alcodon cmap = new Alcodon();
+// if (acf.codons[p] != null)
+// {
+// // Null codons indicate a gapped column in the translated peptide
+// // alignment.
+// cmap.setPos1(acf.codons[p][0]);
+// cmap.setPos2(acf.codons[p][1]);
+// cmap.setPos3(acf.codons[p][2]);
+// }
+// alc.addAlcodon(cmap);
+// }
+// if (acf.getProtMappings() != null
+// && acf.getProtMappings().length > 0)
+// {
+// SequenceI[] dnas = acf.getdnaSeqs();
+// jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
+// for (int m = 0; m < pmaps.length; m++)
+// {
+// AlcodMap alcmap = new AlcodMap();
+// alcmap.setDnasq(seqHash(dnas[m]));
+// alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+// false));
+// alc.addAlcodMap(alcmap);
+// }
+// }
}
}
view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
av.getSequenceSetId()));
view.setId(av.getViewId());
- view.setViewName(av.viewName);
- view.setGatheredViews(av.gatherViewsHere);
-
- if (ap.av.explodedPosition != null)
+ if (av.getCodingComplement() != null)
{
- view.setXpos(av.explodedPosition.x);
- view.setYpos(av.explodedPosition.y);
- view.setWidth(av.explodedPosition.width);
- view.setHeight(av.explodedPosition.height);
+ view.setComplementId(av.getCodingComplement().getViewId());
}
- else
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.isGatherViewsHere());
+
+ Rectangle position = ap.av.getExplodedGeometry();
+ if (position == null)
{
- view.setXpos(ap.alignFrame.getBounds().x);
- view.setYpos(ap.alignFrame.getBounds().y);
- view.setWidth(ap.alignFrame.getBounds().width);
- view.setHeight(ap.alignFrame.getBounds().height);
+ position = ap.alignFrame.getBounds();
}
+ view.setXpos(position.x);
+ view.setYpos(position.y);
+ view.setWidth(position.width);
+ view.setHeight(position.height);
view.setStartRes(av.startRes);
view.setStartSeq(av.startSeq);
view.setFontName(av.font.getName());
view.setFontSize(av.font.getSize());
view.setFontStyle(av.font.getStyle());
- view.setRenderGaps(av.renderGaps);
+ view.setRenderGaps(av.isRenderGaps());
view.setShowAnnotation(av.isShowAnnotation());
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowText(av.getShowText());
view.setShowUnconserved(av.getShowUnconserved());
view.setWrapAlignment(av.getWrapAlignment());
- view.setTextCol1(av.textColour.getRGB());
- view.setTextCol2(av.textColour2.getRGB());
- view.setTextColThreshold(av.thresholdTextColour);
+ view.setTextCol1(av.getTextColour().getRGB());
+ view.setTextCol2(av.getTextColour2().getRGB());
+ view.setTextColThreshold(av.getThresholdTextColour());
view.setShowConsensusHistogram(av.isShowConsensusHistogram());
view.setShowSequenceLogo(av.isShowSequenceLogo());
view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
view.setShowGroupConsensus(av.isShowGroupConsensus());
view.setShowGroupConservation(av.isShowGroupConservation());
- view.setShowNPfeatureTooltip(av.isShowNpFeats());
- view.setShowDbRefTooltip(av.isShowDbRefs());
+ view.setShowNPfeatureTooltip(av.isShowNPFeats());
+ view.setShowDbRefTooltip(av.isShowDBRefs());
view.setFollowHighlight(av.followHighlight);
view.setFollowSelection(av.followSelection);
- view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
+ view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
if (av.getFeaturesDisplayed() != null)
{
jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getRenderOrder().toArray(new String[0]);
+ String[] renderOrder = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer().getRenderOrder()
+ .toArray(new String[0]);
Vector settingsAdded = new Vector();
Object gstyle = null;
}
else
{
- setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ setting.setColour(ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer()
.getColour(renderOrder[ro]).getRGB());
}
settingsAdded.addElement(key);
}
// is groups actually supposed to be a map here ?
- en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().getFeatureGroups()
- .iterator();
+ en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getFeatureGroups().iterator();
Vector groupsAdded = new Vector();
while (en.hasNext())
{
for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
.size(); c++)
{
- int[] region = av.getColumnSelection()
- .getHiddenColumns().get(c);
+ int[] region = av.getColumnSelection().getHiddenColumns()
+ .get(c);
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
hc.setEnd(region[1]);
Pdbids pdb, PDBEntry entry, List<String> viewIds,
String matchedFile, StructureViewerBase viewFrame)
{
- final AAStructureBindingModel bindingModel = viewFrame
- .getBinding();
- for (int peid = 0; peid < bindingModel
- .getPdbCount(); peid++)
+ final AAStructureBindingModel bindingModel = viewFrame.getBinding();
+ for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
{
final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
final String pdbId = pdbentry.getId();
if (!pdbId.equals(entry.getId())
&& !(entry.getId().length() > 4 && entry.getId()
- .toLowerCase()
- .startsWith(pdbId.toLowerCase())))
+ .toLowerCase().startsWith(pdbId.toLowerCase())))
{
continue;
}
{
matchedFile = pdbentry.getFile();
}
- else if (!matchedFile.equals(pdbentry
- .getFile()))
+ else if (!matchedFile.equals(pdbentry.getFile()))
{
Cache.log
.warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
// 1QIP==1qipA)
String statestring = viewFrame.getStateInfo();
- for (int smap = 0; smap < viewFrame.getBinding()
- .getSequence()[peid].length; smap++)
+ for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++)
{
// if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
if (jds == viewFrame.getBinding().getSequence()[peid][smap])
final String viewId = viewFrame.getViewId();
state.setViewId(viewId);
state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
- state.setColourwithAlignPanel(viewFrame
- .isUsedforcolourby(ap));
+ state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
state.setColourByJmol(viewFrame.isColouredByViewer());
/*
* Only store each structure viewer's state once in each XML document.
return false;
}
}
- throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.unsupported_version_calcIdparam", new Object[]
+ { calcIdParam.toString() }));
}
/**
mp = new Mapping();
jalview.util.MapList mlst = jmp.getMap();
- int r[] = mlst.getFromRanges();
- for (int s = 0; s < r.length; s += 2)
+ List<int[]> r = mlst.getFromRanges();
+ for (int[] range : r)
{
MapListFrom mfrom = new MapListFrom();
- mfrom.setStart(r[s]);
- mfrom.setEnd(r[s + 1]);
+ mfrom.setStart(range[0]);
+ mfrom.setEnd(range[1]);
mp.addMapListFrom(mfrom);
}
r = mlst.getToRanges();
- for (int s = 0; s < r.length; s += 2)
+ for (int[] range : r)
{
MapListTo mto = new MapListTo();
- mto.setStart(r[s]);
- mto.setEnd(r[s + 1]);
+ mto.setStart(range[0]);
+ mto.setEnd(range[1]);
mp.addMapListTo(mto);
}
mp.setMapFromUnit(mlst.getFromRatio());
errorMessage = null;
uniqueSetSuffix = null;
seqRefIds = null;
- viewportsAdded = null;
+ viewportsAdded.clear();
frefedSequence = null;
if (file.startsWith("http://"))
{
seqRefIds = new HashMap<String, SequenceI>();
}
- if (viewportsAdded == null)
- {
- viewportsAdded = new Hashtable();
- }
if (frefedSequence == null)
{
frefedSequence = new Vector();
}
- jalview.gui.AlignFrame af = null, _af = null;
- Hashtable gatherToThisFrame = new Hashtable();
+ AlignFrame af = null, _af = null;
+ Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
final String file = jprovider.getFilename();
try
{
if (object.getJalviewModelSequence().getViewportCount() > 0)
{
af = _af;
- if (af.viewport.gatherViewsHere)
+ if (af.viewport.isGatherViewsHere())
{
gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
}
Desktop.instance.stopLoading();
}
- Enumeration en = gatherToThisFrame.elements();
- while (en.hasMoreElements())
+ /*
+ * Regather multiple views (with the same sequence set id) to the frame (if
+ * any) that is flagged as the one to gather to, i.e. convert them to tabbed
+ * views instead of separate frames. Note this doesn't restore a state where
+ * some expanded views in turn have tabbed views - the last "first tab" read
+ * in will play the role of gatherer for all.
+ */
+ for (AlignFrame fr : gatherToThisFrame.values())
{
- Desktop.instance.gatherViews((AlignFrame) en.nextElement());
+ Desktop.instance.gatherViews(fr);
}
+
+ restoreSplitFrames();
+
if (errorMessage != null)
{
reportErrors();
}
/**
+ * Try to reconstruct and display SplitFrame windows, where each contains
+ * complementary dna and protein alignments. Done by pairing up AlignFrame
+ * objects (created earlier) which have complementary viewport ids associated.
+ */
+ protected void restoreSplitFrames()
+ {
+ List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
+ List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
+ Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
+
+ /*
+ * Identify the DNA alignments
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (af.getViewport().getAlignment().isNucleotide())
+ {
+ dna.put(candidate.getKey().getId(), af);
+ }
+ }
+
+ /*
+ * Try to match up the protein complements
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (!af.getViewport().getAlignment().isNucleotide())
+ {
+ String complementId = candidate.getKey().getComplementId();
+ // only non-null complements should be in the Map
+ if (complementId != null && dna.containsKey(complementId))
+ {
+ final AlignFrame dnaFrame = dna.get(complementId);
+ SplitFrame sf = createSplitFrame(dnaFrame, af);
+ addedToSplitFrames.add(dnaFrame);
+ addedToSplitFrames.add(af);
+ if (af.viewport.isGatherViewsHere())
+ {
+ gatherTo.add(sf);
+ }
+ }
+ }
+ }
+
+ /*
+ * Open any that we failed to pair up (which shouldn't happen!) as
+ * standalone AlignFrame's.
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (!addedToSplitFrames.contains(af)) {
+ Viewport view = candidate.getKey();
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
+ System.err.println("Failed to restore view " + view.getTitle()
+ + " to split frame");
+ }
+ }
+
+ /*
+ * Gather back into tabbed views as flagged.
+ */
+ for (SplitFrame sf : gatherTo)
+ {
+ Desktop.instance.gatherViews(sf);
+ }
+
+ splitFrameCandidates.clear();
+ }
+
+ /**
+ * Construct and display one SplitFrame holding DNA and protein alignments.
+ *
+ * @param dnaFrame
+ * @param proteinFrame
+ * @return
+ */
+ protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
+ AlignFrame proteinFrame)
+ {
+ SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
+ String title = MessageManager.getString("label.linked_view_title");
+ int width = (int) dnaFrame.getBounds().getWidth();
+ int height = (int) (dnaFrame.getBounds().getHeight()
+ + proteinFrame.getBounds().getHeight() + 50);
+ Desktop.addInternalFrame(splitFrame, title, width, height);
+ return splitFrame;
+ }
+
+ /**
* check errorMessage for a valid error message and raise an error box in the
* GUI or write the current errorMessage to stderr and then clear the error
* state.
errorMessage = null;
}
- Hashtable<String, String> alreadyLoadedPDB;
+ Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
/**
* when set, local views will be updated from view stored in JalviewXML
String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
- if (alreadyLoadedPDB == null)
- {
- alreadyLoadedPDB = new Hashtable();
- }
-
if (alreadyLoadedPDB.containsKey(pdbId))
{
return alreadyLoadedPDB.get(pdbId).toString();
// ////////////////////////////////
// LOAD SEQUENCES
- Vector hiddenSeqs = null;
+ List<SequenceI> hiddenSeqs = null;
jalview.datamodel.Sequence jseq;
- ArrayList tmpseqs = new ArrayList();
+ List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
boolean multipleView = false;
{
if (hiddenSeqs == null)
{
- hiddenSeqs = new Vector();
+ hiddenSeqs = new ArrayList<SequenceI>();
}
- hiddenSeqs.addElement(seqRefIds.get(seqId));
+ hiddenSeqs.add(seqRefIds.get(seqId));
}
}
// /
// Create the alignment object from the sequence set
// ///////////////////////////////
- jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
- .size()];
-
- tmpseqs.toArray(orderedSeqs);
+ SequenceI[] orderedSeqs = tmpseqs
+ .toArray(new SequenceI[tmpseqs.size()]);
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
- orderedSeqs);
+ Alignment al = new Alignment(orderedSeqs);
// / Add the alignment properties
for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
}
// ///////////////////////////////
- Hashtable pdbloaded = new Hashtable();
+ Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
if (!multipleView)
{
// load sequence features, database references and any associated PDB
}
}
StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance)
- .registerPDBEntry(entry);
+ Desktop.instance).registerPDBEntry(entry);
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
}
AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
for (int i = 0; i < alc.length; i++)
{
- jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
- alc[i].getAlcodonCount());
- if (alc[i].getAlcodonCount() > 0)
- {
- Alcodon[] alcods = alc[i].getAlcodon();
- for (int p = 0; p < cf.codons.length; p++)
- {
- if (alcods[p].hasPos1() && alcods[p].hasPos2()
- && alcods[p].hasPos3())
- {
- // translated codons require three valid positions
- cf.codons[p] = new int[3];
- cf.codons[p][0] = (int) alcods[p].getPos1();
- cf.codons[p][1] = (int) alcods[p].getPos2();
- cf.codons[p][2] = (int) alcods[p].getPos3();
- }
- else
- {
- cf.codons[p] = null;
- }
- }
- }
+ AlignedCodonFrame cf = new AlignedCodonFrame();
if (alc[i].getAlcodMapCount() > 0)
{
AlcodMap[] maps = alc[i].getAlcodMap();
for (int m = 0; m < maps.length; m++)
{
- SequenceI dnaseq = seqRefIds
- .get(maps[m].getDnasq());
+ SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
// Load Mapping
jalview.datamodel.Mapping mapping = null;
// attach to dna sequence reference.
}
al.addCodonFrame(cf);
}
-
}
// ////////////////////////////////
// LOAD ANNOTATIONS
- ArrayList<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
+ List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
/**
* store any annotations which forward reference a group's ID
*/
if (an[i].getId() != null
&& annotationIds.containsKey(an[i].getId()))
{
- jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
- .get(an[i].getId());
+ AlignmentAnnotation jda = annotationIds.get(an[i].getId());
// in principle Visible should always be true for annotation displayed
// in multiple views
if (an[i].hasVisible())
for (int s = 0; s < groups[i].getSeqCount(); s++)
{
String seqId = groups[i].getSeq(s) + "";
- jalview.datamodel.SequenceI ts = seqRefIds
- .get(seqId);
+ jalview.datamodel.SequenceI ts = seqRefIds.get(seqId);
if (ts != null)
{
for (int s = 0; s < structureStateCount; s++)
{
// check to see if we haven't already created this structure view
- final StructureState structureState = ids[p].getStructureState(s);
+ final StructureState structureState = ids[p]
+ .getStructureState(s);
String sviewid = (structureState.getViewId() == null) ? null
- : structureState.getViewId()
- + uniqueSetSuffix;
+ : structureState.getViewId() + uniqueSetSuffix;
jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
// Originally : ids[p].getFile()
// : TODO: verify external PDB file recovery still works in normal
// Desktop.desktop.getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
String pdbFile = loadPDBFile(jprovider, ids[p].getId());
- jalview.datamodel.SequenceI seq = seqRefIds
- .get(jseqs[i].getId() + "");
+ jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
+ .getId() + "");
if (sviewid == null)
{
sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
}
if (!structureViewers.containsKey(sviewid))
{
- structureViewers.put(sviewid, new StructureViewerModel(x, y, width, height,
- false, false, true));
+ structureViewers.put(sviewid, new StructureViewerModel(x, y,
+ width, height, false, false, true));
// Legacy pre-2.7 conversion JAL-823 :
// do not assume any view has to be linked for colour by
// sequence
* pre-2.7 projects)
*/
boolean colourByViewer = jmoldat.isColourByViewer();
- colourByViewer &= structureState
- .hasColourByJmol() ? structureState
+ colourByViewer &= structureState.hasColourByJmol() ? structureState
.getColourByJmol() : true;
jmoldat.setColourByViewer(colourByViewer);
}
}
}
- // Instantiate the associated structure views
- for (Entry<String, StructureViewerModel> entry : structureViewers.entrySet())
+ // Instantiate the associated structure views
+ for (Entry<String, StructureViewerModel> entry : structureViewers
+ .entrySet())
{
- createOrLinkStructureViewer(entry, af, ap);
- }
+ createOrLinkStructureViewer(entry, af, ap);
+ }
}
/**
* @param viewerData
* @param af
*/
- protected void createChimeraViewer(Entry<String, StructureViewerModel> viewerData,
- AlignFrame af)
+ protected void createChimeraViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af)
{
final StructureViewerModel data = viewerData.getValue();
String chimeraSession = data.getStateData();
boolean colourBySequence = data.isColourWithAlignPanel();
// TODO can/should this be done via StructureViewer (like Jmol)?
- final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs
- .size()]);
- final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs.size()][]);
+ final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
+ final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
+ .size()][]);
new ChimeraViewFrame(chimeraSession, af.alignPanel, pdbArray,
- seqsArray,
- colourByChimera, colourBySequence);
+ seqsArray, colourByChimera, colourBySequence);
}
else
{
* @param af
*/
protected void createJmolViewer(
- final Entry<String, StructureViewerModel> viewerData, AlignFrame af)
+ final Entry<String, StructureViewerModel> viewerData,
+ AlignFrame af)
{
final StructureViewerModel svattrib = viewerData.getValue();
String state = svattrib.getStateData();
newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
- seqmaps.add(filedat.getSeqList()
- .toArray(new SequenceI[0]));
+ seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
newFileLoc.append("\"");
cp = ecp + 1; // advance beyond last \" and set cursor so we can
// look for next file statement.
newFileLoc.append(filedat.getFilePath());
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
- seqmaps.add(filedat.getSeqList()
- .toArray(new SequenceI[0]));
+ seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
newFileLoc.append(" \"");
newFileLoc.append(filedat.getFilePath());
newFileLoc.append("\"");
* Post jalview 2.4 schema includes structure view id
*/
if (sviewid != null
- && ((StructureViewerBase) frame).getViewId().equals(
- sviewid))
+ && ((StructureViewerBase) frame).getViewId()
+ .equals(sviewid))
{
comp = (AppJmol) frame;
// todo: break?
}
}
- AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
- Alignment al, JalviewModelSequence jms, Viewport view,
- String uniqueSeqSetId, String viewId,
- ArrayList<JvAnnotRow> autoAlan)
+ AlignFrame loadViewport(String file, JSeq[] JSEQ,
+ List<SequenceI> hiddenSeqs, Alignment al,
+ JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
+ String viewId, List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
.getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
}
- af.viewport.gatherViewsHere = view.getGatheredViews();
+ af.viewport.setGatherViewsHere(view.getGatheredViews());
if (view.getSequenceSetId() != null)
{
- jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
- .get(uniqueSeqSetId);
+ AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
af.viewport.setSequenceSetId(uniqueSeqSetId);
if (av != null)
{
// propagate shared settings to this new view
- af.viewport.historyList = av.historyList;
- af.viewport.redoList = av.redoList;
+ af.viewport.setHistoryList(av.getHistoryList());
+ af.viewport.setRedoList(av.getRedoList());
}
else
{
af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
}
- jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
- .size()];
-
- for (int s = 0; s < hiddenSeqs.size(); s++)
- {
- hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
- }
+ // jalview.datamodel.SequenceI[] hseqs = new
+ // jalview.datamodel.SequenceI[hiddenSeqs
+ // .size()];
+ //
+ // for (int s = 0; s < hiddenSeqs.size(); s++)
+ // {
+ // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
+ // }
+ SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
+ .size()]);
af.viewport.hideSequence(hseqs);
}
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setRightAlignIds(view.getRightAlignIds());
- af.viewport.setFont(new java.awt.Font(view.getFontName(), view
- .getFontStyle(), view.getFontSize()));
- af.alignPanel.fontChanged();
+ af.viewport.setFont(
+ new java.awt.Font(view.getFontName(), view.getFontStyle(), view
+ .getFontSize()), true);
+ // TODO: allow custom charWidth/Heights to be restored by updating them
+ // after setting font - which means set above to false
af.viewport.setRenderGaps(view.getRenderGaps());
af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());
af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
af.viewport.setShowBoxes(view.getShowBoxes());
af.viewport.setShowText(view.getShowText());
- af.viewport.textColour = new java.awt.Color(view.getTextCol1());
- af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
- af.viewport.thresholdTextColour = view.getTextColThreshold();
+ af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
+ af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
+ af.viewport.setThresholdTextColour(view.getTextColThreshold());
af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
.isShowUnconserved() : false);
af.viewport.setStartRes(view.getStartRes());
af.viewport.setStartSeq(view.getStartSeq());
-
+ af.alignPanel.updateLayout();
ColourSchemeI cs = null;
// apply colourschemes
if (view.getBgColour() != null)
}
if (view.hasShowDbRefTooltip())
{
- af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
+ af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
}
if (view.hasShowNPfeatureTooltip())
{
- af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
+ af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
}
if (view.hasShowGroupConsensus())
{
}
}
af.setMenusFromViewport(af.viewport);
+
// TODO: we don't need to do this if the viewport is aready visible.
- Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
- view.getHeight());
- af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
- reorderAutoannotation(af, al, autoAlan);
- af.alignPanel.alignmentChanged();
+ /*
+ * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
+ * has a 'cdna/protein complement' view, in which case save it in order to
+ * populate a SplitFrame once all views have been read in.
+ */
+ String complementaryViewId = view.getComplementId();
+ if (complementaryViewId == null)
+ {
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
+ // recompute any autoannotation
+ af.alignPanel.updateAnnotation(false, true);
+ reorderAutoannotation(af, al, autoAlan);
+ af.alignPanel.alignmentChanged();
+ }
+ else
+ {
+ splitFrameCandidates.put(view, af);
+ }
return af;
}
}
private void reorderAutoannotation(AlignFrame af, Alignment al,
- ArrayList<JvAnnotRow> autoAlan)
+ List<JvAnnotRow> autoAlan)
{
// copy over visualization settings for autocalculated annotation in the
// view
+ auan.template.getCalcId()), auan);
}
int hSize = al.getAlignmentAnnotation().length;
- ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+ List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
// work through any autoCalculated annotation already on the view
// removing it if it should be placed in a different location on the
// annotation panel.
- List<String> remains = new ArrayList(visan.keySet());
+ List<String> remains = new ArrayList<String>(visan.keySet());
for (int h = 0; h < hSize; h++)
{
jalview.datamodel.AlignmentAnnotation jalan = al
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
- jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
- .get(vamsasSeq.getId());
- jalview.datamodel.SequenceI dsq = null;
+ SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+ SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
dsq = sq.getDatasetSequence();
// if (pre || post)
if (sq != dsq)
{
- StringBuffer sb = new StringBuffer();
+ // StringBuffer sb = new StringBuffer();
String newres = jalview.analysis.AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, sq.getSequenceAsString());
if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
* local sequence definition
*/
Sequence ms = mc.getSequence();
- jalview.datamodel.Sequence djs = null;
+ SequenceI djs = null;
String sqid = ms.getDsseqid();
if (sqid != null && sqid.length() > 0)
{
/*
* recover dataset sequence
*/
- djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
+ djs = seqRefIds.get(sqid);
}
else
{
frefedSequence = new Vector();
}
- viewportsAdded = new Hashtable();
+ viewportsAdded.clear();
AlignFrame af = loadFromObject(jm, null, false, null);
af.alignPanels.clear();
}
else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
{
- if (annotationIds == null)
- {
- annotationIds = new Hashtable();
- }
String anid;
- annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
- jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
+ AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
+ annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
if (jvann.annotationId == null)
{
jvann.annotationId = anid;
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.setFont(new java.awt.Font(view.getFontName(), view
- .getFontStyle(), view.getFontSize()));
- af.alignPanel.fontChanged();
+ af.viewport.setFont(
+ new java.awt.Font(view.getFontName(), view.getFontStyle(), view
+ .getFontSize()), true);
af.viewport.setRenderGaps(view.getRenderGaps());
af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
+ af.viewport.setShowAnnotation(view.isShowAnnotation());
af.viewport.setShowBoxes(view.getShowBoxes());
af.viewport.setShowText(view.getShowText());
af.viewport.setGlobalColourScheme(cs);
af.viewport.setColourAppliesToAllGroups(false);
+ af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Font;
+import java.awt.GridLayout;
import java.awt.Rectangle;
import java.awt.event.ActionListener;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
+import javax.swing.JScrollBar;
import javax.swing.SwingConstants;
/**
public static JPanel addtoLayout(JPanel panel, String tooltip,
JComponent label, JComponent valBox)
{
- JPanel laypanel = new JPanel(), labPanel = new JPanel(), valPanel = new JPanel();
+ JPanel laypanel = new JPanel(new GridLayout(1, 2));
+ JPanel labPanel = new JPanel(new BorderLayout());
+ JPanel valPanel = new JPanel();
// laypanel.setSize(panel.getPreferredSize());
// laypanel.setLayout(null);
labPanel.setBounds(new Rectangle(7, 7, 158, 23));
valPanel.setBounds(new Rectangle(172, 7, 270, 23));
// labPanel.setLayout(new GridLayout(1,1));
// valPanel.setLayout(new GridLayout(1,1));
- labPanel.add(label);
+ labPanel.add(label, BorderLayout.WEST);
valPanel.add(valBox);
laypanel.add(labPanel);
laypanel.add(valPanel);
}
}
+ /**
+ * Returns the proportion of its range that a scrollbar's position represents,
+ * as a value between 0 and 1. For example if the whole range is from 0 to
+ * 200, then a position of 40 gives proportion = 0.2.
+ *
+ * @see http://www.javalobby.org/java/forums/t33050.html#91885334
+ *
+ * @param scroll
+ * @return
+ */
+ public static float getScrollBarProportion(JScrollBar scroll)
+ {
+ /*
+ * The extent (scroll handle width) deduction gives the true operating range
+ * of possible positions.
+ */
+ int possibleRange = scroll.getMaximum() - scroll.getMinimum()
+ - scroll.getModel().getExtent();
+ float valueInRange = scroll.getValue()
+ - (scroll.getModel().getExtent() / 2f);
+ float proportion = valueInRange / possibleRange;
+ return proportion;
+ }
+
+ /**
+ * Returns the scroll bar position in its range that would match the given
+ * proportion (between 0 and 1) of the whole. For example if the whole range
+ * is from 0 to 200, then a proportion of 0.25 gives position 50.
+ *
+ * @param scrollbar
+ * @param proportion
+ * @return
+ */
+ public static int getScrollValueForProportion(JScrollBar scrollbar,
+ float proportion)
+ {
+ /*
+ * The extent (scroll handle width) deduction gives the true operating range
+ * of possible positions.
+ */
+ float fraction = proportion
+ * (scrollbar.getMaximum() - scrollbar.getMinimum() - scrollbar
+ .getModel().getExtent())
+ + (scrollbar.getModel().getExtent() / 2f);
+ return Math.min(Math.round(fraction), scrollbar.getMaximum());
+ }
+
public static void jvInitComponent(AbstractButton comp, String i18nString)
{
setColorAndFont(comp);
import jalview.renderer.AnnotationRenderer;
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JPanel;
/**
* DOCUMENT ME!
@Override
public void mouseDragged(MouseEvent evt)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
// TODO: feature: jv2.5 detect shift drag and update selection from
// it.
@Override
public void mousePressed(MouseEvent evt)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
boxX = evt.getX();
boxY = evt.getY();
import jalview.jbgui.GPCAPanel;
import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import java.awt.BorderLayout;
AlignmentPanel ap;
- AlignViewport av;
+ AlignmentViewport av;
PCAModel pcaModel;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.gui;
+
+import jalview.jbgui.GPDBSearchPanel;
+import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.swing.table.DefaultTableModel;
+
+@SuppressWarnings("serial")
+public class PDBSearchPanel extends GPDBSearchPanel
+{
+ private SequenceFetcher seqFetcher;
+
+ private IProgressIndicator progressIdicator;
+
+ private Collection<PDBDocField> wantedFields;
+
+ public PDBSearchPanel(SequenceFetcher seqFetcher)
+ {
+ this.seqFetcher = seqFetcher;
+ this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+ .getProgressIndicator();
+ }
+
+
+ /**
+ * Action performed when an input is detected on txt_search field.
+ */
+ @Override
+ public void txt_search_ActionPerformed()
+ {
+ boolean allowEmptySequence = false;
+ mainFrame.setTitle(MessageManager
+ .getString("label.pdb_sequence_getcher"));
+ tbl_summary.setModel(new DefaultTableModel());
+ if (txt_search.getText().trim().length() > 0)
+ {
+ long startTime = System.currentTimeMillis();
+
+ String searchTarget = ((PDBDocField) cmb_searchTarget
+ .getSelectedItem()).getCode();
+
+ wantedFields = PDBDocFieldPreferences
+ .getSearchSummaryFields();
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(allowEmptySequence);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy(searchTarget + ":");
+ request.setSearchTerm(txt_search.getText());
+ request.setWantedFields(wantedFields);
+
+ PDBRestClient pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
+ if (resultList.getSearchSummary() != null)
+ {
+ tbl_summary.setModel(PDBRestResponse.getTableModel(request,
+ resultList.getSearchSummary()));
+ }
+
+ long endTime = System.currentTimeMillis();
+ int resultSetCount = resultList.getNumberOfItemsFound();
+ String result = (resultSetCount > 1) ? MessageManager
+ .getString("label.results") : MessageManager
+ .getString("label.result");
+ mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
+ + " (" + (endTime - startTime) + " milli secs)");
+ }
+ }
+
+ @Override
+ public void btn_ok_ActionPerformed()
+ {
+ loadSelectedPDBSequencesToAlignment();
+ }
+
+ @Override
+ public void btn_back_ActionPerformed()
+ {
+ mainFrame.dispose();
+ new SequenceFetcher(progressIdicator);
+ }
+
+ @Override
+ public void btn_cancel_ActionPerformed()
+ {
+ mainFrame.dispose();
+ }
+
+ /**
+ * Add the discovered/selected sequences to a target alignment window
+ */
+ public void loadSelectedPDBSequencesToAlignment()
+ {
+ mainFrame.dispose();
+ StringBuilder selectedIds = new StringBuilder();
+ int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
+ int[] selectedRows = tbl_summary.getSelectedRows();
+ for (int summaryRow : selectedRows)
+ {
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ .toString();
+ selectedIds.append(";").append(pdbIdStr);
+ }
+
+ String ids = selectedIds.deleteCharAt(0).toString();
+ seqFetcher.textArea.setText(ids);
+ Thread worker = new Thread(seqFetcher);
+ worker.start();
+ }
+
+ /**
+ * Populates search target combo-box options
+ */
+ public void populateCmbSearchTargetOptions()
+ {
+ List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
+ searchableTargets.add(PDBDocField.PDB_ID);
+ searchableTargets.add(PDBDocField.PFAM_ACCESSION);
+ searchableTargets.add(PDBDocField.MOLECULE_TYPE);
+ searchableTargets.add(PDBDocField.MOLECULE_NAME);
+ searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
+ searchableTargets.add(PDBDocField.GENE_NAME);
+ searchableTargets.add(PDBDocField.GENUS);
+ searchableTargets.add(PDBDocField.ALL);
+
+ Collections.sort(searchableTargets, new Comparator<PDBDocField>()
+ {
+ @Override
+ public int compare(PDBDocField o1, PDBDocField o2)
+ {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
+
+ for (PDBDocField searchTarget : searchableTargets)
+ {
+ cmb_searchTarget.addItem(searchTarget);
+ }
+ }
+
+}
*/
package jalview.gui;
-import java.util.*;
-import java.util.List;
-
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
/**
* Route datamodel/view update events for a sequence set to any display
*/
public class PaintRefresher
{
- static Hashtable components;
+ static Map<String, List<Component>> components = new HashMap<String, List<Component>>();
/**
- * DOCUMENT ME!
+ * Add the given component to those registered under the given sequence set
+ * id. Does nothing if already added.
*
* @param comp
- * DOCUMENT ME!
* @param al
- * DOCUMENT ME!
*/
public static void Register(Component comp, String seqSetId)
{
- if (components == null)
- {
- components = new Hashtable();
- }
-
if (components.containsKey(seqSetId))
{
- Vector comps = (Vector) components.get(seqSetId);
+ List<Component> comps = components.get(seqSetId);
if (!comps.contains(comp))
{
- comps.addElement(comp);
+ comps.add(comp);
}
}
else
{
- Vector vcoms = new Vector();
- vcoms.addElement(comp);
+ List<Component> vcoms = new ArrayList<Component>();
+ vcoms.add(comp);
components.put(seqSetId, vcoms);
}
}
+ /**
+ * Remove this component from all registrations. Also removes a registered
+ * sequence set id if there are no remaining components registered against it.
+ *
+ * @param comp
+ */
public static void RemoveComponent(Component comp)
{
- if (components == null)
- {
- return;
- }
-
- Enumeration en = components.keys();
- while (en.hasMoreElements())
+ List<String> emptied = new ArrayList<String>();
+ for (Entry<String, List<Component>> registered : components.entrySet())
{
- String id = en.nextElement().toString();
- Vector comps = (Vector) components.get(id);
+ String id = registered.getKey();
+ List<Component> comps = components.get(id);
comps.remove(comp);
- if (comps.size() == 0)
+ if (comps.isEmpty())
{
- components.remove(id);
+ emptied.add(id);
}
}
+
+ /*
+ * Remove now empty ids after the above (to avoid
+ * ConcurrentModificationException).
+ */
+ for (String id : emptied)
+ {
+ components.remove(id);
+ }
}
public static void Refresh(Component source, String id)
public static void Refresh(Component source, String id,
boolean alignmentChanged, boolean validateSequences)
{
- if (components == null)
- {
- return;
- }
-
- Component comp;
- Vector comps = (Vector) components.get(id);
+ List<Component> comps = components.get(id);
if (comps == null)
{
return;
}
- Enumeration e = comps.elements();
- while (e.hasMoreElements())
+ for (Component comp : comps)
{
- comp = (Component) e.nextElement();
-
if (comp == source)
{
continue;
static AlignmentPanel[] getAssociatedPanels(String id)
{
- if (components == null)
- {
- return new AlignmentPanel[0];
- }
- ;
- Vector comps = (Vector) components.get(id);
+ List<Component> comps = components.get(id);
if (comps == null)
{
return new AlignmentPanel[0];
}
- ;
- Vector tmp = new Vector();
- int i, iSize = comps.size();
- for (i = 0; i < iSize; i++)
+ List<AlignmentPanel> tmp = new ArrayList<AlignmentPanel>();
+ for (Component comp : comps)
{
- if (comps.elementAt(i) instanceof AlignmentPanel)
+ if (comp instanceof AlignmentPanel)
{
- tmp.addElement(comps.elementAt(i));
+ tmp.add((AlignmentPanel) comp);
}
}
- AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
- tmp.toArray(result);
-
- return result;
+ return tmp.toArray(new AlignmentPanel[tmp.size()]);
}
}
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPairwiseAlignPanel;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.event.ActionEvent;
import java.util.Vector;
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
- AlignViewport av;
+ AlignmentViewport av;
Vector sequences;
* @param av
* DOCUMENT ME!
*/
- public PairwiseAlignPanel(AlignViewport av)
+ public PairwiseAlignPanel(AlignmentViewport av)
{
super();
this.av = av;
*/
package jalview.gui;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
/**
* DOCUMENT ME!
*
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JMenuItem pdbFromFile = new JMenuItem();
- // JBPNote: Commented these out - Should add these services via the web
- // services menu system.
- // JMenuItem ContraFold = new JMenuItem();
-
- // JMenuItem RNAFold = new JMenuItem();
-
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
JMenu seqHideAnnotationsMenu = new JMenu();
- JMenuItem seqAddReferenceAnnotations = new JMenuItem();
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenu groupShowAnnotationsMenu = new JMenu();
JMenu groupHideAnnotationsMenu = new JMenu();
- JMenuItem groupAddReferenceAnnotations = new JMenuItem();
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenuItem sequenceFeature = new JMenuItem();
JMenu jMenu1 = new JMenu();
- JMenu structureMenu = new JMenu();
+ JMenuItem structureMenu = new JMenuItem();
JMenu viewStructureMenu = new JMenu();
- // JMenu colStructureMenu = new JMenu();
JMenuItem editSequence = new JMenuItem();
- // JMenuItem annotationMenuItem = new JMenuItem();
-
JMenu groupLinksMenu;
JMenuItem hideInsertions = new JMenuItem();
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
colours.add(RNAInteractionColour);
- // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
{
structureMenu.remove(viewStructureMenu);
}
- // structureMenu.remove(colStructureMenu);
}
if (ap.av.getAlignment().isNucleotide() == true)
{
final String structureLine = aa[i].label + " (alignment)";
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_structure_line", new String[]
+ "label.2d_rna_structure_line", new Object[]
{ structureLine }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- // // System.out.println("1:"+structureLine);
- // System.out.println("1:sname" + seq.getName());
- // System.out.println("2:seq" + seq);
- //
- // // System.out.println("3:"+seq.getSequenceAsString());
- // System.out.println("3:strucseq" + rnastruc);
- // // System.out.println("4:struc"+seq.getRNA());
- // System.out.println("5:name" + seq.getName());
- // System.out.println("6:ap" + ap);
new AppVarna(structureLine, seq, seq.getSequenceAsString(),
rnastruc, seq.getName(), ap);
- // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
- // seq.getName(), ap);
System.out.println("end");
}
});
}
}
- // SequenceFeatures[] test = seq.getSequenceFeatures();
if (seq.getAnnotation() != null)
{
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_sequence_name", new String[]
+ "label.2d_rna_sequence_name", new Object[]
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
&& ap.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
+ "label.represent_group_with", new Object[]
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
if (sg != null && sg.getSize() > 0)
{
groupName.setText(MessageManager.formatMessage("label.name_param",
- new String[]
+ new Object[]
{ sg.getName() }));
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
new PDBEntry[reppdb.size()]);
final JMenuItem gpdbview, rpdbview;
- if (pdbe.size() == 1)
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_structure_for", new String[]
- { sqass.getDisplayId(false) })));
- }
- else
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_all_structures", new String[]
- { new Integer(pdbe.size()).toString() })));
- }
- gpdbview.setToolTipText(MessageManager
- .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
- gpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(ap, pe, ap.av.collateForPDB(pe));
- }
- });
- if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
- {
- structureMenu.add(rpdbview = new JMenuItem(MessageManager
- .formatMessage(
- "label.view_all_representative_structures",
- new String[]
- { new Integer(reppdb.size()).toString() })));
- rpdbview.setToolTipText(MessageManager
- .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
- rpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- }
- });
- }
}
}
else
final boolean actionIsShow)
{
String label = types.toString(); // [a, b, c]
- label = label.substring(1, label.length() - 1);
+ label = label.substring(1, label.length() - 1); // a, b, c
final JMenuItem item = new JMenuItem(label);
item.setToolTipText(calcId);
item.addActionListener(new java.awt.event.ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- showHideAnnotation_actionPerformed(types, forSequences, allTypes,
- actionIsShow);
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
+ forSequences, allTypes, actionIsShow);
+ refresh();
}
});
showOrHideMenu.add(item);
}
- /**
- * Action on selecting a list of annotation type (or the 'all types' values)
- * to show or hide for the specified sequences.
- *
- * @param types
- * @param forSequences
- * @param anyType
- * @param doShow
- */
- protected void showHideAnnotation_actionPerformed(
- Collection<String> types, List<SequenceI> forSequences,
- boolean anyType, boolean doShow)
- {
- for (AlignmentAnnotation aa : ap.getAlignment()
- .getAlignmentAnnotation())
- {
- if (anyType || types.contains(aa.label))
- {
- if ((aa.sequenceRef != null)
- && forSequences.contains(aa.sequenceRef))
- {
- aa.visible = doShow;
- }
- }
- }
- refresh();
- }
-
private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
{
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
- // System.out.println(urlLink.getGroupURLType()
- // +" "+((String[])urlset[3])[0]);
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
addshowLink(linkMenus[type], label
{
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
- "label.open_url_param", new String[]
+ "label.open_url_param", new Object[]
{ url }));
item.addActionListener(new java.awt.event.ActionListener()
{
pdbFromFile_actionPerformed();
}
});
- // RNAFold.setText("From RNA Fold with predict2D");
- // RNAFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // RNAFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
- // ContraFold.setText("From Contra Fold with predict2D");
- // ContraFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // ContraFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
+
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- structureMenu.setText(MessageManager.getString("label.structure"));
+ structureMenu.setText(MessageManager.getString("label.view_structure"));
+ structureMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
+ }
+ });
+
viewStructureMenu.setText(MessageManager
.getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
if (ap.getAlignment().isNucleotide())
{
// JBPNote - commented since the colourscheme isn't functional
- // colourMenu.add(RNAInteractionColour);
colourMenu.add(purinePyrimidineColour);
}
- // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- // colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
protected void configureReferenceAnnotationsMenu(
JMenuItem menuItem, List<SequenceI> forSequences)
{
- menuItem.setText(MessageManager
- .getString("label.add_reference_annotations"));
menuItem.setEnabled(false);
- if (forSequences == null)
- {
- return;
- }
/*
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
Map<String, String> tipEntries = new TreeMap<String, String>();
- StringBuilder tooltip = new StringBuilder(64);
- tooltip.append(MessageManager.getString("label.add_annotations_for"));
-
- /*
- * For each sequence selected in the alignment, make a list of any
- * annotations on the underlying dataset sequence which are not already on
- * the alignment.
- *
- * Build a map of { alignmentSequence, <List of annotations to add> }
- */
- AlignmentI al = this.ap.av.getAlignment();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
- for (SequenceI seq : forSequences)
- {
- SequenceI dataset = seq.getDatasetSequence();
- if (dataset == null)
- {
- continue;
- }
- AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
- if (datasetAnnotations == null)
- {
- continue;
- }
- final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation dsann : datasetAnnotations)
- {
- /*
- * Find matching annotations on the alignment.
- */
- final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
- .findAnnotations(seq, dsann.getCalcId(),
- dsann.label);
- if (!matchedAlignmentAnnotations.iterator().hasNext())
- {
- result.add(dsann);
- tipEntries.put(dsann.getCalcId(), dsann.label);
- }
- }
- /*
- * Save any addable annotations for this sequence
- */
- if (!result.isEmpty())
- {
- candidates.put(seq, result);
- }
- }
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences,
+ tipEntries, candidates, al);
if (!candidates.isEmpty())
{
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
/*
* Found annotations that could be added. Enable the menu item, and
* configure its tooltip and action.
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- /*
- * Add annotations at the top of the annotation, in the same order as their
- * related sequences.
- */
- for (SequenceI seq : candidates.keySet())
- {
- for (AlignmentAnnotation ann : candidates.get(seq))
- {
- AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
- int startRes = 0;
- int endRes = ann.annotations.length;
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
- if (selectionGroup != null)
- {
- startRes = selectionGroup.getStartRes();
- endRes = selectionGroup.getEndRes();
- }
- copyAnn.restrict(startRes, endRes);
-
- /*
- * Add to the sequence (sets copyAnn.datasetSequence), unless the
- * original annotation is already on the sequence.
- */
- if (!seq.hasAnnotation(ann))
- {
- seq.addAlignmentAnnotation(copyAnn);
- }
- // adjust for gaps
- copyAnn.adjustForAlignment();
- // add to the alignment and set visible
- this.ap.getAlignment().addAnnotation(copyAnn);
- copyAnn.visible = true;
- }
- }
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
refresh();
}
+ MessageManager
.formatMessage(
"label.create_sequence_details_report_annotation_for",
- new String[]
+ new Object[]
{ seq.getDisplayId(true) }) + "</h2></p><p>");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
- "label.sequece_details_for",
- (sequences.length == 1 ? new String[]
- { sequences[0].getDisplayId(true) } : new String[]
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) } : new Object[]
{ MessageManager.getString("label.selection") })), 500, 400);
}
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
else
// remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
refresh();
}
int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
+ SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
ap.av.hideSequence(hseqs);
// refresh(); TODO: ? needed ?
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(),
sg.getEndRes() + 1);
String description;
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new String[]
+ "label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for", new String[]
+ "label.select_pdb_file_for", new Object[]
{ sequence.getDisplayId(false) }));
chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new String[]
+ "label.load_pdb_file_associate_with_sequence", new Object[]
{ sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
}
- // JBNote: commented out - these won't be instantiated here...!
- // public void RNAFold_actionPerformed() throws Exception
- // {
- // Predict2D P2D = new Predict2D();
- // P2D.getStructure2DFromRNAFold("toto");
- // }
- //
- // public void ContraFold_actionPerformed() throws Exception
- // {
- // Predict2D P2D = new Predict2D();
- // P2D.getStructure2DFromContraFold("toto");
- // }
+
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
public class Preferences extends GPreferences
{
+ public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+ public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
public static final String ADD_SS_ANN = "ADD_SS_ANN";
*/
for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
{
- colour.addItem(ColourSchemeProperty.getColourName(i));
+ protColour.addItem(ColourSchemeProperty.getColourName(i));
+ nucColour.addItem(ColourSchemeProperty.getColourName(i));
}
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");
- colour.setSelectedItem(string);
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+ protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+ nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
Color.orange));
maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
/*
* Save Colours settings
*/
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
.getSelectedItem().toString());
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
}
CommandI command = historyList.pop();
- if (ap.av.historyList.contains(command))
+ if (ap.av.getHistoryList().contains(command))
{
command.undoCommand(af.getViewAlignments());
- ap.av.historyList.remove(command);
+ ap.av.getHistoryList().remove(command);
ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
import jalview.datamodel.*;
import jalview.math.*;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
/**
* DOCUMENT ME!
float scalefactor = 1;
- AlignViewport av;
+ AlignmentViewport av;
AlignmentPanel ap;
// Fill the selected columns
ColumnSelection cs = av.getColumnSelection();
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+
int s;
if (cs != null)
{
if ((sel >= startx) && (sel <= endx))
{
- gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
+ gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
getHeight());
}
}
int scalestartx = (startx / 10) * 10;
FontMetrics fm = gg.getFontMetrics(av.getFont());
- int y = av.charHeight - fm.getDescent();
+ int y = avCharHeight - fm.getDescent();
if ((scalestartx % 10) == 0)
{
{
string = String.valueOf(av.getColumnSelection()
.adjustForHiddenColumns(i));
- if ((i - startx - 1) * av.charWidth > maxX)
+ if ((i - startx - 1) * avCharWidth > maxX)
{
- gg.drawString(string, (i - startx - 1) * av.charWidth, y);
- maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
+ gg.drawString(string, (i - startx - 1) * avCharWidth, y);
+ maxX = (i - startx + 1) * avCharWidth + fm.stringWidth(string);
}
- gg.drawLine(
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
y + 2,
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ ((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
y + (fm.getDescent() * 2));
-
}
else
{
- gg.drawLine(
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- y + fm.getDescent(),
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- y + (fm.getDescent() * 2));
+ gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
+ y + fm.getDescent(), ((i - startx - 1) * avCharWidth)
+ + (avCharWidth / 2), y + (fm.getDescent() * 2));
}
}
}
gg.fillPolygon(new int[]
- { res * av.charWidth - av.charHeight / 4,
- res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+ { res * avCharWidth - avCharHeight / 4,
+ res * avCharWidth + avCharHeight / 4, res * avCharWidth },
new int[]
- { y - av.charHeight / 2, y - av.charHeight / 2, y + 8 },
+ { y - avCharHeight / 2, y - avCharHeight / 2, y + 8 },
3);
}
if (reveal != null && reveal[0] > startx && reveal[0] < endx)
{
gg.drawString(MessageManager.getString("label.reveal_columns"),
- reveal[0] * av.charWidth, 0);
+ reveal[0] * avCharWidth, 0);
}
}
public SeqCanvas(AlignmentPanel ap)
{
this.av = ap.av;
+ updateViewport();
fr = new FeatureRenderer(ap);
sr = new SequenceRenderer(av);
setLayout(new BorderLayout());
return fr;
}
+ int charHeight = 0, charWidth = 0;
+
+ private void updateViewport()
+ {
+ charHeight = av.getCharHeight();
+ charWidth = av.getCharWidth();
+ }
/**
* DOCUMENT ME!
*
* @param ypos
* DOCUMENT ME!
*/
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
+ updateViewport();
int scalestartx = startx - (startx % 10) + 10;
g.setColor(Color.black);
-
// NORTH SCALE
for (int i = scalestartx; i < endx; i += 10)
{
value = av.getColumnSelection().adjustForHiddenColumns(value);
}
- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
- ypos - (av.charHeight / 2));
+ g.drawString(String.valueOf(value), (i - startx - 1) * charWidth,
+ ypos - (charHeight / 2));
- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- (ypos + 2) - (av.charHeight / 2),
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
+ (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
+ + (charWidth / 2),
ypos - 2);
}
}
void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
+ ypos += charHeight;
if (av.hasHiddenColumns())
{
if (value != -1)
{
int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- - av.charWidth / 2;
- g.drawString(value + "", x, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ - charWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * charHeight))
+ - (charHeight / 5));
}
}
}
*/
void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
- ypos += av.charHeight;
+ ypos += charHeight;
if (av.hasHiddenColumns())
{
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
+ - (charHeight / 5));
}
}
}
}
fastpainting = true;
fastPaint = true;
-
- gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
- imgWidth, imgHeight, -horizontal * av.charWidth, -vertical
- * av.charHeight);
+ updateViewport();
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
int sr = av.startRes;
int er = av.endRes;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
er++;
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * charWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
}
else
{
- transY = imgHeight - (vertical * av.charHeight);
+ transY = imgHeight - (vertical * charHeight);
}
}
else if (vertical < 0)
// Set this to false to force a full panel paint
public void paintComponent(Graphics g)
{
+ updateViewport();
BufferedImage lcimg = img; // take reference since other threads may null
// img and call later.
super.paintComponent(g);
imgWidth = getWidth();
imgHeight = getHeight();
- imgWidth -= (imgWidth % av.charWidth);
- imgHeight -= (imgHeight % av.charHeight);
+ imgWidth -= (imgWidth % charWidth);
+ imgHeight -= (imgHeight % charHeight);
if ((imgWidth < 1) || (imgHeight < 1))
{
LABEL_EAST = 0;
LABEL_WEST = 0;
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+ return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
}
/**
public void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
+ updateViewport();
AlignmentI al = av.getAlignment();
FontMetrics fm = getFontMetrics(av.getFont());
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += charHeight;
}
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- int cHeight = av.getAlignment().getHeight() * av.charHeight;
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
av.setWrappedWidth(cWidth);
g.setFont(av.getFont());
g.setColor(Color.black);
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
drawWestScale(g, startRes, endx, ypos);
}
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
g.translate(canvasWidth - LABEL_EAST, 0);
drawEastScale(g, startRes, endx, ypos);
g.translate(LABEL_WEST, 0);
- if (av.scaleAboveWrapped)
+ if (av.getScaleAboveWrapped())
{
drawNorthScale(g, startRes, endx, ypos);
}
- if (av.hasHiddenColumns() && av.showHiddenMarkers)
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
g.setColor(Color.blue);
int res;
}
gg.fillPolygon(new int[]
- { res * av.charWidth - av.charHeight / 4,
- res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+ { res * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth },
new int[]
- { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
- ypos - (av.charHeight / 2) + 8 }, 3);
+ { ypos - (charHeight / 2), ypos - (charHeight / 2),
+ ypos - (charHeight / 2) + 8 }, 3);
}
}
if (clip == null)
{
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+ g.setClip(0, 0, cWidth * charWidth, canvasHeight);
}
else
{
- g.setClip(0, (int) clip.getBounds().getY(), cWidth * av.charWidth,
+ g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
(int) clip.getBounds().getHeight());
}
int startSeq,
int endSeq, int offset)
{
+ updateViewport();
if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
int blockStart = startRes;
int blockEnd = endRes;
- for (int i = 0; regions != null && i < regions.size(); i++)
+ for (int[] region : regions)
{
- int[] region = regions.get(i);
int hideStart = region[0];
int hideEnd = region[1];
blockEnd = hideStart - 1;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
{
g1.setColor(Color.blue);
- g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
- 0 + offset, (blockEnd - blockStart + 1) * av.charWidth
- - 1, (endSeq - startSeq) * av.charHeight + offset);
+ g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
+ (endSeq - startSeq) * charHeight + offset);
}
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
blockStart = hideEnd + 1;
}
if (screenY <= (endRes - startRes))
{
blockEnd = blockStart + (endRes - startRes) - screenY;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * charWidth, 0);
}
}
// int startRes, int endRes, int startSeq, int endSeq, int x, int y,
// int x1, int x2, int y1, int y2, int startx, int starty,
- void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
+ private void draw(Graphics g, int startRes, int endRes, int startSeq,
+ int endSeq,
int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.renderGaps);
+ sr.prepare(g, av.isRenderGaps());
SequenceI nextSeq;
continue;
}
sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+ startRes, endRes, offset + ((i - startSeq) * charHeight));
if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * av.charHeight));
+ + ((i - startSeq) * charHeight));
}
// / Highlight search Results once all sequences have been drawn
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
visibleResults[r + 1], (visibleResults[r] - startRes)
- * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
}
}
}
if (av.cursorMode && cursorY == i && cursorX >= startRes
&& cursorX <= endRes)
{
- sr.drawCursor(nextSeq, cursorX,
- (cursorX - startRes) * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
}
}
int sy = -1;
int ex = -1;
int groupIndex = -1;
- int visWidth = (endRes - startRes + 1) * av.charWidth;
+ int visWidth = (endRes - startRes + 1) * charWidth;
if ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
for (i = startSeq; i < endSeq; i++)
{
- sx = (group.getStartRes() - startRes) * av.charWidth;
- sy = offset + ((i - startSeq) * av.charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
+ sx = (group.getStartRes() - startRes) * charWidth;
+ sy = offset + ((i - startSeq) * charHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
if (sx + ex < 0 || sx > visWidth)
{
continue;
}
- if ((sx <= (endRes - startRes) * av.charWidth)
+ if ((sx <= (endRes - startRes) * charWidth)
&& group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i)))
{
&& !group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i + 1)))
{
- bottom = sy + av.charHeight;
+ bottom = sy + charHeight;
}
if (!inGroup)
ex = visWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * charWidth;
}
if (top != -1)
if (inGroup)
{
- sy = offset + ((i - startSeq) * av.charHeight);
+ sy = offset + ((i - startSeq) * charHeight);
if (sx >= 0 && sx < visWidth)
{
g.drawLine(sx, oldY, sx, sy);
{
ex = visWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * charWidth;
}
if (top != -1)
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.structure.SelectionSource;
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.Color;
int res = 0;
int x = evt.getX();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap
+ seqCanvas.getAnnotationHeight();
int y = evt.getY();
int seq = 0;
int y = evt.getY();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap
+ seqCanvas.getAnnotationHeight();
y -= hgap;
return seq;
}
+ /**
+ * When all of a sequence of edits are complete, put the resulting edit list
+ * on the history stack (undo list), and reset flags for editing in progress.
+ */
void endEditing()
{
- if (editCommand != null && editCommand.getSize() > 0)
+ try
+ {
+ if (editCommand != null && editCommand.getSize() > 0)
+ {
+ ap.alignFrame.addHistoryItem(editCommand);
+ av.firePropertyChange("alignment", null, av.getAlignment()
+ .getSequences());
+ }
+ } finally
{
- ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null, av.getAlignment()
- .getSequences());
+ /*
+ * Tidy up come what may...
+ */
+ startseq = -1;
+ lastres = -1;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = null;
+ editCommand = null;
}
-
- startseq = -1;
- lastres = -1;
- editingSeqs = false;
- groupEditing = false;
- keyboardNo1 = null;
- keyboardNo2 = null;
- editCommand = null;
}
void setCursorRow()
}
endEditing();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
ap.scrollToWrappedVisible(seqCanvas.cursorX);
}
{
ap.scrollUp(false);
}
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
while (seqCanvas.cursorX < av.getColumnSelection()
.adjustForHiddenColumns(av.startRes))
seqCanvas.revalidate();
}
}
+ setStatusMessage(results);
seqCanvas.highlightSearchResults(results);
}
@Override
+ public VamsasSource getVamsasSource()
+ {
+ return this.ap == null ? null : this.ap.av;
+ }
+ @Override
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
*/
int setStatusMessage(SequenceI sequence, int res, int seq)
{
- int pos = -1;
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
- + sequence.getName());
+ StringBuilder text = new StringBuilder(32);
- Object obj = null;
+ /*
+ * Sequence number (if known), and sequence name.
+ */
+ String seqno = seq == -1 ? "" : " " + (seq + 1);
+ text.append("Sequence" + seqno + " ID: " + sequence.getName());
+
+ String residue = null;
+ /*
+ * Try to translate the display character to residue name (null for gap).
+ */
+ final String displayChar = String.valueOf(sequence.getCharAt(res));
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
- + "");
- if (obj != null)
+ residue = ResidueProperties.nucleotideName.get(displayChar);
+ if (residue != null)
{
- text.append(" Nucleotide: ");
+ text.append(" Nucleotide: ").append(residue);
}
}
else
{
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
- if (obj != null)
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ResidueProperties.aa2Triplet.get(displayChar);
+ if (residue != null)
{
- text.append(" Residue: ");
+ text.append(" Residue: ").append(residue);
}
}
- if (obj != null)
+ int pos = -1;
+ if (residue != null)
{
pos = sequence.findPosition(res);
- if (obj != "")
- {
- text.append(obj + " (" + pos + ")");
- }
+ text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
return pos;
}
/**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ */
+ private void setStatusMessage(SearchResults results)
+ {
+ List<Match> matches = results.getResults();
+ if (!matches.isEmpty())
+ {
+ Match m = matches.get(0);
+ SequenceI seq = m.getSequence();
+ int sequenceIndex = this.av.getAlignment().findIndex(seq);
+
+ /*
+ * Convert position in sequence (base 1) to sequence character array index
+ * (base 0)
+ */
+ int start = m.getStart() - 1;
+ setStatusMessage(seq, start, sequenceIndex);
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @param evt
{
if (mouseWheelPressed)
{
- int oldWidth = av.charWidth;
+ int oldWidth = av.getCharWidth();
// Which is bigger, left-right or up-down?
if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
fontSize = 1;
}
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
+ av.setFont(
+ new Font(av.font.getName(), av.font.getStyle(), fontSize),
+ true);
+ av.setCharWidth(oldWidth);
ap.fontChanged();
}
else
{
- if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+ if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
{
- av.charWidth--;
+ av.setCharWidth(av.getCharWidth() - 1);
}
else if (evt.getX() > lastMousePress.getX())
{
- av.charWidth++;
+ av.setCharWidth(av.getCharWidth() + 1);
}
ap.paintAlignment(false);
}
FontMetrics fm = getFontMetrics(av.getFont());
- av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
lastMousePress = evt.getPoint();
}
}
- StringBuffer message = new StringBuffer();
+ StringBuilder message = new StringBuilder(64);
if (groupEditing)
{
message.append("Edit group:");
}
else
{
- editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.getAlignment(), true);
+ appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
+ - lastres);
}
}
else
}
else
{
- editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
+ - startres);
}
}
}
else
{
- editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.getAlignment(), true);
+ appendEdit(Action.INSERT_GAP, new SequenceI[]
+ { seq }, lastres, startres - lastres);
}
}
else
{
for (int j = lastres; j > startres; j--)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ if (!Comparison.isGap(seq.getCharAt(startres)))
{
endEditing();
break;
int max = 0;
for (int m = startres; m < lastres; m++)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ if (!Comparison.isGap(seq.getCharAt(m)))
{
break;
}
if (max > 0)
{
- editCommand.appendEdit(Action.DELETE_GAP,
- new SequenceI[]
- { seq }, startres, max, av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, new SequenceI[]
+ { seq }, startres, max);
}
}
}
}
else
{
- editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[]
- { seq }, lastres, startres - lastres, av.getAlignment(), true);
+ appendEdit(Action.INSERT_NUC, new SequenceI[]
+ { seq }, lastres, startres - lastres);
}
}
}
}
}
- editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
- av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
- editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
- av.getAlignment(), true);
+ appendEdit(Action.INSERT_GAP, seq, j, 1);
}
+ /**
+ * Helper method to add and perform one edit action.
+ *
+ * @param action
+ * @param seq
+ * @param pos
+ * @param count
+ */
+ protected void appendEdit(Action action, SequenceI[] seq, int pos,
+ int count)
+ {
+
+ final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
+ av.getAlignment().getGapCharacter());
+
+ editCommand.appendEdit(edit, av.getAlignment(),
+ true, null);
+ }
+
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
- av.getAlignment(), true);
+ appendEdit(Action.DELETE_GAP, seq, j, 1);
- editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
- av.getAlignment(), true);
+ appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
}
/**
startWrapBlock = wrappedBlock;
- if (av.wrapAlignment && seq > av.getAlignment().getHeight())
+ if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.cannot_edit_annotations_in_wrapped_view"),
// handles selection messages...
// TODO: extend config options to allow user to control if selections may be
// shared between viewports.
- if (av == source
- || !av.followSelection
- || (av.isSelectionGroupChanged(false) || av
- .isColSelChanged(false))
- || (source instanceof AlignViewport && ((AlignViewport) source)
- .getSequenceSetId().equals(av.getSequenceSetId())))
+ boolean iSentTheSelection = (av == source
+ || (source instanceof AlignViewport && ((AlignmentViewport) source)
+ .getSequenceSetId().equals(av.getSequenceSetId())));
+ if (iSentTheSelection || !av.followSelection)
+ {
+ return;
+ }
+
+ /*
+ * Ignore the selection if there is one of our own pending.
+ */
+ if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ {
+ return;
+ }
+
+ /*
+ * Check for selection in a view of which this one is a dna/protein
+ * complement.
+ */
+ if (selectionFromTranslation(seqsel, colsel, source))
{
return;
}
+
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
// rules are: colsel is copied if there is a real intersection between
// sequence selection
- boolean repaint = false, copycolsel = true;
- // if (!av.isSelectionGroupChanged(false))
+ boolean repaint = false;
+ boolean copycolsel = true;
+
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize() > 0)
{
- SequenceGroup sgroup = null;
- if (seqsel != null && seqsel.getSize() > 0)
- {
- if (av.getAlignment() == null)
- {
- jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
- + av.getSequenceSetId() + " ViewId=" + av.getViewId()
- + " 's alignment is NULL! returning immediatly.");
- return;
- }
- sgroup = seqsel.intersect(av.getAlignment(),
- (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
- if ((sgroup == null || sgroup.getSize() == 0)
- || (colsel == null || colsel.size() == 0))
- {
- // don't copy columns if the region didn't intersect.
- copycolsel = false;
- }
- }
- if (sgroup != null && sgroup.getSize() > 0)
+ if (av.getAlignment() == null)
{
- av.setSelectionGroup(sgroup);
+ jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediately.");
+ return;
}
- else
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
+ if ((sgroup == null || sgroup.getSize() == 0)
+ || (colsel == null || colsel.size() == 0))
{
- av.setSelectionGroup(null);
+ // don't copy columns if the region didn't intersect.
+ copycolsel = false;
}
- av.isSelectionGroupChanged(true);
- repaint = true;
}
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
+ {
+ av.setSelectionGroup(null);
+ }
+ av.isSelectionGroupChanged(true);
+ repaint = true;
+
if (copycolsel)
{
// the current selection is unset or from a previous message
av.isColSelChanged(true);
repaint = true;
}
+
if (copycolsel
&& av.hasHiddenColumns()
&& (av.getColumnSelection() == null || av.getColumnSelection()
{
System.err.println("Bad things");
}
- if (repaint)
+ if (repaint) // always true!
{
// probably finessing with multiple redraws here
PaintRefresher.Refresh(this, av.getSequenceSetId());
// ap.paintAlignment(false);
}
}
+
+ /**
+ * If this panel is a cdna/protein translation view of the selection source,
+ * tries to map the source selection to a local one, and returns true. Else
+ * returns false.
+ *
+ * @param seqsel
+ * @param colsel
+ * @param source
+ */
+ protected boolean selectionFromTranslation(SequenceGroup seqsel,
+ ColumnSelection colsel, SelectionSource source)
+ {
+ if (!(source instanceof AlignViewportI)) {
+ return false;
+ }
+ final AlignViewportI sourceAv = (AlignViewportI) source;
+ if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+ {
+ return false;
+ }
+
+ /*
+ * Map sequence selection
+ */
+ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
+ av.setSelectionGroup(sg);
+ av.isSelectionGroupChanged(true);
+
+ /*
+ * Map column selection
+ */
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+ av);
+ av.setColumnSelection(cs);
+ av.isColSelChanged(true);
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+
+ return true;
+ }
}
*/
package jalview.gui;
-import java.util.*;
-import java.util.List;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.seqfetcher.DbSourceProxy;
+
import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import com.stevesoft.pat.Regex;
public class SequenceFetcher extends JPanel implements Runnable
{
- // ASequenceFetcher sfetch;
+ JLabel dbeg = new JLabel();
+
+ JDatabaseTree database;
+
+ JButton databaseButt;
+
+ JLabel jLabel1 = new JLabel();
+
+ JCheckBox replacePunctuation = new JCheckBox();
+
+ JButton ok = new JButton();
+
+ JButton clear = new JButton();
+
+ JButton example = new JButton();
+
+ JButton close = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JTextArea textArea = new JTextArea();
+
+ JScrollPane jScrollPane1 = new JScrollPane();
+
+ JPanel jPanel2 = new JPanel();
+
+ JPanel jPanel3 = new JPanel();
+
+ JPanel jPanel4 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ BorderLayout borderLayout3 = new BorderLayout();
+
JInternalFrame frame;
IProgressIndicator guiWindow;
private static Thread initingThread = null;
+ int debounceTrap = 0;
/**
* Blocking method that initialises and returns the shared instance of the
* SequenceFetcher client
return sfetch;
}
+ private IProgressIndicator progressIndicator;
public SequenceFetcher(IProgressIndicator guiIndic)
{
- final IProgressIndicator guiWindow = guiIndic;
+ this.progressIndicator = guiIndic;
final SequenceFetcher us = this;
// launch initialiser thread
Thread sf = new Thread(new Runnable()
@Override
public void run()
{
- if (getSequenceFetcherSingleton(guiWindow) != null)
+ if (getSequenceFetcherSingleton(progressIndicator) != null)
{
- us.initGui(guiWindow);
+ us.initGui(progressIndicator);
}
else
{
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
ok_actionPerformed();
+ }
}
});
jPanel3.setLayout(borderLayout1);
databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- try
- {
- databaseButt.setText(database.getSelectedItem()
- + (database.getSelectedSources().size() > 1 ? " (and "
- + database.getSelectedSources().size()
- + " others)" : ""));
- String eq = database.getExampleQueries();
- dbeg.setText(MessageManager.formatMessage(
- "label.example_query_param", new String[]
- { eq }));
- boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
- for (DbSourceProxy dbs : database.getSelectedSources())
- {
- if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
- {
- enablePunct = false;
- break;
- }
- }
- replacePunctuation.setEnabled(enablePunct);
+ debounceTrap++;
+ String currentSelection = database.getSelectedItem();
- } catch (Exception ex)
+ if (!currentSelection.equalsIgnoreCase("pdb"))
{
- dbeg.setText("");
- replacePunctuation.setEnabled(true);
+ otherSourceAction();
}
- jPanel2.repaint();
+ if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
+ {
+ pdbSourceAction();
+ }
+
}
});
dbeg.setText("");
}
+ private void pdbSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new PDBSearchPanel(this);
+ frame.dispose();
+ }
+
+ private void otherSourceAction()
+ {
+ try
+ {
+ databaseButt.setText(database.getSelectedItem()
+ + (database.getSelectedSources().size() > 1 ? " (and "
+ + database.getSelectedSources().size() + " others)"
+ : ""));
+ String eq = database.getExampleQueries();
+ dbeg.setText(MessageManager.formatMessage(
+ "label.example_query_param", new String[]
+ { eq }));
+ boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+ for (DbSourceProxy dbs : database.getSelectedSources())
+ {
+ if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ {
+ enablePunct = false;
+ break;
+ }
+ }
+ replacePunctuation.setEnabled(enablePunct);
+
+ } catch (Exception ex)
+ {
+ dbeg.setText("");
+ replacePunctuation.setEnabled(true);
+ }
+ jPanel2.repaint();
+ }
+
protected void example_actionPerformed()
{
DbSourceProxy db = null;
jPanel3.repaint();
}
- JLabel dbeg = new JLabel();
-
- JDatabaseTree database;
-
- JButton databaseButt;
-
- JLabel jLabel1 = new JLabel();
-
- JCheckBox replacePunctuation = new JCheckBox();
-
- JButton ok = new JButton();
-
- JButton clear = new JButton();
-
- JButton example = new JButton();
-
- JButton close = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- JTextArea textArea = new JTextArea();
-
- JScrollPane jScrollPane1 = new JScrollPane();
-
- JPanel jPanel2 = new JPanel();
-
- JPanel jPanel3 = new JPanel();
-
- JPanel jPanel4 = new JPanel();
- BorderLayout borderLayout1 = new BorderLayout();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
- BorderLayout borderLayout3 = new BorderLayout();
public void close_actionPerformed(ActionEvent e)
{
if (al != null && al.getHeight() > 0)
{
+ if (title == null)
+ {
+ title = getDefaultRetrievalTitle();
+ }
if (alignFrame == null)
{
AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
// Alignments?
}
- if (title == null)
- {
- title = getDefaultRetrievalTitle();
- }
SequenceFeature[] sfs = null;
List<SequenceI> alsqs;
synchronized (alsqs = al.getSequences())
{
for (SequenceI sq : alsqs)
{
- if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
+ if ((sfs = sq.getSequenceFeatures()) != null)
{
if (sfs.length > 0)
{
}
else
{
- for (int i = 0; i < al.getHeight(); i++)
- {
- alignFrame.viewport.getAlignment().addSequence(
- al.getSequenceAt(i)); // this
- // also
- // creates
- // dataset
- // sequence
- // entries
- }
- alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
- .getHeight());
- alignFrame.viewport.getAlignment().getWidth();
- alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.getAlignment().getSequences());
+ alignFrame.viewport.addAlignment(al, title);
}
}
return al;
}
});
}
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
}
package jalview.gui;
import jalview.api.FeatureRenderer;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
*/
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
+ final static int CHAR_TO_UPPER = 'A' - 'a';
+
AlignViewport av;
FontMetrics fm;
// If EPS graphics, stringWidth will be a double, not an int
double dwidth = fm.getStringBounds("M", g).getWidth();
- monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av.charWidth == dwidth);
+ monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av
+ .getCharWidth() == dwidth);
this.renderGaps = renderGaps;
}
int length = seq.getLength();
int curStart = -1;
- int curWidth = av.charWidth;
+ int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = av
+ .getCharHeight();
Color tempColour = null;
{
if (tempColour != null)
{
- graphics.fillRect(av.charWidth * (curStart - start), y1,
- curWidth, av.charHeight);
+ graphics.fillRect(avWidth * (curStart - start), y1, curWidth,
+ avHeight);
}
graphics.setColor(resBoxColour);
curStart = i;
- curWidth = av.charWidth;
+ curWidth = avWidth;
tempColour = resBoxColour;
}
else
{
- curWidth += av.charWidth;
+ curWidth += avWidth;
}
i++;
}
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
- av.charHeight);
+ graphics.fillRect(avWidth * (curStart - start), y1, curWidth, avHeight);
}
*/
public void drawText(SequenceI seq, int start, int end, int y1)
{
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+ y1 += av.getCharHeight() - av.getCharHeight() / 5; // height/5 replaces pady
int charOffset = 0;
char s;
{
end = seq.getLength() - 1;
}
- graphics.setColor(av.textColour);
+ graphics.setColor(av.getTextColour());
- if (monospacedFont && av.showText && allGroups.length == 0
- && !av.getColourText() && av.thresholdTextColour == 0)
+ if (monospacedFont && av.getShowText() && allGroups.length == 0
+ && !av.getColourText() && av.getThresholdTextColour() == 0)
{
- if (av.renderGaps)
+ if (av.isRenderGaps())
{
graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
}
boolean getboxColour = false;
for (int i = start; i <= end; i++)
{
- graphics.setColor(av.textColour);
+ graphics.setColor(av.getTextColour());
getboxColour = false;
s = seq.getCharAt(i);
if (!renderGaps && jalview.util.Comparison.isGap(s))
}
}
- if (av.thresholdTextColour > 0)
+ if (av.getThresholdTextColour() > 0)
{
if (!getboxColour)
{
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
- + resBoxColour.getGreen() < av.thresholdTextColour)
+ + resBoxColour.getGreen() < av.getThresholdTextColour())
{
- graphics.setColor(av.textColour2);
+ graphics.setColor(av.getTextColour2());
}
}
if (av.getShowUnconserved())
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + av.getCharWidth()
* (i - start), y1);
}
}
}
+ /**
+ * Returns 'conservedChar' to represent the given position if the sequence
+ * character at that position is equal to the consensus (ignoring case), else
+ * returns the sequence character
+ *
+ * @param usesrep
+ * @param position
+ * @param sequenceChar
+ * @param conservedChar
+ * @return
+ */
private char getDisplayChar(final boolean usesrep, int position,
- char s, char c)
+ char sequenceChar, char conservedChar)
{
- // TODO - use currentSequenceGroup rather than alignemnt
+ // TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
.charAt(0);
- if (conschar != '-' && s == conschar)
+ if (conschar != '-'
+ && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
{
- s = c;
+ sequenceChar = conservedChar;
}
- return s;
+ return sequenceChar;
}
/**
public void drawHighlightedText(SequenceI seq, int start, int end,
int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.BLACK);
- graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
- av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth() * (end - start + 1),
+ av.getCharHeight());
graphics.setColor(Color.white);
char s = '~';
// Need to find the sequence position here.
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
for (int i = start; i <= end; i++)
{
s = seq.getCharAt(i);
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1
- + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady);
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + x1 + (av.getCharWidth() * (i - start)),
+ (y1 + av.getCharHeight()) - pady);
}
}
}
public void drawCursor(SequenceI seq, int res, int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
graphics.setColor(Color.white);
char s = seq.getCharAt(res);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ (y1 + av.getCharHeight()) - pady);
}
}
*/
package jalview.gui;
-import java.util.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Iterator;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.util.MessageManager;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
/**
* DOCUMENT ME!
}
else
{
- toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+ toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
}
if (allGroups != null && allGroups.hasNext())
{
while ((toChange = allGroups.next().cs) == null
&& allGroups.hasNext())
+ {
;
+ }
}
else
{
--- /dev/null
+package jalview.gui;
+
+import java.awt.Component;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.beans.PropertyVetoException;
+import java.util.Map.Entry;
+
+import javax.swing.AbstractAction;
+import javax.swing.InputMap;
+import javax.swing.JComponent;
+import javax.swing.JMenuItem;
+import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
+import jalview.datamodel.AlignmentI;
+import jalview.jbgui.GAlignFrame;
+import jalview.jbgui.GSplitFrame;
+import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.AlignmentViewport;
+
+/**
+ * An internal frame on the desktop that hosts a horizontally split view of
+ * linked DNA and Protein alignments. Additional views can be created in linked
+ * pairs, expanded to separate split frames, or regathered into a single frame.
+ * <p>
+ * (Some) operations on each alignment are automatically mirrored on the other.
+ * These include mouseover (highlighting), sequence and column selection,
+ * sequence ordering and sorting, and grouping, colouring and sorting by tree.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class SplitFrame extends GSplitFrame implements SplitContainerI
+{
+ private static final long serialVersionUID = 1L;
+
+ public SplitFrame(GAlignFrame top, GAlignFrame bottom)
+ {
+ super(top, bottom);
+ init();
+ }
+
+ /**
+ * Initialise this frame.
+ */
+ protected void init()
+ {
+ getTopFrame().setSplitFrame(this);
+ getBottomFrame().setSplitFrame(this);
+ getTopFrame().setVisible(true);
+ getBottomFrame().setVisible(true);
+
+ ((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
+ ((AlignFrame) getBottomFrame()).getViewport());
+
+ int width = ((AlignFrame) getTopFrame()).getWidth();
+ // about 50 pixels for the SplitFrame's title bar etc
+ int height = ((AlignFrame) getTopFrame()).getHeight()
+ + ((AlignFrame) getBottomFrame()).getHeight() + 50;
+ height = Math.min(height, Desktop.instance.getHeight() - 20);
+ // setSize(AlignFrame.DEFAULT_WIDTH, Desktop.instance.getHeight() - 20);
+ setSize(width, height);
+
+ adjustLayout();
+
+ addCloseFrameListener();
+
+ addKeyListener();
+
+ addKeyBindings();
+
+ addCommandListeners();
+ }
+
+ /**
+ * Set the top and bottom frames to listen to each others Commands (e.g. Edit,
+ * Order).
+ */
+ protected void addCommandListeners()
+ {
+ // TODO if CommandListener is only ever 1:1 for complementary views,
+ // may change broadcast pattern to direct messaging (more efficient)
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
+ ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
+ }
+
+ /**
+ * Do any tweaking and twerking of the layout wanted.
+ */
+ public void adjustLayout()
+ {
+ /*
+ * Ensure sequence ids are the same width for good alignment.
+ */
+ int w1 = ((AlignFrame) getTopFrame()).getViewport().getIdWidth();
+ int w2 = ((AlignFrame) getBottomFrame()).getViewport().getIdWidth();
+ int w3 = Math.max(w1, w2);
+ if (w1 != w3)
+ {
+ ((AlignFrame) getTopFrame()).getViewport().setIdWidth(w3);
+ }
+ if (w2 != w3)
+ {
+ ((AlignFrame) getBottomFrame()).getViewport().setIdWidth(w3);
+ }
+
+ /*
+ * Set the character width for protein to 3 times that for dna.
+ */
+ boolean scaleThreeToOne = true; // TODO a new Preference option?
+ if (scaleThreeToOne)
+ {
+ final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
+ final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
+ final AlignmentI topAlignment = topViewport.getAlignment();
+ final AlignmentI bottomAlignment = bottomViewport.getAlignment();
+ AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
+ : (bottomAlignment.isNucleotide() ? bottomViewport : null);
+ AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
+ : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
+ if (protein != null && cdna != null)
+ {
+ ViewStyleI vs = cdna.getViewStyle();
+ ViewStyleI vs2 = protein.getViewStyle();
+ vs2.setCharWidth(3 * vs.getCharWidth());
+ protein.setViewStyle(vs2);
+ }
+ }
+ }
+
+ /**
+ * Add a listener to tidy up when the frame is closed.
+ */
+ protected void addCloseFrameListener()
+ {
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent evt)
+ {
+ if (getTopFrame() instanceof AlignFrame)
+ {
+ ((AlignFrame) getTopFrame())
+ .closeMenuItem_actionPerformed(true);
+ }
+ if (getBottomFrame() instanceof AlignFrame)
+ {
+ ((AlignFrame) getBottomFrame())
+ .closeMenuItem_actionPerformed(true);
+ }
+ };
+ });
+ }
+
+ /**
+ * Add a key listener that delegates to whichever split component the mouse is
+ * in (or does nothing if neither).
+ */
+ protected void addKeyListener()
+ {
+ addKeyListener(new KeyAdapter() {
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ AlignFrame af = (AlignFrame) getFrameAtMouse();
+
+ /*
+ * Intercept and override any keys here if wanted.
+ */
+ if (!overrideKey(e, af))
+ {
+ if (af != null)
+ {
+ for (KeyListener kl : af.getKeyListeners())
+ {
+ kl.keyPressed(e);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ Component c = getFrameAtMouse();
+ if (c != null)
+ {
+ for (KeyListener kl : c.getKeyListeners())
+ {
+ kl.keyReleased(e);
+ }
+ }
+ }
+
+ });
+ }
+
+ /**
+ * Returns true if the key event is overriden and actioned (or ignored) here,
+ * else returns false, indicating it should be delegated to the AlignFrame's
+ * usual handler.
+ * <p>
+ * We can't handle Cmd-Key combinations here, instead this is done by
+ * overriding key bindings.
+ *
+ * @see addKeyOverrides
+ * @param e
+ * @param af
+ * @return
+ */
+ protected boolean overrideKey(KeyEvent e, AlignFrame af)
+ {
+ boolean actioned = false;
+ int keyCode = e.getKeyCode();
+ switch (keyCode)
+ {
+ case KeyEvent.VK_DOWN:
+ if (e.isAltDown() || !af.viewport.cursorMode)
+ {
+ /*
+ * Key down (or Alt-key-down in cursor mode) - move selected sequences
+ */
+ ((AlignFrame) getTopFrame()).moveSelectedSequences(false);
+ ((AlignFrame) getBottomFrame()).moveSelectedSequences(false);
+ actioned = true;
+ e.consume();
+ }
+ break;
+ case KeyEvent.VK_UP:
+ if (e.isAltDown() || !af.viewport.cursorMode)
+ {
+ /*
+ * Key up (or Alt-key-up in cursor mode) - move selected sequences
+ */
+ ((AlignFrame) getTopFrame()).moveSelectedSequences(true);
+ ((AlignFrame) getBottomFrame()).moveSelectedSequences(true);
+ actioned = true;
+ e.consume();
+ }
+ default:
+ }
+ return actioned;
+ }
+
+ /**
+ * Set key bindings (recommended for Swing over key accelerators).
+ */
+ private void addKeyBindings()
+ {
+ overrideDelegatedKeyBindings();
+
+ overrideImplementedKeyBindings();
+ }
+
+ /**
+ * Override key bindings with alternative action methods implemented in this
+ * class.
+ */
+ protected void overrideImplementedKeyBindings()
+ {
+ overrideFind();
+ overrideNewView();
+ overrideCloseView();
+ overrideExpandViews();
+ overrideGatherViews();
+ }
+
+ /**
+ * Replace Cmd-W close view action with our version.
+ */
+ protected void overrideCloseView()
+ {
+ AbstractAction action;
+ /*
+ * Ctrl-W / Cmd-W - close view or window
+ */
+ KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ closeView_actionPerformed();
+ }
+ };
+ overrideKeyBinding(key_cmdW, action);
+ }
+
+ /**
+ * Replace Cmd-T new view action with our version.
+ */
+ protected void overrideNewView()
+ {
+ /*
+ * Ctrl-T / Cmd-T open new view
+ */
+ KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ AbstractAction action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ newView_actionPerformed();
+ }
+ };
+ overrideKeyBinding(key_cmdT, action);
+ }
+
+ /**
+ * For now, delegates key events to the corresponding key accelerator for the
+ * AlignFrame that the mouse is in. Hopefully can be simplified in future if
+ * AlignFrame is changed to use key bindings rather than accelerators.
+ */
+ protected void overrideDelegatedKeyBindings()
+ {
+ if (getTopFrame() instanceof AlignFrame)
+ {
+ /*
+ * Get all accelerator keys in the top frame (the bottom should be
+ * identical) and override each one.
+ */
+ for (Entry<KeyStroke, JMenuItem> acc : ((AlignFrame) getTopFrame())
+ .getAccelerators().entrySet())
+ {
+ overrideKeyBinding(acc);
+ }
+ }
+ }
+
+ /**
+ * Overrides an AlignFrame key accelerator with our version which delegates to
+ * the action listener in whichever frame has the mouse (and does nothing if
+ * neither has).
+ *
+ * @param acc
+ */
+ private void overrideKeyBinding(Entry<KeyStroke, JMenuItem> acc)
+ {
+ final KeyStroke ks = acc.getKey();
+ InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED);
+ inputMap.put(ks, ks);
+ this.getActionMap().put(ks, new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Component c = getFrameAtMouse();
+ if (c != null && c instanceof AlignFrame)
+ {
+ for (ActionListener a : ((AlignFrame) c).getAccelerators()
+ .get(ks).getActionListeners())
+ {
+ a.actionPerformed(null);
+ }
+ }
+ }
+ });
+ }
+
+ /**
+ * Replace an accelerator key's action with the specified action.
+ *
+ * @param ks
+ */
+ protected void overrideKeyBinding(KeyStroke ks, AbstractAction action)
+ {
+ this.getActionMap().put(ks, action);
+ overrideMenuItem(ks, action);
+ }
+
+ /**
+ * Create and link new views (with matching names) in both panes.
+ * <p>
+ * Note this is _not_ multiple tabs, each hosting a split pane view, rather it
+ * is a single split pane with each split holding multiple tabs which are
+ * linked in pairs.
+ * <p>
+ * TODO implement instead with a tabbed holder in the SplitView, each tab
+ * holding a single JSplitPane. Would avoid a duplicated tab, at the cost of
+ * some additional coding.
+ */
+ protected void newView_actionPerformed()
+ {
+ AlignFrame topFrame = (AlignFrame) getTopFrame();
+ AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
+
+ AlignmentPanel newTopPanel = topFrame.newView(null, true);
+ AlignmentPanel newBottomPanel = bottomFrame.newView(null, true);
+
+ /*
+ * This currently (for the first new view only) leaves the top pane on tab 0
+ * but the bottom on tab 1. This results from 'setInitialTabVisible' echoing
+ * from the bottom back to the first frame. Next line is a fudge to work
+ * around this. TODO find a better way.
+ */
+ if (topFrame.getTabIndex() != bottomFrame.getTabIndex())
+ {
+ topFrame.setDisplayedView(newTopPanel);
+ }
+
+ newBottomPanel.av.viewName = newTopPanel.av.viewName;
+ newTopPanel.av.setCodingComplement(newBottomPanel.av);
+
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addCommandListener(newTopPanel.av);
+ ssm.addCommandListener(newBottomPanel.av);
+ }
+
+ /**
+ * Close the currently selected view in both panes. If there is only one view,
+ * close this split frame.
+ */
+ protected void closeView_actionPerformed()
+ {
+ int viewCount = ((AlignFrame) getTopFrame()).getAlignPanels().size();
+ if (viewCount < 2)
+ {
+ close();
+ return;
+ }
+
+ AlignmentPanel topPanel = ((AlignFrame) getTopFrame()).alignPanel;
+ AlignmentPanel bottomPanel = ((AlignFrame) getBottomFrame()).alignPanel;
+
+ ((AlignFrame) getTopFrame()).closeView(topPanel);
+ ((AlignFrame) getBottomFrame()).closeView(bottomPanel);
+
+ }
+
+ /**
+ * Close child frames and this split frame.
+ */
+ public void close()
+ {
+ ((AlignFrame) getTopFrame()).closeMenuItem_actionPerformed(true);
+ ((AlignFrame) getBottomFrame()).closeMenuItem_actionPerformed(true);
+ try
+ {
+ this.setClosed(true);
+ } catch (PropertyVetoException e)
+ {
+ // ignore
+ }
+ }
+
+ /**
+ * Replace AlignFrame 'expand views' action with SplitFrame version.
+ */
+ protected void overrideExpandViews()
+ {
+ KeyStroke key_X = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
+ AbstractAction action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ expandViews_actionPerformed();
+ }
+ };
+ overrideMenuItem(key_X, action);
+ }
+
+ /**
+ * Replace AlignFrame 'gather views' action with SplitFrame version.
+ */
+ protected void overrideGatherViews()
+ {
+ KeyStroke key_G = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
+ AbstractAction action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ gatherViews_actionPerformed();
+ }
+ };
+ overrideMenuItem(key_G, action);
+ }
+
+ /**
+ * Override the menu action associated with the keystroke in the child frames,
+ * replacing it with the given action.
+ *
+ * @param ks
+ * @param action
+ */
+ private void overrideMenuItem(KeyStroke ks, AbstractAction action)
+ {
+ overrideMenuItem(ks, action, getTopFrame());
+ overrideMenuItem(ks, action, getBottomFrame());
+ }
+
+ /**
+ * Override the menu action associated with the keystroke in one child frame,
+ * replacing it with the given action. Mwahahahaha.
+ *
+ * @param key
+ * @param action
+ * @param comp
+ */
+ private void overrideMenuItem(KeyStroke key, final AbstractAction action,
+ JComponent comp)
+ {
+ if (comp instanceof AlignFrame)
+ {
+ JMenuItem mi = ((AlignFrame) comp).getAccelerators().get(key);
+ if (mi != null)
+ {
+ for (ActionListener al : mi.getActionListeners())
+ {
+ mi.removeActionListener(al);
+ }
+ mi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ action.actionPerformed(e);
+ }
+ });
+ }
+ }
+ }
+
+ /**
+ * Expand any multiple views (which are always in pairs) into separate split
+ * frames.
+ */
+ protected void expandViews_actionPerformed()
+ {
+ Desktop.instance.explodeViews(this);
+ }
+
+ /**
+ * Gather any other SplitFrame views of this alignment back in as multiple
+ * (pairs of) views in this SplitFrame.
+ */
+ protected void gatherViews_actionPerformed()
+ {
+ Desktop.instance.gatherViews(this);
+ }
+
+ /**
+ * Returns the alignment in the complementary frame to the one given.
+ */
+ @Override
+ public AlignmentI getComplement(Object alignFrame)
+ {
+ if (alignFrame == this.getTopFrame())
+ {
+ return ((AlignFrame) getBottomFrame()).viewport.getAlignment();
+ }
+ else if (alignFrame == this.getBottomFrame())
+ {
+ return ((AlignFrame) getTopFrame()).viewport.getAlignment();
+ }
+ return null;
+ }
+
+ /**
+ * Returns the title of the complementary frame to the one given.
+ */
+ @Override
+ public String getComplementTitle(Object alignFrame)
+ {
+ if (alignFrame == this.getTopFrame())
+ {
+ return ((AlignFrame) getBottomFrame()).getTitle();
+ }
+ else if (alignFrame == this.getBottomFrame())
+ {
+ return ((AlignFrame) getTopFrame()).getTitle();
+ }
+ return null;
+ }
+
+ /**
+ * Set the 'other half' to hidden / revealed.
+ */
+ @Override
+ public void setComplementVisible(Object alignFrame, boolean show)
+ {
+ /*
+ * Hiding the AlignPanel suppresses unnecessary repaints
+ */
+ if (alignFrame == getTopFrame())
+ {
+ ((AlignFrame) getBottomFrame()).alignPanel.setVisible(show);
+ }
+ else if (alignFrame == getBottomFrame())
+ {
+ ((AlignFrame) getTopFrame()).alignPanel.setVisible(show);
+ }
+ super.setComplementVisible(alignFrame, show);
+ }
+
+ /**
+ * Replace Cmd-F Find action with our version. This is necessary because the
+ * 'default' Finder searches in the first AlignFrame it finds. We need it to
+ * search in the half of the SplitFrame that has the mouse.
+ */
+ protected void overrideFind()
+ {
+ /*
+ * Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
+ */
+ KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ AbstractAction action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Component c = getFrameAtMouse();
+ if (c != null && c instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) c;
+ new Finder(af.viewport, af.alignPanel);
+ }
+ }
+ };
+ overrideKeyBinding(key_cmdF, action);
+ }
+}
+
--- /dev/null
+/*
+
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.gui;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
+import java.awt.event.ItemEvent;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+
+/**
+ * Provides the behaviors for the Structure chooser Panel
+ *
+ * @author tcnofoegbu
+ *
+ */
+@SuppressWarnings("serial")
+public class StructureChooser extends GStructureChooser
+{
+ private boolean structuresDiscovered = false;
+
+ private SequenceI selectedSequence;
+
+ private SequenceI[] selectedSequences;
+
+ private IProgressIndicator progressIndicator;
+
+ private Collection<PDBResponseSummary> discoveredStructuresSet;
+
+ private PDBRestRequest lastPdbRequest;
+
+ private PDBRestClient pdbRestCleint;
+
+ private String selectedPdbFileName;
+
+ private boolean isValidPBDEntry;
+
+ public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+ AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.selectedSequence = selectedSeq;
+ this.selectedSequences = selectedSeqs;
+ this.progressIndicator = (ap == null) ? null : ap.alignFrame;
+ init();
+ }
+
+ /**
+ * Initializes parameters used by the Structure Chooser Panel
+ */
+ public void init()
+ {
+ Thread discoverPDBStructuresThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ long startTime = System.currentTimeMillis();
+ String msg = MessageManager.getString("status.fetching_db_refs");
+ updateProgressIndicator(msg, startTime);
+ fetchStructuresMetaData();
+ populateFilterComboBox();
+ updateProgressIndicator(null, startTime);
+ mainFrame.setVisible(true);
+ updateCurrentView();
+ }
+ });
+ discoverPDBStructuresThread.start();
+ }
+
+ /**
+ * Updates the progress indicator with the specified message
+ *
+ * @param message
+ * displayed message for the operation
+ * @param id
+ * unique handle for this indicator
+ */
+ public void updateProgressIndicator(String message, long id)
+ {
+ if (progressIndicator != null)
+ {
+ progressIndicator.setProgressBar(message, id);
+ }
+ }
+
+ /**
+ * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
+ * selection group
+ */
+ public void fetchStructuresMetaData()
+ {
+ long startTime = System.currentTimeMillis();
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+
+ discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ for (SequenceI seq : selectedSequences)
+ {
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ discoveredStructuresSet.addAll(resultList.getSearchSummary());
+ updateSequenceDbRef(seq, resultList.getSearchSummary());
+ }
+ }
+
+ int noOfStructuresFound = 0;
+ if (discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty())
+ {
+ tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
+ discoveredStructuresSet));
+ structuresDiscovered = true;
+ noOfStructuresFound = discoveredStructuresSet.size();
+ }
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+ + " Found (" + totalTime + ")");
+ }
+
+ /**
+ * Update the DBRef entry for a given sequence with values retrieved from
+ * PDBResponseSummary
+ *
+ * @param seq
+ * the Sequence to update its DBRef entry
+ * @param responseSummaries
+ * a collection of PDBResponseSummary
+ */
+ public void updateSequenceDbRef(SequenceI seq,
+ Collection<PDBResponseSummary> responseSummaries)
+ {
+ for (PDBResponseSummary response : responseSummaries)
+ {
+ PDBEntry newEntry = new PDBEntry();
+ newEntry.setId(response.getPdbId());
+ newEntry.setType("PDB");
+ seq.getDatasetSequence().addPDBId(newEntry);
+ }
+ }
+
+ /**
+ * Builds a query string for a given sequences using its DBRef entries
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+ @SuppressWarnings("unchecked")
+ public static String buildQuery(SequenceI seq)
+ {
+ String query = seq.getName();
+ StringBuilder queryBuilder = new StringBuilder();
+ int count = 0;
+
+ if (seq.getPDBId() != null)
+ {
+ for (PDBEntry entry : (Vector<PDBEntry>) seq.getPDBId())
+ {
+ queryBuilder.append("text:").append(entry.getId()).append(" OR ");
+ }
+ }
+
+ if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+ {
+ for (DBRefEntry dbRef : seq.getDBRef())
+ {
+ queryBuilder.append("text:")
+ .append(dbRef.getAccessionId().replaceAll("GO:", ""))
+ .append(" OR ");
+ ++count;
+ if (count > 10)
+ {
+ break;
+ }
+ }
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ query = queryBuilder.toString().substring(5, endIndex);
+ }
+ return query;
+ }
+
+ /**
+ * Filters a given list of discovered structures based on supplied argument
+ *
+ * @param fieldToFilterBy
+ * the field to filter by
+ */
+ public void filterResultSet(final String fieldToFilterBy)
+ {
+ Thread filterThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ long startTime = System.currentTimeMillis();
+ try
+ {
+ lbl_loading.setVisible(true);
+
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+ Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ for (SequenceI seq : selectedSequences)
+ {
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint
+ .executeRequest(pdbRequest);
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
+
+ if (!filteredResponse.isEmpty())
+ {
+ final int filterResponseCount = filteredResponse.size();
+ Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ tbl_summary.setModel(PDBRestResponse.getTableModel(
+ lastPdbRequest, reorderedStructuresSet));
+
+ // Update table selection model here
+ tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+
+ }
+
+ lbl_loading.setVisible(false);
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ mainFrame.setTitle("Structure Chooser - Filter time ("
+ + totalTime + ")");
+
+ validateSelections();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ });
+ filterThread.start();
+ }
+
+
+ /**
+ * Handles action event for btn_pdbFromFile
+ */
+ public void pdbFromFile_actionPerformed()
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle(MessageManager.formatMessage(
+ "label.select_pdb_file_for", new String[]
+ { selectedSequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { selectedSequence.getDisplayId(false) }));
+
+ int value = chooser.showOpenDialog(null);
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ selectedPdbFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ validateSelections();
+ }
+ }
+
+ /**
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
+ */
+ protected void populateFilterComboBox()
+ {
+ if (isStructuresDiscovered())
+ {
+ cmb_filterOption.addItem(new FilterOption("Best Quality",
+ PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
+ PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Resolution",
+ PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
+ PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
+ PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
+ PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
+ }
+ cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
+ VIEWS_ENTER_ID));
+ cmb_filterOption.addItem(new FilterOption("From File", "-",
+ VIEWS_FROM_FILE));
+ }
+
+ /**
+ * Updates the displayed view based on the selected filter option
+ */
+ protected void updateCurrentView()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ layout_switchableViews.show(pnl_switchableViews,
+ selectedFilterOpt.getView());
+ String filterTitle = mainFrame.getTitle();
+ mainFrame.setTitle(frameTitle);
+ chk_invertFilter.setVisible(false);
+ if (selectedFilterOpt.getView() == VIEWS_FILTER)
+ {
+ mainFrame.setTitle(filterTitle);
+ chk_invertFilter.setVisible(true);
+ filterResultSet(selectedFilterOpt.getValue());
+ }
+ else
+ {
+ idInputAssSeqPanel.loadCmbAssSeq();
+ fileChooserAssSeqPanel.loadCmbAssSeq();
+ }
+ validateSelections();
+ }
+
+ /**
+ * Validates user selection and activates the view button if all parameters
+ * are correct
+ */
+ public void validateSelections()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ btn_view.setEnabled(false);
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ if (tbl_summary.getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ validateAssociationEnterPdb();
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ validateAssociationFromFile();
+ }
+ }
+
+ /**
+ * Validates inputs from the Manual PDB entry panel
+ */
+ public void validateAssociationEnterPdb()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ if (selectedSequences.length == 1
+ || !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-"))
+ {
+ txt_search.setEnabled(true);
+ if (isValidPBDEntry)
+ {
+ btn_view.setEnabled(true);
+ lbl_pdbManualFetchStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ txt_search.setEnabled(false);
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ }
+ }
+
+ /**
+ * Validates inputs for the manual PDB file selection options
+ */
+ public void validateAssociationFromFile()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_fromFileStatus.setIcon(errorImage);
+ if (selectedSequences.length == 1
+ || (assSeqOpt != null
+ && !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-")))
+ {
+ btn_pdbFromFile.setEnabled(true);
+ if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+ {
+ btn_view.setEnabled(true);
+ lbl_fromFileStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ btn_pdbFromFile.setEnabled(false);
+ lbl_fromFileStatus.setIcon(errorImage);
+ }
+ }
+
+ @Override
+ public void cmbAssSeqStateChanged()
+ {
+ validateSelections();
+ }
+
+ /**
+ * Handles the state change event for the 'filter' combo-box and 'invert'
+ * check-box
+ */
+ @Override
+ protected void stateChanged(ItemEvent e)
+ {
+ if (e.getSource() instanceof JCheckBox)
+ {
+ updateCurrentView();
+ }
+ else
+ {
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ {
+ updateCurrentView();
+ }
+ }
+
+ }
+
+ /**
+ * Handles action event for btn_ok
+ */
+ @Override
+ public void ok_ActionPerformed()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
+ lastPdbRequest.getWantedFields(), true);
+ int[] selectedRows = tbl_summary.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ for (int summaryRow : selectedRows)
+ {
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ .toString();
+ PDBEntry pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType("PDB");
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pdbEntriesToView,
+ ap.av.collateForPDB(pdbEntriesToView));
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ PDBEntry pdbEntry = new PDBEntry();
+ pdbEntry.setId(txt_search.getText());
+ pdbEntry.setType("PDB");
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ PDBEntry[] pdbEntriesToView = new PDBEntry[]
+ { pdbEntry };
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pdbEntriesToView,
+ ap.av.collateForPDB(pdbEntriesToView));
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+ selectedSequence, true, Desktop.instance);
+ }
+ mainFrame.dispose();
+ }
+
+ /**
+ * Populates the combo-box used in associating manually fetched structures to
+ * a unique sequence when more than one sequence selection is made.
+ */
+ public void populateCmbAssociateSeqOptions(
+ JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
+ {
+ cmb_assSeq.removeAllItems();
+ cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
+ null));
+ // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
+ lbl_associateSeq.setVisible(false);
+ if (selectedSequences.length > 1)
+ {
+ for (SequenceI seq : selectedSequences)
+ {
+ cmb_assSeq.addItem(new AssociateSeqOptions(seq));
+ }
+ }
+ else
+ {
+ String seqName = selectedSequence.getDisplayId(false);
+ seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
+ lbl_associateSeq.setText(seqName);
+ lbl_associateSeq.setVisible(true);
+ cmb_assSeq.setVisible(false);
+ }
+ }
+
+ public boolean isStructuresDiscovered()
+ {
+ return structuresDiscovered;
+ }
+
+ public void setStructuresDiscovered(boolean structuresDiscovered)
+ {
+ this.structuresDiscovered = structuresDiscovered;
+ }
+
+ public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ {
+ return discoveredStructuresSet;
+ }
+
+ @Override
+ protected void txt_search_ActionPerformed()
+ {
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.PDB_ID);
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(txt_search.getText() + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
+ }
+ validateSelections();
+ }
+
+ @Override
+ public void tabRefresh()
+ {
+ if (selectedSequences != null)
+ {
+ Thread refreshThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ fetchStructuresMetaData();
+ filterResultSet(((FilterOption) cmb_filterOption
+ .getSelectedItem()).getValue());
+ }
+ });
+ refreshThread.start();
+ }
+ }
+
+}
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.JColorChooser;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
public class TextColourChooser
{
AlignmentPanel ap;
int original1, original2, originalThreshold;
if (sg == null)
{
- original1 = ap.av.textColour.getRGB();
- original2 = ap.av.textColour2.getRGB();
- originalThreshold = ap.av.thresholdTextColour;
+ original1 = ap.av.getTextColour().getRGB();
+ original2 = ap.av.getTextColour2().getRGB();
+ originalThreshold = ap.av.getThresholdTextColour();
}
else
{
{
if (sg == null)
{
- ap.av.textColour = new Color(original1);
- ap.av.textColour2 = new Color(original2);
- ap.av.thresholdTextColour = originalThreshold;
+ ap.av.setTextColour(new Color(original1));
+ ap.av.setTextColour2(new Color(original2));
+ ap.av.setThresholdTextColour(originalThreshold);
}
else
{
{
if (sg == null)
{
- ap.av.textColour = col;
+ ap.av.setTextColour(col);
if (ap.av.getColourAppliesToAllGroups())
{
setGroupTextColour();
{
if (sg == null)
{
- ap.av.textColour2 = col;
+ ap.av.setTextColour2(col);
if (ap.av.getColourAppliesToAllGroups())
{
setGroupTextColour();
{
if (sg == null)
{
- ap.av.thresholdTextColour = value;
+ ap.av.setThresholdTextColour(value);
if (ap.av.getColourAppliesToAllGroups())
{
setGroupTextColour();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- sg.textColour = ap.av.textColour;
- sg.textColour2 = ap.av.textColour2;
- sg.thresholdTextColour = ap.av.thresholdTextColour;
+ sg.textColour = ap.av.getTextColour();
+ sg.textColour2 = ap.av.getTextColour2();
+ sg.thresholdTextColour = ap.av.getThresholdTextColour();
}
}
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.SelectionSource;
+import jalview.util.Format;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JColorChooser;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
* @version $Revision$
*/
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
- Printable, MouseMotionListener
+ Printable, MouseMotionListener, SelectionSource
{
/** DOCUMENT ME!! */
public static final String PLACEHOLDER = " * ";
if (node.element() instanceof SequenceI)
{
- SequenceI seq = (SequenceI) ((SequenceNode) node).element();
+ SequenceI seq = (SequenceI) node.element();
if (av.getSequenceColour(seq) == Color.white)
{
Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2,
charWidth, charHeight);
- nameHash.put((SequenceI) node.element(), rect);
+ nameHash.put(node.element(), rect);
// Colour selected leaves differently
SequenceGroup selected = av.getSelectionGroup();
if ((selected != null)
&& selected.getSequences(null).contains(
- (SequenceI) node.element()))
+ node.element()))
{
g.setColor(Color.gray);
int xend = (int) (height * scale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
- g.setColor(((SequenceNode) node).color.darker());
+ g.setColor(node.color.darker());
// Draw horizontal line
g.drawLine(xstart, ypos, xend, ypos);
{
for (int a = 0; a < aps.length; a++)
{
- aps[a].av.setSequenceColour((SequenceI) node.element(), c);
+ final SequenceI seq = (SequenceI) node.element();
+ aps[a].av.setSequenceColour(seq, c);
}
}
}
labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
- float wscale = (float) (width - labelLength - (offx * 2))
+ float wscale = (width - labelLength - (offx * 2))
/ tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
g2.setColor(Color.gray);
}
- int x = (int) ((threshold * (float) (getWidth() - labelLength - (2 * offx))) + offx);
+ int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx);
g2.drawLine(x, 0, x, getHeight());
}
AlignmentPanel[] aps = getAssociatedPanels();
+ // TODO push calls below into a single AlignViewportI method?
+ // see also AlignViewController.deleteGroups
for (int a = 0; a < aps.length; a++)
{
aps[a].av.setSelectionGroup(null);
aps[a].av.getAlignment().deleteAllGroups();
aps[a].av.clearSequenceColours();
}
+ if (av.getCodingComplement() != null)
+ {
+ av.getCodingComplement().setSelectionGroup(null);
+ av.getCodingComplement().getAlignment().deleteAllGroups();
+ av.getCodingComplement().clearSequenceColours();
+ }
colourGroups();
}
if (cs != null)
{
cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.getIgnoreGapsConsensus());
+ av.isIgnoreGapsConsensus());
}
}
sg.cs = cs;
// sg.recalcConservation();
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
+
for (int a = 0; a < aps.length; a++)
{
if (aps[a].av.getGlobalColourScheme() != null
aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
}
+
+ // TODO can we push all of the below into AlignViewportI?
+ av.getAlignment().addGroup(sg);
+ final AlignViewportI codingComplement = av.getCodingComplement();
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+ codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq, col.brighter());
+ }
+ }
+ }
}
+
// notify the panel to redo any group specific stuff.
for (int a = 0; a < aps.length; a++)
{
// to any Jmols listening in
}
+ if (av.getCodingComplement() != null)
+ {
+ ((AlignViewport) av.getCodingComplement()).getAlignPanel().updateAnnotation();
+ /*
+ * idPanel. repaint ()
+ */
+ }
}
/**
import jalview.jbgui.GTreePanel;
import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Font;
import java.awt.Graphics;
return treeCanvas.av.getAlignment();
}
- public AlignViewport getViewPort()
+ public AlignmentViewport getViewPort()
{
return treeCanvas.av;
}
associateLeavesMenu.add(item);
}
- final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ "label.all_views");
buttonGroup.add(itemf);
itemf.setSelected(treeCanvas.applyToAllViews);
itemf.addActionListener(new ActionListener()
av.setCurrentTree(tree);
if (av.getSortByTree())
{
- sortByTree_actionPerformed(null);
+ sortByTree_actionPerformed();
}
}
}
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params", new String[]
+ "label.original_data_for_params", new Object[]
{ this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
*
* @param e
*/
- public void sortByTree_actionPerformed(ActionEvent e)
+ @Override
+ public void sortByTree_actionPerformed()
{
if (treeCanvas.applyToAllViews)
public CommandI sortAlignmentIn(AlignmentPanel ap)
{
- AlignViewport av = ap.av;
+ AlignmentViewport av = ap.av;
SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
AlignmentSorter.sortByTree(av.getAlignment(), tree);
CommandI undo;
}
}else{
for (int i = 0; i < 24; i++){
- JButton button = (JButton) upperCaseButtons.get(i);
+ JButton button = upperCaseButtons.get(i);
newColours[i] = button.getBackground();
}
}
}
}else{
for (int i = 0; i < 23; i++){
- JButton button = (JButton) lowerCaseButtons.get(i);
+ JButton button = lowerCaseButtons.get(i);
newColours[i] = button.getBackground();
}
}
if (ap != null)
{
- ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
return ucs;
import jalview.structure.VamsasListener;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.IOException;
-import java.util.Enumeration;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
public void end_session(boolean promptUser)
{
if (!inSession())
+ {
throw new Error(MessageManager.getString("error.jalview_no_connected_vamsas_session"));
+ }
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
{
int i = -1;
- public void mouseOver(SequenceI seq, int index,
+ @Override
+ public void mouseOverSequence(SequenceI seq, int index,
VamsasSource source)
{
if (jv2vobj == null)
+ {
return;
+ }
if (seq != last || i != index)
{
VorbaId v = (VorbaId) jv2vobj.get(seq);
AlignmentI visal = null;
if (source instanceof AlignViewport)
{
- visal = ((AlignViewport) source).getAlignment();
+ visal = ((AlignmentViewport) source).getAlignment();
}
SelectionMessage sm = null;
if ((seqsel == null || seqsel.getSize() == 0)
{
// the empty selection.
sm = new SelectionMessage("jalview", new String[]
- { ((AlignViewport) source).getSequenceSetId() }, null,
+ { ((AlignmentViewport) source).getSequenceSetId() }, null,
true);
}
else
{
// gather selected columns outwith the sequence positions
// too
- Enumeration cols = colsel.getSelected().elements();
- while (cols.hasMoreElements())
+ for (Object obj : colsel.getSelected())
{
- int ival = ((Integer) cols.nextElement()).intValue();
+ int ival = ((Integer) obj).intValue();
Pos p = new Pos();
p.setI(ival + 1);
range.addPos(p);
*/
protected void updateWebServiceMenus()
{
- for (AlignFrame alignFrame : Desktop.getAlignframes())
+ for (AlignFrame alignFrame : Desktop.getAlignFrames())
{
alignFrame.BuildWebServiceMenu();
}
* List of valid format strings used in the isValidFormat method
*/
public static final String[] READABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, "HTML" }; // ,
- // "SimpleBLAST"
- // };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+ "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, "HTML" };
+
+ /**
+ * List of readable format file extensions by application in order
+ * corresponding to READABLE_FNAMES
+ */
+ public static final String[] READABLE_EXTENSIONS = new String[]
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, "jar,jvp", "html" };
+
+ /**
+ * List of readable formats by application in order corresponding to
+ * READABLE_EXTENSIONS
+ */
+ public static final String[] READABLE_FNAMES = new String[]
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
+ "RNAML", PhylipFile.FILE_DESC, "Jalview", "HTML" };
/**
* List of valid format strings for use by callers of the formatSequences
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
PhylipFile.FILE_DESC, "Jalview" };
- /**
- * List of readable format file extensions by application in order
- * corresponding to READABLE_FNAMES
- */
- public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT,
- "html" }; // ".blast"
-
- /**
- * List of readable formats by application in order corresponding to
- * READABLE_EXTENSIONS
- */
- public static final String[] READABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm", "RNAML", PhylipFile.FILE_DESC, "HTML" };// ,
-
- // "SimpleBLAST"
- // };
-
public static String INVALID_CHARACTERS = "Contains invalid characters";
// TODO: make these messages dynamic
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.json.binding.v1.BioJsAlignmentPojo;
import jalview.json.binding.v1.BioJsSeqPojo;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.io.BufferedReader;
public class BioJsHTMLOutput
{
- private AlignViewport av;
+ private AlignmentViewport av;
private jalview.api.FeatureRenderer fr;
seqPojo.setName(name.toString());
seqPojo.setSeq(seq.getSequenceAsString());
- SequenceFeature[] seqFeatures = seq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
if (seqFeatures != null)
{
ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
}
if (viewport != null)
{
- // TODO: create undo object for this JAL-1101
- for (int i = 0; i < al.getHeight(); i++)
- {
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
- }
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.addAlignment(al, title);
}
else
{
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* DOCUMENT ME!
super(source);
}
- {
- // TODO Auto-generated constructor stub
- }
-
/**
* DOCUMENT ME!
*/
*/
package jalview.io;
+
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
}
// ADD NON POSITIONAL SEQUENCE INFO
- SequenceFeature[] features = ds.getSequenceFeatures();
+ SequenceFeature[] features = sequence.getSequenceFeatures();
if (showNpFeats && features != null)
{
for (int i = 0; i < features.length; i++)
{
feature = ds.getSequenceFeatures()[0].type;
}
+ // ?bug - feature may still have previous loop value
String key = type2id(feature);
if (key == null)
import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.io.IOException;
import java.util.Enumeration;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.List;
+import java.util.Set;
import java.util.Vector;
import java.util.jar.JarInputStream;
import java.util.jar.JarOutputStream;
-import uk.ac.vamsas.client.*;
-import uk.ac.vamsas.objects.core.*;
+import uk.ac.vamsas.client.IClientAppdata;
+import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation;
+import uk.ac.vamsas.objects.core.AnnotationElement;
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DataSetAnnotations;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Glyph;
+import uk.ac.vamsas.objects.core.Local;
+import uk.ac.vamsas.objects.core.MapType;
+import uk.ac.vamsas.objects.core.Mapped;
+import uk.ac.vamsas.objects.core.Property;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.RangeAnnotation;
+import uk.ac.vamsas.objects.core.RangeType;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.core.VAMSAS;
import uk.ac.vamsas.objects.utils.Properties;
/*
private void buildSkipList()
{
skipList = new Hashtable();
- AlignFrame[] al = Desktop.getAlignframes();
+ AlignFrame[] al = Desktop.getAlignFrames();
for (int f = 0; al != null && f < al.length; f++)
{
skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
* @return true if alignment associated with this view will be stored in
* document.
*/
- public boolean alignmentWillBeSkipped(AlignViewport av)
+ public boolean alignmentWillBeSkipped(AlignmentViewport av)
{
return (!av.getAlignment().isAligned());
}
- private void addToSkipList(AlignViewport av)
+ private void addToSkipList(AlignmentViewport av)
{
if (skipList == null)
{
an.addProperty(Properties.newProperty(THRESHOLD,
Properties.FLOATTYPE, "" + alan.getThreshold().value));
if (alan.getThreshold().label != null)
+ {
an.addProperty(Properties.newProperty(THRESHOLD + "Name",
Properties.STRINGTYPE, "" + alan.getThreshold().label));
+ }
}
((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
bindjvvobj(alan, an);
// sync,
// and if any contain more than one view, then remove the one generated by
// document update.
- AlignViewport views[], av = null;
+ AlignmentViewport views[], av = null;
AlignFrame af = null;
Iterator newviews = newAlignmentViews.iterator();
while (newviews.hasNext())
{
- av = (AlignViewport) newviews.next();
+ av = (AlignmentViewport) newviews.next();
af = Desktop.getAlignFrameFor(av);
// TODO implement this : af.getNumberOfViews
String seqsetidobj = av.getSequenceSetId();
// to the align frames.
boolean gathered = false;
String newviewid = null;
- AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames();
+ Set<AlignedCodonFrame> mappings = av.getAlignment()
+ .getCodonFrames();
for (int i = 0; i < views.length; i++)
{
if (views[i] != av)
{
// ensure sequence mappings from vamsas document view still
// active
- if (mappings != null && mappings.length > 0)
+ if (mappings != null)
{
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(Desktop.instance)
uk.ac.vamsas.objects.core.Alignment alignment = dataset
.getAlignment(al);
// TODO check this handles multiple views properly
- AlignViewport av = findViewport(alignment);
+ AlignmentViewport av = findViewport(alignment);
jalview.datamodel.AlignmentI jal = null;
if (av != null)
return newAlignmentViews.size();
}
- public AlignViewport findViewport(Alignment alignment)
+ public AlignmentViewport findViewport(Alignment alignment)
{
- AlignViewport av = null;
- AlignViewport[] avs = Desktop
+ AlignmentViewport av = null;
+ AlignmentViewport[] avs = Desktop
.getViewports((String) getvObj2jv(alignment));
if (avs != null)
{
Cache.log.warn("Failed to parse threshold property");
}
if (val != null)
+ {
if (gl == null)
{
gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
{
gl.value = val.floatValue();
}
+ }
}
else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
{
if (gl == null)
+ {
gl = new GraphLine(0, "", java.awt.Color.black);
+ }
gl.label = props[p].getContent();
}
}
* initialise a range type object from a set of start/end inclusive intervals
*
* @param mrt
- * @param range
+ * @param ranges
*/
- private void initRangeType(RangeType mrt, int[] range)
+ private void initRangeType(RangeType mrt, List<int[]> ranges)
{
- for (int i = 0; i < range.length; i += 2)
+ for (int[] range : ranges)
{
Seg vSeg = new Seg();
- vSeg.setStart(range[i]);
- vSeg.setEnd(range[i + 1]);
+ vSeg.setStart(range[0]);
+ vSeg.setEnd(range[1]);
mrt.addSeg(vSeg);
}
}
return vobj2jv;
}
- public void storeSequenceMappings(AlignViewport viewport, String title)
+ public void storeSequenceMappings(AlignmentViewport viewport, String title)
throws Exception
{
- AlignViewport av = viewport;
+ AlignmentViewport av = viewport;
try
{
jalview.datamodel.AlignmentI jal = av.getAlignment();
}
// Store any sequence mappings.
- if (av.getAlignment().getCodonFrames() != null
- && av.getAlignment().getCodonFrames().length > 0)
+ Set<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
+ if (cframes != null)
{
- jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment()
- .getCodonFrames();
- for (int cf = 0; cf < cframes.length; cf++)
+ for (AlignedCodonFrame acf : cframes)
{
- if (cframes[cf].getdnaSeqs() != null
- && cframes[cf].getdnaSeqs().length > 0)
+ if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
{
- jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
- jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
+ jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
+ jalview.datamodel.Mapping[] mps = acf.getProtMappings();
for (int smp = 0; smp < mps.length; smp++)
{
uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);
*/
package jalview.io.vamsas;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
+
+import java.util.List;
import java.util.Vector;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.Mapped;
import uk.ac.vamsas.objects.core.RangeType;
import uk.ac.vamsas.objects.core.Seg;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.MessageManager;
/**
* Enhances DatastoreItem objects with additional functions to do with RangeType
* initialise a range type object from a set of start/end inclusive intervals
*
* @param mrt
- * @param range
+ * @param ranges
*/
- protected void initRangeType(RangeType mrt, int[] range)
+ protected void initRangeType(RangeType mrt, List<int[]> ranges)
{
- for (int i = 0; i < range.length; i += 2)
+ for (int[] range : ranges)
{
Seg vSeg = new Seg();
- vSeg.setStart(range[i]);
- vSeg.setEnd(range[i + 1]);
+ vSeg.setStart(range[0]);
+ vSeg.setEnd(range[1]);
vSeg.setInclusive(true);
mrt.addSeg(vSeg);
}
*/
package jalview.io.vamsas;
-import java.util.Vector;
-
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceI;
import jalview.gui.Desktop;
import jalview.io.VamsasAppDatastore;
-import uk.ac.vamsas.client.Vobject;
+
+import java.util.Vector;
+
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.Sequence;
jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
return;
}
- mobj = this.getvObj2jv((Vobject) sdloc);
+ mobj = this.getvObj2jv(sdloc);
if (mobj instanceof SequenceI)
{
from = (SequenceI) mobj;
}
- mobj = this.getvObj2jv((Vobject) sdmap);
+ mobj = this.getvObj2jv(sdmap);
if (mobj instanceof SequenceI)
{
to = (SequenceI) mobj;
}
// create mapping storage object and make each dataset alignment reference
// it.
- jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc
- .getV_parent());
- jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap
- .getV_parent());
- AlignedCodonFrame afc = new AlignedCodonFrame(0);
+ AlignmentI dsLoc = (AlignmentI) getvObj2jv(sdloc.getV_parent());
+ AlignmentI dsMap = (AlignmentI) getvObj2jv(sdmap.getV_parent());
+ AlignedCodonFrame acf = new AlignedCodonFrame();
if (dsLoc != null && dsLoc != dsMap)
{
- dsLoc.addCodonFrame(afc);
+ dsLoc.addCodonFrame(acf);
}
if (dsMap != null)
{
- dsMap.addCodonFrame(afc);
+ dsMap.addCodonFrame(acf);
}
// create and add the new mapping to (each) dataset's codonFrame
mapping = new jalview.util.MapList(mapping.getToRanges(),
mapping.getFromRanges(), mapping.getToRatio(),
mapping.getFromRatio());
- afc.addMap(to, from, mapping);
+ acf.addMap(to, from, mapping);
}
else
{
mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
- afc.addMap(from, to, mapping);
+ acf.addMap(from, to, mapping);
}
}
else
{
mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
- afc.addMap(from, to, mapping);
+ acf.addMap(from, to, mapping);
}
bindjvvobj(mapping, sequenceMapping);
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).addMappings(
- new AlignedCodonFrame[]
- { afc });
+ .getStructureSelectionManager(Desktop.instance).addMapping(acf);
// Try to link up any conjugate database references in the two sequences
// matchConjugateDBRefs(from, to, mapping);
// Try to propagate any dbrefs across this mapping.
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignViewport;
import jalview.gui.TreePanel;
import jalview.io.NewickFile;
import jalview.io.VamsasAppDatastore;
+import jalview.viewmodel.AlignmentViewport;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.Entry;
*/
public Object[] recoverInputData(Provenance tp)
{
- AlignViewport javport = null;
+ AlignmentViewport javport = null;
jalview.datamodel.AlignmentI jal = null;
jalview.datamodel.CigarArray view = null;
for (int pe = 0; pe < tp.getEntryCount(); pe++)
return null;
}
- private AlignViewport getViewport(Vobject v_parent)
+ private AlignmentViewport getViewport(Vobject v_parent)
{
if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
{
int i = -1;
- public void mouseOver(SequenceI seq, int index, VamsasSource source)
+ @Override
+ public void mouseOverSequence(SequenceI seq, int index,
+ VamsasSource source)
{
if (seq != last || i != index)
{
*/
package jalview.javascript;
-import java.awt.Color;
-import java.util.ArrayList;
-
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.bin.JalviewLite;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolCommands;
+import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Propagate events involving PDB structures associated with sequences to a
* javascript function. Generally, the javascript handler is called with a
return modelSet;
}
- @Override
public void mouseOverStructure(int atomIndex, String strInfo)
{
}
@Override
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbId)
+ public void highlightAtoms(List<AtomSpec> atoms)
{
- String[] st = new String[0];
- try
- {
- executeJavascriptFunction(_listenerfn, st = new String[]
- { "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),
- "" + atomIndex });
- } catch (Exception ex)
+ for (AtomSpec atom : atoms)
{
- System.err.println("Couldn't execute callback with " + _listenerfn
- + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
- + "," + st[3] + "\n");
- ex.printStackTrace();
-
+ try
+ {
+ // TODO is this right? StructureSelectionManager passes pdbFile as the
+ // field that is interpreted (in 2.8.2) as pdbId?
+ // JBPComment: yep - this is right! the Javascript harness uses the
+ // absolute pdbFile URI to locate the PDB file in the external viewer
+ executeJavascriptFunction(_listenerfn, new String[]
+ { "mouseover", "" + atom.getPdbFile(),
+ "" + atom.getChain(),
+ "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't execute callback with " + _listenerfn
+ + " for atomSpec: " + atom);
+ ex.printStackTrace();
+ }
}
-
}
@Override
}
@Override
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbId)
- {
- return null;
- }
-
- @Override
public AlignFrame getAlignFrame()
{
// associated with all alignframes, always.
*/
package jalview.jbgui;
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.FocusEvent;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.JTabbedPane;
+import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import javax.swing.event.ChangeEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
public class GAlignFrame extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
- protected JMenu fileMenu = new JMenu();
-
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu editMenu = new JMenu();
-
- protected JMenu viewMenu = new JMenu();
-
- protected JMenu annotationsMenu = new JMenu();
-
protected JMenu colourMenu = new JMenu();
- protected JMenu calculateMenu = new JMenu();
-
protected JMenu webService = new JMenu();
protected JMenuItem webServiceNoServices;
- protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
-
- protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
-
- protected JMenuItem invertSequenceMenuItem = new JMenuItem();
-
- protected JMenuItem remove2LeftMenuItem = new JMenuItem();
-
- protected JMenuItem remove2RightMenuItem = new JMenuItem();
-
- protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
-
- protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-
public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
- protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
-
- protected JMenuItem sortIDMenuItem = new JMenuItem();
-
- protected JMenuItem sortLengthMenuItem = new JMenuItem();
-
- protected JMenuItem sortGroupMenuItem = new JMenuItem();
-
protected JMenu sortByAnnotScore = new JMenu();
- protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
-
- protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
-
- protected JMenuItem PCAMenuItem = new JMenuItem();
-
- protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
-
- protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
public JLabel statusBar = new JLabel();
- protected JMenuItem saveAs = new JMenuItem();
-
protected JMenu outputTextboxMenu = new JMenu();
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
- JMenuItem njTreeBlosumMenuItem = new JMenuItem();
-
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-
public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
- JMenuItem htmlMenuItem = new JMenuItem();
-
- JMenuItem overviewMenuItem = new JMenuItem();
-
protected JMenuItem undoMenuItem = new JMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
- JMenuItem printMenuItem = new JMenuItem();
-
public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
- JMenuItem findMenuItem = new JMenuItem();
-
public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
- JMenuItem deleteGroups = new JMenuItem();
-
- JMenuItem createGroup = new JMenuItem();
-
- JMenuItem unGroup = new JMenuItem();
-
- JMenuItem delete = new JMenuItem();
-
JMenuItem copy = new JMenuItem();
JMenuItem cut = new JMenuItem();
JMenu pasteMenu = new JMenu();
- JMenuItem pasteNew = new JMenuItem();
-
- JMenuItem pasteThis = new JMenuItem();
-
public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
- JMenuItem createPNG = new JMenuItem();
-
- JMenuItem createBioJS = new JMenuItem();
-
- JMenuItem createSVG = new JMenuItem();
-
- protected JMenuItem font = new JMenuItem();
-
public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
- JMenuItem epsFile = new JMenuItem();
-
- JMenuItem LoadtreeMenuItem = new JMenuItem();
-
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- protected JMenuItem modifyPID = new JMenuItem();
-
protected JMenuItem modifyConservation = new JMenuItem();
protected JMenu sortByTreeMenu = new JMenu();
protected JMenu calculateTree = new JMenu();
- JMenu jMenu2 = new JMenu();
-
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
protected ButtonGroup colours = new ButtonGroup();
- JMenuItem vamsasStore = new JMenuItem();
-
protected JMenuItem showTranslation = new JMenuItem();
- protected JMenuItem extractScores = new JMenuItem();
-
- protected JMenuItem expandAlignment = new JMenuItem();
-
protected JMenu showProducts = new JMenu();
- public JMenuItem openFeatureSettings = new JMenuItem();
-
- JMenuItem fetchSequence = new JMenuItem();
-
- JMenuItem annotationColour = new JMenuItem();
-
- JMenuItem annotationColumn = new JMenuItem();
-
protected JMenuItem rnahelicesColour = new JMenuItem();
- JMenuItem associatedData = new JMenuItem();
-
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
- JMenu addSequenceMenu = new JMenu();
-
- JMenuItem addFromFile = new JMenuItem();
-
- JMenuItem addFromText = new JMenuItem();
-
- JMenuItem addFromURL = new JMenuItem();
-
- JMenuItem exportAnnotations = new JMenuItem();
-
- JMenuItem exportFeatures = new JMenuItem();
-
protected JPanel statusPanel = new JPanel();
- GridLayout gridLayout1 = new GridLayout();
-
- JMenu jMenu3 = new JMenu();
-
- JMenuItem showAllSeqs = new JMenuItem();
-
- JMenuItem showAllColumns = new JMenuItem();
-
- JMenu hideMenu = new JMenu();
-
- JMenuItem hideSelSequences = new JMenuItem();
-
- JMenuItem hideSelColumns = new JMenuItem();
-
- JMenuItem hideAllButSelection = new JMenuItem();
-
- JMenuItem hideAllSelection = new JMenuItem();
-
- JMenuItem showAllhidden = new JMenuItem();
-
protected JMenuItem showAllSeqAnnotations = new JMenuItem();
protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
protected JMenuItem hideAllAlAnnotations = new JMenuItem();
- protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
-
- protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
- JMenuItem invertColSel = new JMenuItem();
-
protected JTabbedPane tabbedPane = new JTabbedPane();
- JMenuItem save = new JMenuItem();
-
protected JMenuItem reload = new JMenuItem();
- JMenuItem newView = new JMenuItem();
-
- JMenuItem textColour = new JMenuItem();
-
- JMenu formatMenu = new JMenu();
-
- JMenu selectMenu = new JMenu();
+ protected JMenu formatMenu = new JMenu();
protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
protected JMenuItem expandViews = new JMenuItem();
- JMenuItem pageSetup = new JMenuItem();
-
- JMenuItem alignmentProperties = new JMenuItem();
-
- JMenu tooltipSettingsMenu = new JMenu();
-
- private JMenuItem justifyLeftMenuItem = new JMenuItem();
-
- private JMenuItem justifyRightMenuItem = new JMenuItem();
-
- JMenu autoAnnMenu = new JMenu();
-
protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
-
- private JMenuItem grpsFromSelection = new JMenuItem();
-
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+
+ private SplitContainerI splitFrame;
+
public GAlignFrame()
{
try
JMenuItem item = new JMenuItem(
jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
// colours.add(covariationColour);
colours.add(tcoffeeColour);
colours.add(RNAInteractionColour);
- setColourSelected(jalview.bin.Cache
- .getDefault("DEFAULT_COLOUR", "None"));
-
+ setColourSelected(jalview.bin.Cache.getDefault(
+ Preferences.DEFAULT_COLOUR, "None"));
}
public void setColourSelected(String defaultColour)
private void jbInit() throws Exception
{
- fileMenu.setText(MessageManager.getString("action.file"));
- saveAs.setText(MessageManager.getString("action.save_as") + "...");
- saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- saveAs.addActionListener(new ActionListener()
+ JMenuItem saveAs = new JMenuItem(
+ MessageManager.getString("action.save_as") + "...");
+ ActionListener al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
saveAs_actionPerformed(e);
}
- });
+ };
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ addMenuActionAndAccelerator(keyStroke, saveAs, al);
+
closeMenuItem.setText(MessageManager.getString("action.close"));
- closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
closeMenuItem_actionPerformed(false);
}
- });
- editMenu.setText(MessageManager.getString("action.edit"));
- viewMenu.setText(MessageManager.getString("action.view"));
- annotationsMenu.setText(MessageManager.getString("action.annotations"));
+ };
+ addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
+
+ JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
+ JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
+ JMenu annotationsMenu = new JMenu(
+ MessageManager.getString("action.annotations"));
+ JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
colourMenu.setText(MessageManager.getString("action.colour"));
- calculateMenu.setText(MessageManager.getString("action.calculate"));
+ JMenu calculateMenu = new JMenu(
+ MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
- selectAllSequenceMenuItem.setText(MessageManager
+ JMenuItem selectAllSequenceMenuItem = new JMenuItem(
+ MessageManager
.getString("action.select_all"));
- selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- selectAllSequenceMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- selectAllSequenceMenuItem_actionPerformed(e);
- }
- });
- deselectAllSequenceMenuItem.setText(MessageManager
- .getString("action.deselect_all"));
- deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
- deselectAllSequenceMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- deselectAllSequenceMenuItem_actionPerformed(e);
- }
- });
- invertSequenceMenuItem.setText(MessageManager
- .getString("action.invert_sequence_selection"));
- invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- invertSequenceMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- invertSequenceMenuItem_actionPerformed(e);
- }
- });
- grpsFromSelection.setText(MessageManager
- .getString("action.make_groups_selection"));
- grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ selectAllSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
+
+ JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
+ MessageManager.getString("action.deselect_all"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ deselectAllSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
+
+ JMenuItem invertSequenceMenuItem = new JMenuItem(
+ MessageManager.getString("action.invert_sequence_selection"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ invertSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
+
+ JMenuItem grpsFromSelection = new JMenuItem(
+ MessageManager.getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
makeGrpsFromSelection_actionPerformed(e);
}
});
- expandAlignment.setText(MessageManager
- .getString("action.view_flanking_regions"));
+ JMenuItem expandAlignment = new JMenuItem(
+ MessageManager.getString("action.view_flanking_regions"));
expandAlignment.setToolTipText(MessageManager
.getString("label.view_flanking_regions"));
- expandAlignment.addActionListener(new java.awt.event.ActionListener()
+ expandAlignment.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
expand_newalign(e);
}
});
- remove2LeftMenuItem.setText(MessageManager
- .getString("action.remove_left"));
- remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- remove2LeftMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- remove2LeftMenuItem_actionPerformed(e);
- }
- });
- remove2RightMenuItem.setText(MessageManager
- .getString("action.remove_right"));
- remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- remove2RightMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- remove2RightMenuItem_actionPerformed(e);
- }
- });
- removeGappedColumnMenuItem.setText(MessageManager
- .getString("action.remove_empty_columns"));
- removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- removeGappedColumnMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeGappedColumnMenuItem_actionPerformed(e);
- }
- });
- removeAllGapsMenuItem.setText(MessageManager
- .getString("action.remove_all_gaps"));
- removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- removeAllGapsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeAllGapsMenuItem_actionPerformed(e);
- }
- });
- justifyLeftMenuItem.setText(MessageManager
- .getString("action.left_justify_alignment"));
- justifyLeftMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- justifyLeftMenuItem_actionPerformed(e);
- }
- });
- justifyRightMenuItem.setText(MessageManager
- .getString("action.right_justify_alignment"));
- justifyRightMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- justifyRightMenuItem_actionPerformed(e);
- }
- });
+ JMenuItem remove2LeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_left"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2LeftMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
+
+ JMenuItem remove2RightMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_right"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2RightMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
+
+ JMenuItem removeGappedColumnMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_empty_columns"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeGappedColumnMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
+
+ JMenuItem removeAllGapsMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_all_gaps"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeAllGapsMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
+
+ JMenuItem justifyLeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.left_justify_alignment"));
+ justifyLeftMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyLeftMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem justifyRightMenuItem = new JMenuItem(
+ MessageManager.getString("action.right_justify_alignment"));
+ justifyRightMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyRightMenuItem_actionPerformed(e);
+ }
+ });
viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewBoxesMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
viewTextMenuItem.setText(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewTextMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
showNonconservedMenuItem.setText(MessageManager
.getString("label.show_non_conversed"));
showNonconservedMenuItem.setState(false);
- showNonconservedMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- showUnconservedMenuItem_actionPerformed(e);
- }
- });
- sortPairwiseMenuItem.setText(MessageManager
- .getString("action.by_pairwise_id"));
- sortPairwiseMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sortPairwiseMenuItem_actionPerformed(e);
- }
- });
- sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showNonconservedMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showUnconservedMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem sortPairwiseMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortPairwiseMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem sortIDMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
sortIDMenuItem_actionPerformed(e);
}
});
- sortLengthMenuItem
- .setText(MessageManager.getString("action.by_length"));
- sortLengthMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sortLengthMenuItem_actionPerformed(e);
- }
- });
- sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sortLengthMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_length"));
+ sortLengthMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortLengthMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem sortGroupMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
sortGroupMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText(MessageManager
+
+ JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
.getString("action.remove_redundancy").concat("..."));
- removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- removeRedundancyMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeRedundancyMenuItem_actionPerformed(e);
- }
- });
- pairwiseAlignmentMenuItem.setText(MessageManager
- .getString("action.pairwise_alignment"));
- pairwiseAlignmentMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- pairwiseAlignmentMenuItem_actionPerformed(e);
- }
- });
- PCAMenuItem.setText(MessageManager
- .getString("label.principal_component_analysis"));
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeRedundancyMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
+ JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
+ MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem PCAMenuItem = new JMenuItem(
+ MessageManager.getString("label.principal_component_analysis"));
+ PCAMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem.setText(MessageManager
- .getString("label.average_distance_identity"));
- averageDistanceTreeMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_actionPerformed(e);
- }
- });
- neighbourTreeMenuItem.setText(MessageManager
- .getString("label.neighbour_joining_identity"));
- neighbourTreeMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- neighbourTreeMenuItem_actionPerformed(e);
- }
- });
- this.getContentPane().setLayout(borderLayout1);
+ JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ averageDistanceTreeMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem neighbourTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ neighbourTreeMenuItem_actionPerformed(e);
+ }
+ });
+
+ this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
outputTextboxMenu.setText(MessageManager
.getString("label.out_to_textbox"));
clustalColour.setText(MessageManager.getString("label.clustalx"));
-
- clustalColour.addActionListener(new java.awt.event.ActionListener()
+ clustalColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new java.awt.event.ActionListener()
+ zappoColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new java.awt.event.ActionListener()
+ taylorColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
hydrophobicityColour.setText(MessageManager
.getString("label.hydrophobicity"));
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
+ hydrophobicityColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed(e);
+ }
+ });
helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new java.awt.event.ActionListener()
+ helixColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
strandColour.setText(MessageManager
.getString("label.strand_propensity"));
- strandColour.addActionListener(new java.awt.event.ActionListener()
+ strandColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new java.awt.event.ActionListener()
+ turnColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ buriedColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
userDefinedColour.setText(MessageManager
.getString("action.user_defined"));
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ userDefinedColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
PIDColour
.setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+ PIDColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
BLOSUM62Colour
.setText(MessageManager.getString("label.blosum62_score"));
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ BLOSUM62Colour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ nucleotideColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
purinePyrimidineColour.setText(MessageManager
.getString("label.purine_pyrimidine"));
- purinePyrimidineColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed(e);
- }
- });
+ purinePyrimidineColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
RNAInteractionColour.setText("RNA Interaction type");
- RNAInteractionColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- RNAInteractionColour_actionPerformed(e);
- }
- });
+ RNAInteractionColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
/*
* covariationColour.setText("Covariation");
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(e); } });
+ * covariationColour.addActionListener(new ActionListener() { public void
+ * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
+ * });
*/
- avDistanceTreeBlosumMenuItem.setText(MessageManager
- .getString("label.average_distance_bloslum62"));
- avDistanceTreeBlosumMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
- njTreeBlosumMenuItem.setText(MessageManager
- .getString("label.neighbour_blosum62"));
- njTreeBlosumMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- njTreeBlosumMenuItem_actionPerformed(e);
- }
- });
+ JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
+ MessageManager.getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ avTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem njTreeBlosumMenuItem = new JMenuItem(
+ MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ njTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem.setText(MessageManager
.getString("label.show_annotations"));
SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
.valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name()));
- sortAnnBySequence.setText(MessageManager
- .getString("label.sort_annotations_by_sequence"));
+ final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_sequence"));
+ final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_label"));
+
sortAnnBySequence
.setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
sortAnnotations_actionPerformed();
}
});
- sortAnnByLabel.setText(MessageManager
- .getString("label.sort_annotations_by_label"));
sortAnnByLabel
.setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
sortAnnByLabel.addActionListener(new ActionListener()
});
colourTextMenuItem.setText(MessageManager
.getString("label.colour_text"));
- colourTextMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- colourTextMenuItem_actionPerformed(e);
- }
- });
- htmlMenuItem.setText(MessageManager.getString("label.html"));
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ colourTextMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ colourTextMenuItem_actionPerformed(e);
+ }
+ });
+
+ JMenuItem htmlMenuItem = new JMenuItem(
+ MessageManager.getString("label.html"));
+ htmlMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
- // TODO uncomment when supported by MassageManager
- // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
- createBioJS.setText("BioJS");
+ JMenuItem createBioJS = new JMenuItem(
+ MessageManager.getString("label.biojs_html_export"));
createBioJS.addActionListener(new java.awt.event.ActionListener()
{
@Override
}
});
- overviewMenuItem.setText(MessageManager
- .getString("label.overview_window"));
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem overviewMenuItem = new JMenuItem(
+ MessageManager.getString("label.overview_window"));
+ overviewMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
overviewMenuItem_actionPerformed(e);
}
});
+
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
- undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
undoMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
+
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
- redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
redoMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+
conservationMenuItem.setText(MessageManager
.getString("action.by_conservation"));
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed(e);
- }
- });
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(e);
+ }
+ });
noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ noColourmenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+ wrapMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
wrapMenuItem_actionPerformed(e);
}
});
- printMenuItem.setText(MessageManager.getString("action.print") + "...");
- printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- printMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem printMenuItem = new JMenuItem(
+ MessageManager.getString("action.print") + "...");
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
printMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
+
renderGapsMenuItem
.setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
- renderGapsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- renderGapsMenuItem_actionPerformed(e);
- }
- });
- findMenuItem.setText(MessageManager.getString("action.find"));
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ renderGapsMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ renderGapsMenuItem_actionPerformed(e);
+ }
+ });
+
+ JMenuItem findMenuItem = new JMenuItem(
+ MessageManager.getString("action.find"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
- findMenuItem.addActionListener(new java.awt.event.ActionListener()
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
findMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+
abovePIDThreshold.setText(MessageManager
.getString("label.above_identity_threshold"));
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+ abovePIDThreshold.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
ButtonGroup buttonGroup = new ButtonGroup();
+ final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_first"));
+ final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_last"));
buttonGroup.add(showAutoFirst);
buttonGroup.add(showAutoLast);
- showAutoFirst.setText(MessageManager.getString("label.show_first"));
showAutoFirst.setSelected(Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE,
- false));
+ Preferences.SHOW_AUTOCALC_ABOVE, false));
showAutoFirst.addActionListener(new ActionListener()
{
@Override
sortAnnotations_actionPerformed();
}
});
- showAutoLast.setText(MessageManager.getString("label.show_last"));
showAutoLast.setSelected(!showAutoFirst.isSelected());
showAutoLast.addActionListener(new ActionListener()
{
});
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ nucleotideColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
- deleteGroups
- .setText(MessageManager.getString("action.undefine_groups"));
- deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- deleteGroups.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem deleteGroups = new JMenuItem(
+ MessageManager.getString("action.undefine_groups"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
deleteGroups_actionPerformed(e);
}
- });
- createGroup.setText(MessageManager.getString("action.create_groups"));
- createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- createGroup.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+
+ JMenuItem createGroup = new JMenuItem(
+ MessageManager.getString("action.create_groups"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
createGroup_actionPerformed(e);
}
- });
- unGroup.setText(MessageManager.getString("action.remove_group"));
- unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- unGroup.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
+ JMenuItem unGroup = new JMenuItem(
+ MessageManager.getString("action.remove_group"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
unGroup_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, unGroup, al);
+
copy.setText(MessageManager.getString("action.copy"));
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
- copy.addActionListener(new java.awt.event.ActionListener()
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, copy, al);
+
cut.setText(MessageManager.getString("action.cut"));
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- cut.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed(e);
}
- });
- delete.setText(MessageManager.getString("action.delete"));
- delete.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, cut, al);
+
+ JMenuItem delete = new JMenuItem(
+ MessageManager.getString("action.delete"));
+ delete.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
delete_actionPerformed(e);
}
});
+
pasteMenu.setText(MessageManager.getString("action.paste"));
- pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
- pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- pasteNew.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem pasteNew = new JMenuItem(
+ MessageManager.getString("label.to_new_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
pasteNew_actionPerformed(e);
}
- });
- pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
- pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- pasteThis.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteNew, al);
+
+ JMenuItem pasteThis = new JMenuItem(
+ MessageManager.getString("label.to_this_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
pasteThis_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteThis, al);
+
applyToAllGroups.setText(MessageManager
.getString("label.apply_colour_to_all_groups"));
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+ applyToAllGroups.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
applyToAllGroups_actionPerformed(e);
}
});
- createPNG.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem createPNG = new JMenuItem("PNG");
+ createPNG.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
createPNG.setActionCommand(MessageManager
.getString("label.save_png_image"));
- createPNG.setText("PNG");
- font.setText(MessageManager.getString("action.font"));
- font.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
+ font.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
seqLimits.setText(MessageManager
.getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
- seqLimits.addActionListener(new java.awt.event.ActionListener()
+ seqLimits.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
seqLimit_actionPerformed(e);
}
});
- epsFile.setText("EPS");
- epsFile.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem epsFile = new JMenuItem("EPS");
+ epsFile.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
- createSVG.setText("SVG");
- createSVG.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem createSVG = new JMenuItem("SVG");
+ createSVG.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
- LoadtreeMenuItem.setActionCommand(MessageManager
+ JMenuItem loadTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.load_associated_tree"));
+ loadTreeMenuItem.setActionCommand(MessageManager
.getString("label.load_tree_for_sequence_set"));
- LoadtreeMenuItem.setText(MessageManager
- .getString("label.load_associated_tree"));
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ loadTreeMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- LoadtreeMenuItem_actionPerformed(e);
+ loadTreeMenuItem_actionPerformed(e);
}
});
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
- scaleAbove.addActionListener(new java.awt.event.ActionListener()
+ scaleAbove.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
scaleLeft.setVisible(false);
scaleLeft.setSelected(true);
scaleLeft.setText(MessageManager.getString("action.scale_left"));
- scaleLeft.addActionListener(new java.awt.event.ActionListener()
+ scaleLeft.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
scaleRight.setVisible(false);
scaleRight.setSelected(true);
scaleRight.setText(MessageManager.getString("action.scale_right"));
- scaleRight.addActionListener(new java.awt.event.ActionListener()
+ scaleRight.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
centreColumnLabelsMenuItem.setState(false);
centreColumnLabelsMenuItem.setText(MessageManager
.getString("label.centre_column_labels"));
- centreColumnLabelsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- centreColumnLabels_actionPerformed(e);
- }
- });
+ centreColumnLabelsMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ centreColumnLabels_actionPerformed(e);
+ }
+ });
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
followHighlightMenuItem.setText(MessageManager
});
- modifyPID.setText(MessageManager
- .getString("label.modify_identity_thereshold"));
- modifyPID.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_thereshold"));
+ modifyPID.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
modifyConservation.setText(MessageManager
.getString("label.modify_conservation_thereshold"));
- modifyConservation
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- modifyConservation_actionPerformed(e);
- }
- });
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed(e);
+ }
+ });
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
calculateTree
.setText(MessageManager.getString("action.calculate_tree"));
- jMenu2.setText(MessageManager.getString("label.export_image"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem.setState(jalview.bin.Cache
.getDefault("PAD_GAPS", false));
padGapsMenuitem_actionPerformed(e);
}
});
+ JMenuItem vamsasStore = new JMenuItem(
+ MessageManager.getString("label.vamsas_store"));
vamsasStore.setVisible(false);
- vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
vamsasStore.addActionListener(new ActionListener()
{
@Override
showTranslation_actionPerformed(e);
}
});
- extractScores.setText(MessageManager.getString("label.extract_scores")
- + "...");
+
+ JMenuItem extractScores = new JMenuItem(
+ MessageManager.getString("label.extract_scores") + "...");
extractScores.addActionListener(new ActionListener()
{
@Override
extractScores_actionPerformed(e);
}
});
- extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
- // score extraction
+ extractScores.setVisible(true);
+ // JBPNote: TODO: make gui for regex based score extraction
+
+ // for show products actions see AlignFrame.canShowProducts
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
- /*
- * showProducts.addActionListener(new ActionListener() {
- *
- * public void actionPerformed(ActionEvent e) {
- * showProducts_actionPerformed(e); } });
- */
- openFeatureSettings.setText(MessageManager
- .getString("label.feature_settings"));
+
+ JMenuItem openFeatureSettings = new JMenuItem(
+ MessageManager.getString("label.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
@Override
featureSettings_actionPerformed(e);
}
});
- fetchSequence
- .setText(MessageManager.getString("label.fetch_sequences"));
+ JMenuItem fetchSequence = new JMenuItem(
+ MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
@Override
}
});
- annotationColour.setText(MessageManager
- .getString("action.by_annotation"));
+ JMenuItem annotationColour = new JMenuItem(
+ MessageManager.getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
@Override
}
});
- annotationColumn.setText(MessageManager
- .getString("action.select_by_annotation"));
+ JMenuItem annotationColumn = new JMenuItem(
+ MessageManager.getString("action.select_by_annotation"));
annotationColumn.addActionListener(new ActionListener()
{
@Override
}
});
- associatedData.setText(MessageManager
- .getString("label.load_features_annotations"));
+ JMenuItem associatedData = new JMenuItem(
+ MessageManager.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
{
@Override
}
});
- addSequenceMenu
- .setText(MessageManager.getString("label.add_sequences"));
- addFromFile.setText(MessageManager.getString("label.from_file"));
+ JMenu addSequenceMenu = new JMenu(
+ MessageManager.getString("label.add_sequences"));
+ JMenuItem addFromFile = new JMenuItem(
+ MessageManager.getString("label.from_file"));
addFromFile.addActionListener(new ActionListener()
{
@Override
addFromFile_actionPerformed(e);
}
});
- addFromText.setText(MessageManager.getString("label.from_textbox"));
+ JMenuItem addFromText = new JMenuItem(
+ MessageManager.getString("label.from_textbox"));
addFromText.addActionListener(new ActionListener()
{
@Override
addFromText_actionPerformed(e);
}
});
- addFromURL.setText(MessageManager.getString("label.from_url"));
+ JMenuItem addFromURL = new JMenuItem(
+ MessageManager.getString("label.from_url"));
addFromURL.addActionListener(new ActionListener()
{
@Override
addFromURL_actionPerformed(e);
}
});
- exportFeatures.setText(MessageManager
- .getString("label.export_features"));
+ JMenuItem exportFeatures = new JMenuItem(
+ MessageManager.getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
@Override
exportFeatures_actionPerformed(e);
}
});
- exportAnnotations.setText(MessageManager
- .getString("label.export_annotations"));
+ JMenuItem exportAnnotations = new JMenuItem(
+ MessageManager.getString("label.export_annotations"));
exportAnnotations.addActionListener(new ActionListener()
{
@Override
exportAnnotations_actionPerformed(e);
}
});
- statusPanel.setLayout(gridLayout1);
- jMenu3.setText(MessageManager.getString("action.show"));
- showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
+ statusPanel.setLayout(new GridLayout());
+ JMenuItem showAllSeqs = new JMenuItem(
+ MessageManager.getString("label.all_sequences"));
showAllSeqs.setToolTipText(MessageManager
.getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
showAllSeqs_actionPerformed(e);
}
});
- showAllColumns.setText(MessageManager.getString("label.all_columns"));
+ JMenuItem showAllColumns = new JMenuItem(
+ MessageManager.getString("label.all_columns"));
showAllColumns.setToolTipText(MessageManager
.getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
showAllColumns_actionPerformed(e);
}
});
- hideMenu.setText(MessageManager.getString("action.hide"));
- hideSelSequences.setText(MessageManager
- .getString("label.selected_sequences"));
+ JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
+ JMenuItem hideSelSequences = new JMenuItem(
+ MessageManager.getString("label.selected_sequences"));
hideSelSequences.setToolTipText(MessageManager
.getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
hideSelSequences_actionPerformed(e);
}
});
- hideSelColumns.setText(MessageManager
- .getString("label.selected_columns"));
+ JMenuItem hideSelColumns = new JMenuItem(
+ MessageManager.getString("label.selected_columns"));
hideSelColumns.setToolTipText(MessageManager
.getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
hideSelColumns_actionPerformed(e);
}
});
- hideAllSelection.setText(MessageManager
- .getString("label.selected_region"));
+ JMenuItem hideAllSelection = new JMenuItem(
+ MessageManager.getString("label.selected_region"));
hideAllSelection.addActionListener(new ActionListener()
{
@Override
}
});
// TODO: should be hidden if no selection exists.
- hideAllButSelection.setText(MessageManager
- .getString("label.all_but_selected_region"));
+ JMenuItem hideAllButSelection = new JMenuItem(
+ MessageManager.getString("label.all_but_selected_region"));
hideAllButSelection.addActionListener(new ActionListener()
{
@Override
hideAllButSelection_actionPerformed(e);
}
});
- showAllhidden.setText(MessageManager
- .getString("label.all_sequences_columns"));
+ JMenuItem showAllhidden = new JMenuItem(
+ MessageManager.getString("label.all_sequences_columns"));
showAllhidden.setToolTipText(MessageManager
.getString("label.toggles_visibility_hidden_selected_regions"));
showAllhidden.addActionListener(new ActionListener()
hiddenMarkers_actionPerformed(e);
}
});
- invertColSel.setText(MessageManager
- .getString("action.invert_column_selection"));
- invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.ALT_MASK, false));
- invertColSel.addActionListener(new ActionListener()
+
+ JMenuItem invertColSel = new JMenuItem(
+ MessageManager.getString("action.invert_column_selection"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
invertColSel_actionPerformed(e);
}
+ };
+ addMenuActionAndAccelerator(keyStroke, invertColSel, al);
+
+ showComplementMenuItem.setVisible(false);
+ showComplementMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showComplement_actionPerformed(showComplementMenuItem.getState());
+ }
});
+
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
@Override
tabbedPane_focusGained(e);
}
});
- save.setText(MessageManager.getString("action.save"));
- save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- save.addActionListener(new ActionListener()
+
+ JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
save_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, save, al);
+
reload.setEnabled(false);
reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
reload_actionPerformed(e);
}
});
- newView.setText(MessageManager.getString("action.new_view"));
- newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- newView.addActionListener(new ActionListener()
+
+ JMenuItem newView = new JMenuItem(
+ MessageManager.getString("action.new_view"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
newView_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, newView, al);
+
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
- textColour.setText(MessageManager.getString("label.colour_text")
- + "...");
+ JMenuItem textColour = new JMenuItem(
+ MessageManager.getString("label.colour_text") + "...");
textColour.addActionListener(new ActionListener()
{
@Override
}
});
formatMenu.setText(MessageManager.getString("action.format"));
- selectMenu.setText(MessageManager.getString("action.select"));
+ JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
idRightAlign.setText(MessageManager
.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
idRightAlign_actionPerformed(e);
}
});
+
gatherViews.setEnabled(false);
gatherViews.setText(MessageManager.getString("action.gather_views"));
- gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, 0, false));
- gatherViews.addActionListener(new ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
gatherViews_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, gatherViews, al);
+
expandViews.setEnabled(false);
expandViews.setText(MessageManager.getString("action.expand_views"));
- expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_X, 0, false));
- expandViews.addActionListener(new ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
expandViews_actionPerformed(e);
}
- });
- pageSetup
- .setText(MessageManager.getString("action.page_setup") + "...");
+ };
+ addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
+ JMenuItem pageSetup = new JMenuItem(
+ MessageManager.getString("action.page_setup") + "...");
pageSetup.addActionListener(new ActionListener()
{
@Override
pageSetup_actionPerformed(e);
}
});
- alignmentProperties.setText(MessageManager
- .getString("label.alignment_props") + "...");
+ JMenuItem alignmentProperties = new JMenuItem(
+ MessageManager.getString("label.alignment_props") + "...");
alignmentProperties.addActionListener(new ActionListener()
{
@Override
alignmentProperties();
}
});
- tooltipSettingsMenu.setText(MessageManager
- .getString("label.sequence_id_tooltip"));
- autoAnnMenu.setText(MessageManager
- .getString("label.autocalculated_annotation"));
+ JMenu tooltipSettingsMenu = new JMenu(
+ MessageManager.getString("label.sequence_id_tooltip"));
+ JMenu autoAnnMenu = new JMenu(
+ MessageManager.getString("label.autocalculated_annotation"));
+
+ JMenu exportImageMenu = new JMenu(
+ MessageManager.getString("label.export_image"));
+ JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
fileMenu.add(pageSetup);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
- fileMenu.add(jMenu2);
+ fileMenu.add(exportImageMenu);
fileMenu.add(exportFeatures);
fileMenu.add(exportAnnotations);
- fileMenu.add(LoadtreeMenuItem);
+ fileMenu.add(loadTreeMenuItem);
fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+
viewMenu.add(newView);
viewMenu.add(expandViews);
viewMenu.add(gatherViews);
viewMenu.addSeparator();
- viewMenu.add(jMenu3);
+ viewMenu.add(showMenu);
viewMenu.add(hideMenu);
+ viewMenu.add(showComplementMenuItem);
viewMenu.addSeparator();
viewMenu.add(followHighlightMenuItem);
+ viewMenu.addSeparator();
+ viewMenu.add(showSeqFeatures);
+ // viewMenu.add(showSeqFeaturesHeight);
+ viewMenu.add(openFeatureSettings);
+ tooltipSettingsMenu.add(showDbRefsMenuitem);
+ tooltipSettingsMenu.add(showNpFeatsMenuitem);
+ viewMenu.add(tooltipSettingsMenu);
+ viewMenu.addSeparator();
+ viewMenu.add(alignmentProperties);
+ viewMenu.addSeparator();
+ viewMenu.add(overviewMenuItem);
+
annotationsMenu.add(annotationPanelMenuItem);
annotationsMenu.addSeparator();
annotationsMenu.add(showAllAlAnnotations);
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
- viewMenu.addSeparator();
- viewMenu.add(showSeqFeatures);
- // viewMenu.add(showSeqFeaturesHeight);
- viewMenu.add(openFeatureSettings);
- tooltipSettingsMenu.add(showDbRefsMenuitem);
- tooltipSettingsMenu.add(showNpFeatsMenuitem);
- viewMenu.add(tooltipSettingsMenu);
- viewMenu.addSeparator();
- viewMenu.add(alignmentProperties);
- viewMenu.addSeparator();
- viewMenu.add(overviewMenuItem);
colourMenu.add(applyToAllGroups);
colourMenu.add(textColour);
colourMenu.addSeparator();
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
sort.add(sortByTreeMenu);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
- jMenu2.add(createBioJS);
- jMenu2.add(createSVG);
+ exportImageMenu.add(htmlMenuItem);
+ exportImageMenu.add(epsFile);
+ exportImageMenu.add(createPNG);
+ exportImageMenu.add(createBioJS);
+ exportImageMenu.add(createSVG);
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
- jMenu3.add(showAllColumns);
- jMenu3.add(showAllSeqs);
- jMenu3.add(showAllhidden);
+ showMenu.add(showAllColumns);
+ showMenu.add(showAllSeqs);
+ showMenu.add(showAllhidden);
hideMenu.add(hideSelColumns);
hideMenu.add(hideSelSequences);
hideMenu.add(hideAllSelection);
}
/**
+ * Adds the given action listener and key accelerator to the given menu item.
+ * Also saves in a lookup table to support lookup of action by key stroke.
+ *
+ * @param keyStroke
+ * @param menuItem
+ * @param actionListener
+ */
+ protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
+ JMenuItem menuItem, ActionListener actionListener)
+ {
+ menuItem.setAccelerator(keyStroke);
+ accelerators.put(keyStroke, menuItem);
+ menuItem.addActionListener(actionListener);
+ }
+
+ /**
* Action on clicking sort annotations by type.
*
* @param sortOrder
{
}
- protected void showProducts_actionPerformed(ActionEvent e)
- {
- }
-
protected void buildSortByAnnotationScoresMenu()
{
}
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
}
{
this.annotationSortOrder = annotationSortOrder;
}
+
+ public Map<KeyStroke, JMenuItem> getAccelerators()
+ {
+ return this.accelerators;
+ }
+
+ /**
+ * Returns the selected index of the tabbed pane, or -1 if none selected
+ * (including the case where the tabbed pane has not been made visible).
+ *
+ * @return
+ */
+ public int getTabIndex()
+ {
+ return tabbedPane.getSelectedIndex();
+ }
+
+ public JPanel getStatusPanel()
+ {
+ return statusPanel;
+ }
+
+ /**
+ * Sets a reference to the containing split frame. Also makes the 'toggle
+ * split view' menu item visible and checked.
+ *
+ * @param sf
+ */
+ public void setSplitFrame(SplitContainerI sf)
+ {
+ this.splitFrame = sf;
+ if (sf != null)
+ {
+ this.showComplementMenuItem.setVisible(true);
+ this.showComplementMenuItem.setState(true);
+ }
+ }
+
+ public SplitContainerI getSplitViewContainer()
+ {
+ return this.splitFrame;
+ }
+
+ protected void showComplement_actionPerformed(boolean state)
+ {
+ }
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.jbgui;
+
+import jalview.gui.Desktop;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+
+/**
+ * GUI layout for PDB Fetch Panel
+ *
+ * @author tcnofoegbu
+ *
+ */
+@SuppressWarnings("serial")
+public abstract class GPDBSearchPanel extends JPanel
+{
+ protected String frameTitle = MessageManager
+ .getString("label.pdb_sequence_getcher");
+
+ protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
+
+ protected JComboBox<PDBDocField> cmb_searchTarget = new JComboBox<PDBDocField>();
+
+ protected JButton btn_ok = new JButton();
+
+ protected JButton btn_back = new JButton();
+
+ protected JButton btn_cancel = new JButton();
+
+ protected JTextField txt_search = new JTextField(20);
+
+ protected JTable tbl_summary = new JTable();
+
+ protected JScrollPane scrl_searchResult = new JScrollPane(
+tbl_summary);
+
+ private JTabbedPane tabbedPane = new JTabbedPane();
+
+ private PDBDocFieldPreferences pdbDocFieldPrefs = new PDBDocFieldPreferences(
+ PreferenceSource.SEARCH_SUMMARY);
+
+ private JPanel pnl_actions = new JPanel();
+
+ private JPanel pnl_results = new JPanel();
+
+ private JPanel pnl_inputs = new JPanel();
+
+ private BorderLayout mainLayout = new BorderLayout();
+
+ public GPDBSearchPanel()
+ {
+ try
+ {
+ jbInit();
+ mainFrame.invalidate();
+ mainFrame.pack();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Initializes the GUI default properties
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ tbl_summary.setAutoCreateRowSorter(true);
+ btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_back.setText(MessageManager.getString("action.back"));
+ btn_back.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ btn_back_ActionPerformed();
+ }
+ });
+ btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_ok.setText(MessageManager.getString("action.ok"));
+ btn_ok.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ btn_ok_ActionPerformed();
+ }
+ });
+ btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_cancel.setText(MessageManager.getString("action.cancel"));
+ btn_cancel.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ btn_cancel_ActionPerformed();
+ }
+ });
+
+ scrl_searchResult.setPreferredSize(new Dimension(500, 300));
+ scrl_searchResult
+ .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
+ cmb_searchTarget.setFont(new java.awt.Font("Verdana", 0, 12));
+ cmb_searchTarget.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+ });
+
+ populateCmbSearchTargetOptions();
+
+ txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
+ txt_search.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+ });
+
+ final String searchTabTitle = MessageManager
+ .getString("label.search_result");
+ ChangeListener changeListener = new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent changeEvent)
+ {
+ JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
+ .getSource();
+ int index = sourceTabbedPane.getSelectedIndex();
+ if (sourceTabbedPane.getTitleAt(index).equals(searchTabTitle))
+ {
+ txt_search_ActionPerformed();
+ }
+ }
+ };
+ tabbedPane.addChangeListener(changeListener);
+ tabbedPane.setPreferredSize(new Dimension(500, 300));
+ tabbedPane.add(searchTabTitle, scrl_searchResult);
+ tabbedPane.add(
+ MessageManager.getString("label.configure_displayed_columns"),
+ pdbDocFieldPrefs);
+
+ pnl_actions.add(btn_back);
+ pnl_actions.add(btn_ok);
+ pnl_actions.add(btn_cancel);
+
+ pnl_results.add(tabbedPane);
+ pnl_inputs.add(cmb_searchTarget);
+ pnl_inputs.add(txt_search);
+
+ this.setLayout(mainLayout);
+ this.add(pnl_inputs, java.awt.BorderLayout.NORTH);
+ this.add(pnl_results, java.awt.BorderLayout.CENTER);
+ this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
+ mainFrame.setVisible(true);
+ mainFrame.setContentPane(this);
+ mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ }
+
+ public JComboBox<PDBDocField> getCmbSearchTarget()
+ {
+ return cmb_searchTarget;
+ }
+
+ public JTextField getTxtSearch()
+ {
+ return txt_search;
+ }
+
+ public JInternalFrame getMainFrame()
+ {
+ return mainFrame;
+ }
+
+ public abstract void txt_search_ActionPerformed();
+
+ public abstract void btn_ok_ActionPerformed();
+
+ public abstract void btn_back_ActionPerformed();
+
+ public abstract void btn_cancel_ActionPerformed();
+
+ public abstract void populateCmbSearchTargetOptions();
+
+}
import jalview.gui.JvSwingUtils;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
protected JTextField chimeraPath = new JTextField();
+
/*
* Colours tab components
*/
protected JPanel maxColour = new JPanel();
- protected JComboBox<String> colour = new JComboBox<String>();
+ protected JComboBox<String> protColour = new JComboBox<String>();
+
+ protected JComboBox<String> nucColour = new JComboBox<String>();
/*
* Connections tab components
maxColour_actionPerformed(maxColour);
}
});
- colour.setFont(verdana11);
- colour.setBounds(new Rectangle(172, 225, 155, 21));
- JLabel colourLabel = new JLabel();
- colourLabel.setFont(verdana11);
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText(MessageManager.getString("label.alignment_colour")
+
+ protColour.setFont(verdana11);
+ protColour.setBounds(new Rectangle(172, 225, 155, 21));
+ JLabel protColourLabel = new JLabel();
+ protColourLabel.setFont(verdana11);
+ protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ protColourLabel.setText(MessageManager
+ .getString("label.prot_alignment_colour") + " ");
+ JvSwingUtils.addtoLayout(coloursTab, MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ protColourLabel, protColour);
+
+ nucColour.setFont(verdana11);
+ nucColour.setBounds(new Rectangle(172, 240, 155, 21));
+ JLabel nucColourLabel = new JLabel();
+ nucColourLabel.setFont(verdana11);
+ nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ nucColourLabel.setText(MessageManager
+ .getString("label.nuc_alignment_colour")
+ " ");
JvSwingUtils.addtoLayout(coloursTab, MessageManager
.getString("label.default_colour_scheme_for_alignment"),
- colourLabel, colour);
+ nucColourLabel, nucColour);
+
JPanel annotationShding = new JPanel();
annotationShding.setBorder(new TitledBorder(MessageManager
.getString("label.annotation_shading_default")));
.getString("label.structure_options")));
structureTab.setLayout(null);
final int width = 400;
- final int height = 23;
- final int lineSpacing = 30;
+ final int height = 22;
+ final int lineSpacing = 25;
int ypos = 30;
structFromPdb.setFont(verdana11);
});
structureTab.add(chimeraPath);
+ ypos += lineSpacing;
+ // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
+ // scrl_pdbDocFieldConfig
+ // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ // scrl_pdbDocFieldConfig.setBounds();
+ PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
+ PreferenceSource.PREFERENCES);
+ docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
+ structureTab.add(docFieldPref);
+
+
+
+
return structureTab;
}
+
/**
* Action on choosing a structure viewer from combobox options.
*
--- /dev/null
+package jalview.jbgui;
+
+import java.awt.Component;
+import java.awt.MouseInfo;
+import java.awt.Point;
+import java.awt.Rectangle;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
+import javax.swing.plaf.basic.BasicInternalFrameUI;
+
+import jalview.util.Platform;
+
+public class GSplitFrame extends JInternalFrame
+{
+ private static final long serialVersionUID = 1L;
+
+ private GAlignFrame topFrame;
+
+ private GAlignFrame bottomFrame;
+
+ private JSplitPane splitPane;
+
+ /**
+ * Constructor
+ *
+ * @param top
+ * @param bottom
+ */
+ public GSplitFrame(GAlignFrame top, GAlignFrame bottom)
+ {
+ this.topFrame = top;
+ this.bottomFrame = bottom;
+
+ hideTitleBars();
+
+ addSplitPane();
+ }
+
+ /**
+ * Create and add the split pane containing the top and bottom components.
+ */
+ protected void addSplitPane()
+ {
+ splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, topFrame,
+ bottomFrame);
+ splitPane.setVisible(true);
+ final double ratio = topFrame.getHeight()
+ / (double) (topFrame.getHeight() + bottomFrame.getHeight());
+ splitPane.setDividerLocation(ratio);
+ splitPane.setResizeWeight(ratio);
+ splitPane.setDividerSize(5);
+ add(splitPane);
+ }
+
+ /**
+ * Try to hide the title bars as a waste of precious space.
+ *
+ * @see http
+ * ://stackoverflow.com/questions/7218971/java-method-works-on-windows
+ * -but-not-macintosh -java
+ */
+ protected void hideTitleBars()
+ {
+ if (new Platform().isAMac())
+ {
+ // this saves some space - but doesn't hide the title bar
+ topFrame.putClientProperty("JInternalFrame.isPalette", true);
+ // topFrame.getRootPane().putClientProperty("Window.style", "small");
+ bottomFrame.putClientProperty("JInternalFrame.isPalette", true);
+ }
+ else
+ {
+ ((BasicInternalFrameUI) topFrame.getUI()).setNorthPane(null);
+ ((BasicInternalFrameUI) bottomFrame.getUI()).setNorthPane(null);
+ }
+ }
+
+ public GAlignFrame getTopFrame()
+ {
+ return topFrame;
+ }
+
+ public GAlignFrame getBottomFrame()
+ {
+ return bottomFrame;
+ }
+
+ /**
+ * Returns the split pane component the mouse is in, or null if neither.
+ *
+ * @return
+ */
+ protected GAlignFrame getFrameAtMouse()
+ {
+ Point loc = MouseInfo.getPointerInfo().getLocation();
+
+ if (isIn(loc, splitPane.getTopComponent()))
+ {
+ return getTopFrame();
+ }
+ else if (isIn(loc, splitPane.getBottomComponent()))
+ {
+ return getBottomFrame();
+ }
+ return null;
+ }
+
+ private boolean isIn(Point loc, Component comp)
+ {
+ if (!comp.isVisible())
+ {
+ return false;
+ }
+ Point p = comp.getLocationOnScreen();
+ Rectangle r = new Rectangle(p.x, p.y, comp.getWidth(), comp.getHeight());
+ return r.contains(loc);
+ }
+
+ /**
+ * Make the complement of the specified split component visible or hidden,
+ * adjusting the position of the split divide.
+ */
+ public void setComplementVisible(Object alignFrame, boolean show)
+ {
+ if (alignFrame == this.topFrame)
+ {
+ this.bottomFrame.setVisible(show);
+ }
+ else if (alignFrame == this.bottomFrame)
+ {
+ this.topFrame.setVisible(show);
+ }
+ if (show)
+ {
+ // SplitPane needs nudging to restore 50-50 split
+ // TODO save/restore other ratios
+ splitPane.setDividerLocation(0.5d);
+ }
+ validate();
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.jbgui;
+
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.CardLayout;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+
+@SuppressWarnings("serial")
+/**
+ * GUI layout for structure chooser
+ * @author tcnofoegbu
+ *
+ */
+public abstract class GStructureChooser extends JPanel implements
+ ItemListener
+{
+ protected String frameTitle = MessageManager
+ .getString("label.structure_chooser");
+
+ protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
+
+ protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<FilterOption>();
+
+ protected AlignmentPanel ap;
+
+ protected JLabel lbl_result = new JLabel(
+ MessageManager.getString("label.select"));
+
+ protected JButton btn_view = new JButton();
+
+ protected JButton btn_cancel = new JButton();
+
+ protected JButton btn_pdbFromFile = new JButton();
+
+ protected JTextField txt_search = new JTextField(14);
+
+ private JPanel pnl_actions = new JPanel();
+
+ private JPanel pnl_filter = new JPanel();
+
+ private JPanel pnl_idInput = new JPanel(new FlowLayout());
+
+ private JPanel pnl_fileChooser = new JPanel(new FlowLayout());
+
+ private JPanel pnl_idInputBL = new JPanel(new BorderLayout());
+
+ private JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
+
+ protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
+
+ protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
+ .getLayout());
+
+ private BorderLayout mainLayout = new BorderLayout();
+
+ protected JCheckBox chk_rememberSettings = new JCheckBox(
+ MessageManager.getString("label.dont_ask_me_again"));
+
+ protected JCheckBox chk_invertFilter = new JCheckBox(
+ MessageManager.getString("label.invert"));
+
+ protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
+ "/images/loading.gif"));
+
+ protected ImageIcon goodImage = new ImageIcon(getClass().getResource(
+ "/images/good.png"));
+
+ protected ImageIcon errorImage = new ImageIcon(getClass().getResource(
+ "/images/error.png"));
+
+ protected JLabel lbl_loading = new JLabel(loadingImage);
+
+ protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
+
+ protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
+
+
+ protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel();
+
+ protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel();
+
+ protected static final String VIEWS_FILTER = "VIEWS_FILTER";
+
+ protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
+
+ protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
+
+ protected JTable tbl_summary = new JTable();
+
+ protected JScrollPane scrl_foundStructures = new JScrollPane(
+ tbl_summary);
+
+ private JTabbedPane tabbedPane = new JTabbedPane();
+
+ private PDBDocFieldPreferences pdbDocFieldPrefs = new PDBDocFieldPreferences(
+ PreferenceSource.STRUCTURE_CHOOSER);
+
+ public GStructureChooser()
+ {
+ try
+ {
+ jbInit();
+ mainFrame.setVisible(false);
+ mainFrame.invalidate();
+ mainFrame.pack();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Initializes the GUI default properties
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ tbl_summary.setAutoCreateRowSorter(true);
+ btn_view.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_view.setText(MessageManager.getString("action.view"));
+ btn_view.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_ActionPerformed();
+ }
+ });
+ btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_cancel.setText(MessageManager.getString("action.cancel"));
+ btn_cancel.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ mainFrame.dispose();
+ }
+ });
+
+ btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
+ String btn_title = MessageManager.getString("label.select_pdb_file");
+ btn_pdbFromFile.setText(btn_title + " ");
+ btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pdbFromFile_actionPerformed();
+ }
+ });
+
+ scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
+ scrl_foundStructures
+ .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
+ cmb_filterOption.setFont(new java.awt.Font("Verdana", 0, 12));
+ chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
+ chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
+
+
+ txt_search.setToolTipText(MessageManager
+ .getString("label.enter_pdb_id"));
+ cmb_filterOption.setToolTipText(MessageManager
+ .getString("info.select_filter_option"));
+ txt_search.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+ });
+
+ cmb_filterOption.addItemListener(this);
+ chk_invertFilter.addItemListener(this);
+
+ pnl_actions.add(chk_rememberSettings);
+ pnl_actions.add(btn_view);
+ pnl_actions.add(btn_cancel);
+
+ // pnl_filter.add(lbl_result);
+ pnl_filter.add(cmb_filterOption);
+ pnl_filter.add(lbl_loading);
+ pnl_filter.add(chk_invertFilter);
+ lbl_loading.setVisible(false);
+
+ pnl_idInput.add(txt_search);
+ pnl_idInput.add(lbl_pdbManualFetchStatus);
+
+ pnl_fileChooser.add(btn_pdbFromFile);
+ pnl_fileChooser.add(lbl_fromFileStatus);
+
+ pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
+ pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
+
+ pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
+ pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
+
+ final String foundStructureSummary = MessageManager
+ .getString("label.found_structures_summary");
+
+ ChangeListener changeListener = new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent changeEvent)
+ {
+ JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
+ .getSource();
+ int index = sourceTabbedPane.getSelectedIndex();
+ if (sourceTabbedPane.getTitleAt(index)
+ .equals(foundStructureSummary))
+ {
+ tabRefresh();
+ }
+ }
+ };
+ tabbedPane.addChangeListener(changeListener);
+ tabbedPane.setPreferredSize(new Dimension(500, 300));
+ tabbedPane.add(foundStructureSummary, scrl_foundStructures);
+ tabbedPane.add(
+ MessageManager.getString("label.configure_displayed_columns"),
+ pdbDocFieldPrefs);
+
+
+ pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
+ pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
+ pnl_switchableViews.add(tabbedPane, VIEWS_FILTER);
+
+ this.setLayout(mainLayout);
+ this.add(pnl_filter, java.awt.BorderLayout.NORTH);
+ this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
+ this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
+
+ mainFrame.setVisible(true);
+ mainFrame.setContentPane(this);
+ mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ }
+
+
+ @Override
+ /**
+ * Event listener for the 'filter' combo-box and 'invert' check-box
+ */
+ public void itemStateChanged(ItemEvent e)
+ {
+ stateChanged(e);
+ }
+
+ /**
+ * This inner class provides the data model for the structure filter combo-box
+ *
+ * @author tcnofoegbu
+ *
+ */
+ public class FilterOption
+ {
+ private String name;
+
+ private String value;
+
+ private String view;
+
+ public FilterOption(String name, String value, String view)
+ {
+ this.name = name;
+ this.value = value;
+ this.view = view;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public String getValue()
+ {
+ return value;
+ }
+
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ public String getView()
+ {
+ return view;
+ }
+
+ public void setView(String view)
+ {
+ this.view = view;
+ }
+
+ public String toString()
+ {
+ return this.name;
+ }
+ }
+
+ /**
+ * This inner class provides the provides the data model for associate
+ * sequence combo-box - cmb_assSeq
+ *
+ * @author tcnofoegbu
+ *
+ */
+ public class AssociateSeqOptions
+ {
+ private SequenceI sequence;
+ private String name;
+
+ public AssociateSeqOptions(SequenceI seq)
+ {
+ this.sequence = seq;
+ this.name = (seq.getName().length() >= 23) ? seq.getName().substring(
+ 0, 23) : seq.getName();
+ }
+
+ public AssociateSeqOptions(String name, SequenceI seq)
+ {
+ this.name = name;
+ this.sequence = seq;
+ }
+
+ public String toString()
+ {
+ return name;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ public void setSequence(SequenceI sequence)
+ {
+ this.sequence = sequence;
+ }
+
+ }
+
+ /**
+ * This inner class holds the Layout and configuration of the panel which
+ * handles association of manually fetched structures to a unique sequence
+ * when more than one sequence selection is made
+ *
+ * @author tcnofoegbu
+ *
+ */
+ public class AssciateSeqPanel extends JPanel implements ItemListener
+ {
+ private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<AssociateSeqOptions>();
+
+ private JLabel lbl_associateSeq = new JLabel();
+
+ public AssciateSeqPanel()
+ {
+ this.setLayout(new FlowLayout());
+ this.add(cmb_assSeq);
+ this.add(lbl_associateSeq);
+ cmb_assSeq.setToolTipText(MessageManager
+ .getString("info.associate_wit_sequence"));
+ cmb_assSeq.addItemListener(this);
+ }
+
+ public void loadCmbAssSeq()
+ {
+ populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq);
+ }
+
+ public JComboBox<AssociateSeqOptions> getCmb_assSeq()
+ {
+ return cmb_assSeq;
+ }
+
+ public void setCmb_assSeq(JComboBox<AssociateSeqOptions> cmb_assSeq)
+ {
+ this.cmb_assSeq = cmb_assSeq;
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ {
+ cmbAssSeqStateChanged();
+ }
+ }
+ }
+
+ public JComboBox<FilterOption> getCmbFilterOption()
+ {
+ return cmb_filterOption;
+ }
+
+ protected abstract void stateChanged(ItemEvent e);
+
+ protected abstract void updateCurrentView();
+
+ protected abstract void populateFilterComboBox();
+
+ protected abstract void ok_ActionPerformed();
+
+ protected abstract void pdbFromFile_actionPerformed();
+
+ protected abstract void txt_search_ActionPerformed();
+
+ public abstract void populateCmbAssociateSeqOptions(
+ JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq);
+
+ public abstract void cmbAssSeqStateChanged();
+
+ public abstract void tabRefresh();
+}
import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
public class GTreePanel extends JInternalFrame
{
{
public void actionPerformed(ActionEvent e)
{
- sortByTree_actionPerformed(e);
+ sortByTree_actionPerformed();
}
});
font.setText(MessageManager.getString("action.font"));
{
}
- public void sortByTree_actionPerformed(ActionEvent e)
+ public void sortByTree_actionPerformed()
{
}
--- /dev/null
+package jalview.jbgui;
+
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.table.AbstractTableModel;
+
+@SuppressWarnings("serial")
+public class PDBDocFieldPreferences extends JScrollPane
+{
+ protected JTable tbl_pdbDocFieldConfig = new JTable();
+
+ protected JScrollPane scrl_pdbDocFieldConfig = new JScrollPane(
+ tbl_pdbDocFieldConfig);
+
+ private HashMap<String, PDBDocField> map = new HashMap<String, PDBDocField>();
+
+ private static Collection<PDBDocField> searchSummaryFields = new HashSet<PDBDocField>();
+
+ private static Collection<PDBDocField> structureSummaryFields = new HashSet<PDBDocField>();
+
+ public enum PreferenceSource
+ {
+ SEARCH_SUMMARY, STRUCTURE_CHOOSER, PREFERENCES;
+ }
+
+ private PreferenceSource currentSource;
+
+ static
+ {
+ searchSummaryFields.add(PDBDocField.PDB_ID);
+ searchSummaryFields.add(PDBDocField.TITLE);
+
+ structureSummaryFields.add(PDBDocField.PDB_ID);
+ structureSummaryFields.add(PDBDocField.TITLE);
+ }
+
+ public PDBDocFieldPreferences(PreferenceSource source)
+ {
+ tbl_pdbDocFieldConfig.setAutoCreateRowSorter(true);
+ this.getViewport().add(tbl_pdbDocFieldConfig);
+ this.currentSource = source;
+
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[]
+ { "PDB Feild", "Show in search summary" };
+ break;
+ case STRUCTURE_CHOOSER:
+ columnNames = new String[]
+ { "PDB Feild", "Show in structure summary" };
+ break;
+ case PREFERENCES:
+ columnNames = new String[]
+ { "PDB Feild", "Show in search summary", "Show in structure summary" };
+ break;
+ default:
+ break;
+ }
+
+ Object[][] data = new Object[PDBDocField.values().length - 1][3];
+ int x = 0;
+ for (PDBDocField field : PDBDocField.values())
+ {
+ if (field.getName().equalsIgnoreCase("all"))
+ {
+ continue;
+ }
+
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ data[x++] = new Object[]
+ { field.getName(), searchSummaryFields.contains(field) };
+ break;
+ case STRUCTURE_CHOOSER:
+ data[x++] = new Object[]
+ { field.getName(), structureSummaryFields.contains(field) };
+ break;
+ case PREFERENCES:
+ data[x++] = new Object[]
+ { field.getName(), searchSummaryFields.contains(field),
+ structureSummaryFields.contains(field) };
+ break;
+ default:
+ break;
+ }
+ map.put(field.getName(), field);
+ }
+
+ PDBFieldTableModel model = new PDBFieldTableModel(columnNames, data);
+ tbl_pdbDocFieldConfig.setModel(model);
+ }
+
+ public static Collection<PDBDocField> getSearchSummaryFields()
+ {
+ return searchSummaryFields;
+ }
+
+ public static void setSearchSummaryFields(
+ Collection<PDBDocField> searchSummaryFields)
+ {
+ PDBDocFieldPreferences.searchSummaryFields = searchSummaryFields;
+ }
+
+ public static Collection<PDBDocField> getStructureSummaryFields()
+ {
+ return structureSummaryFields;
+ }
+
+ public static void setStructureSummaryFields(
+ Collection<PDBDocField> structureSummaryFields)
+ {
+ PDBDocFieldPreferences.structureSummaryFields = structureSummaryFields;
+ }
+
+ class PDBFieldTableModel extends AbstractTableModel
+ {
+
+ public PDBFieldTableModel(String[] columnNames, Object[][] data)
+ {
+ this.data = data;
+ this.columnNames = columnNames;
+ }
+
+ private Object[][] data;
+
+ private String[] columnNames;
+
+ public int getColumnCount()
+ {
+ return columnNames.length;
+ }
+
+ public int getRowCount()
+ {
+ return data.length;
+ }
+
+ public String getColumnName(int col)
+ {
+ return columnNames[col];
+ }
+
+ public Object getValueAt(int row, int col)
+ {
+ return data[row][col];
+ }
+
+ /*
+ * JTable uses this method to determine the default renderer/ editor for
+ * each cell. If we didn't implement this method, then the last column would
+ * contain text ("true"/"false"), rather than a check box.
+ */
+ public Class getColumnClass(int c)
+ {
+ return getValueAt(0, c).getClass();
+ }
+
+ /*
+ * Don't need to implement this method unless your table's editable.
+ */
+ public boolean isCellEditable(int row, int col)
+ {
+ // Note that the data/cell address is constant,
+ // no matter where the cell appears onscreen.
+ return col == 1 || col == 2;
+
+ }
+
+ /*
+ * Don't need to implement this method unless your table's data can change.
+ */
+ public void setValueAt(Object value, int row, int col)
+ {
+ data[row][col] = value;
+ fireTableCellUpdated(row, col);
+
+ String name = getValueAt(row, 0).toString();
+ boolean selected = ((Boolean) value).booleanValue();
+
+ PDBDocField pdbField = map.get(name);
+
+ if (currentSource == PreferenceSource.SEARCH_SUMMARY)
+ {
+ updatePrefs(searchSummaryFields, pdbField, selected);
+ }
+ else if (currentSource == PreferenceSource.STRUCTURE_CHOOSER)
+ {
+ updatePrefs(structureSummaryFields, pdbField, selected);
+ }
+ else if (currentSource == PreferenceSource.PREFERENCES)
+ {
+ if (col == 1)
+ {
+ updatePrefs(searchSummaryFields, pdbField, selected);
+ }
+ else if (col == 2)
+ {
+ updatePrefs(structureSummaryFields, pdbField, selected);
+ }
+ }
+ }
+
+ private void updatePrefs(Collection<PDBDocField> prefConfig,
+ PDBDocField pdbField,
+ boolean selected)
+ {
+ if (prefConfig.contains(pdbField) && !selected)
+ {
+ prefConfig.remove(pdbField);
+ }
+
+ if (!prefConfig.contains(pdbField) && selected)
+ {
+ prefConfig.add(pdbField);
+ }
+ }
+
+ }
+}
package jalview.renderer;
import jalview.analysis.AAFrequency;
+import jalview.analysis.CodingUtils;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
private Hashtable[] hconsensus;
+ private Hashtable[] complementConsensus;
+
private Hashtable[] hStrucConsensus;
private boolean av_ignoreGapsConsensus;
profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
: new jalview.schemes.ZappoColourScheme();
}
- boolean rna = av.getAlignment().isNucleotide();
columnSelection = av.getColumnSelection();
- hconsensus = av.getSequenceConsensusHash();// hconsensus;
- hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
- av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
+ hconsensus = av.getSequenceConsensusHash();
+ complementConsensus = av.getComplementConsensusHash();
+ hStrucConsensus = av.getRnaStructureConsensusHash();
+ av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
}
+ /**
+ * Returns profile data; the first element is the profile type, the second is
+ * the number of distinct values, the third the total count, and the remainder
+ * depend on the profile type.
+ *
+ * @param aa
+ * @param column
+ * @return
+ */
public int[] getProfileFor(AlignmentAnnotation aa, int column)
{
// TODO : consider refactoring the global alignment calculation
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
- if (aa.autoCalculated && aa.label.startsWith("Consensus"))
+ if (aa.autoCalculated
+ && (aa.label.startsWith("Consensus") || aa.label
+ .startsWith("cDNA Consensus")))
{
+ boolean forComplement = aa.label.startsWith("cDNA Consensus");
if (aa.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
+ // TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
aa.groupRef.consensusData[column],
aa.groupRef.getIgnoreGapsConsensus());
// be stored
if (aa.groupRef == null && aa.sequenceRef == null)
{
- return AAFrequency.extractProfile(hconsensus[column],
- av_ignoreGapsConsensus);
+ if (forComplement)
+ {
+ return AAFrequency.extractCdnaProfile(
+ complementConsensus[column], av_ignoreGapsConsensus);
+ }
+ else
+ {
+ return AAFrequency.extractProfile(hconsensus[column],
+ av_ignoreGapsConsensus);
+ }
}
}
else
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
- boolean centreColLabels, centreColLabelsDef = av
- .getCentreColumnLabels();
+ boolean centreColLabels;
+ boolean centreColLabelsDef = av.isCentreColumnLabels();
boolean scaleColLabel = false;
- AlignmentAnnotation consensusAnnot = av
- .getAlignmentConsensusAnnotation(), structConsensusAnnot = av
+ final AlignmentAnnotation consensusAnnot = av
+ .getAlignmentConsensusAnnotation();
+ final AlignmentAnnotation structConsensusAnnot = av
.getAlignmentStrucConsensusAnnotation();
+ final AlignmentAnnotation complementConsensusAnnot = av
+ .getComplementConsensusAnnotation();
boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
BitSet graphGroupDrawn = new BitSet();
renderProfile = row.groupRef.isShowSequenceLogo();
normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
}
- else if (row == consensusAnnot || row == structConsensusAnnot)
+ else if (row == consensusAnnot || row == structConsensusAnnot
+ || row == complementConsensusAnnot)
{
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;
{
validRes = true;
}
+ final String displayChar = validRes ? row_annotations[column].displayCharacter
+ : null;
if (x > -1)
{
if (activeRow == i)
g.setColor(Color.orange.darker());
g.fillRect(x * charWidth, y, charWidth, charHeight);
}
- if (validCharWidth
- && validRes
- && row_annotations[column].displayCharacter != null
- && (row_annotations[column].displayCharacter.length() > 0))
+ if (validCharWidth && validRes && displayChar != null
+ && (displayChar.length() > 0))
{
- if (centreColLabels || scaleColLabel)
+ fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
+ displayChar.length());
+ if (/* centreColLabels || */scaleColLabel)
{
- fmWidth = fm.charsWidth(
- row_annotations[column].displayCharacter
- .toCharArray(), 0,
- row_annotations[column].displayCharacter.length());
-
- if (scaleColLabel)
- {
+ // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
+ // displayChar.length());
+ //
+ // if (scaleColLabel)
+ // {
// justify the label and scale to fit in column
if (fmWidth > charWidth)
{
// and update the label's width to reflect the scaling.
fmWidth = charWidth;
}
- }
- }
- else
- {
- fmWidth = fm
- .charWidth(row_annotations[column].displayCharacter
- .charAt(0));
+ // }
}
+ // TODO is it ok to use width of / show all characters here?
+ // else
+ // {
+ // fmWidth = fm.charWidth(displayChar.charAt(0));
+ // }
charOffset = (int) ((charWidth - fmWidth) / 2f);
if (row_annotations[column].colour == null)
if (column == 0 || row.graph > 0)
{
- g.drawString(row_annotations[column].displayCharacter,
- (x * charWidth) + charOffset, y + iconOffset);
+ g.drawString(displayChar, (x * charWidth) + charOffset, y
+ + iconOffset);
}
else if (row_annotations[column - 1] == null
|| (labelAllCols
- || !row_annotations[column].displayCharacter
- .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
+ || !displayChar
+ .equals(row_annotations[column - 1].displayCharacter) || (displayChar
.length() < 2 && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(row_annotations[column].displayCharacter, x
- * charWidth + charOffset, y + iconOffset);
+ g.drawString(displayChar, x * charWidth + charOffset, y
+ + iconOffset);
}
g.setFont(ofont);
}
if (ss == '(')
{
// distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf(')') > -1)
+ if (displayChar.indexOf(')') > -1)
{
ss = ')';
}
if (ss == '[')
{
- if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
+ if ((displayChar.indexOf(']') > -1))
{
ss = ']';
if (ss == '{')
{
// distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf('}') > -1)
+ if (displayChar.indexOf('}') > -1)
{
ss = '}';
if (ss == '<')
{
// distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf('<') > -1)
+ if (displayChar.indexOf('<') > -1)
{
ss = '>';
if (ss >= 65)
{
// distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf(ss + 32) > -1)
+ if (displayChar.indexOf(ss + 32) > -1)
{
ss = (char) (ss + 32);
if (renderProfile)
{
+ /*
+ * {profile type, #values, total count, char1, pct1, char2, pct2...}
+ */
int profl[] = getProfileFor(_aa, column);
+
// just try to draw the logo if profl is not null
- if (profl != null && profl[1] != 0)
+ if (profl != null && profl[2] != 0)
{
+ boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
+ boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
float ht = normaliseProfile ? y - _aa.graphHeight : y1;
double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
double hght;
char[] dc;
/**
- * profl.length == 74 indicates that the profile of a secondary
- * structure conservation row was accesed. Therefore dc gets length 2,
- * to have space for a basepair instead of just a single nucleotide
+ * Render a single base for a sequence profile, a base pair for
+ * structure profile, and a triplet for a cdna profile
*/
- if (profl.length == 74)
- {
- dc = new char[2];
- }
- else
- {
- dc = new char[1];
- }
+ dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
+
LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
- double scale = 1f / (normaliseProfile ? profl[1] : 100f);
+ double scale = 1f / (normaliseProfile ? profl[2] : 100f);
float ofontHeight = 1f / lm.getAscent();// magnify to fill box
double scl = 0.0;
- for (int c = 2; c < profl[0];)
- {
- dc[0] = (char) profl[c++];
- if (_aa.label.startsWith("StrucConsensus"))
+ /*
+ * Traverse the character(s)/percentage data in the array
+ */
+ int c = 3;
+ int valuesProcessed = 0;
+ // profl[1] is the number of values in the profile
+ while (valuesProcessed < profl[1])
+ {
+ if (isStructureProfile)
{
+ // todo can we encode a structure pair as an int, like codons?
+ dc[0] = (char) profl[c++];
dc[1] = (char) profl[c++];
}
+ else if (isCdnaProfile)
+ {
+ dc = CodingUtils.decodeCodon(profl[c++]);
+ }
+ else
+ {
+ dc[0] = (char) profl[c++];
+ }
wdth = charWidth;
wdth /= fm.charsWidth(dc, 0, dc.length);
ht += scl;
+ // next profl[] position is profile % for the character(s)
+ scl = htn * scale * profl[c++];
+ lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
+ .getFontRenderContext());
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, scl / lm.getAscent())));
+ lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
+
+ // Debug - render boxes around characters
+ // g.setColor(Color.red);
+ // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
+ // (int)(scl));
+ // g.setColor(profcolour.findColour(dc[0]).darker());
+
+ /*
+ * Set character colour as per alignment colour scheme; use the
+ * codon translation if a cDNA profile
+ */
+ Color colour = null;
+ if (isCdnaProfile)
{
- scl = htn * scale * profl[c++];
- lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
- .getFontRenderContext());
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl / lm.getAscent())));
- lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
-
- // Debug - render boxes around characters
- // g.setColor(Color.red);
- // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
- // (int)(scl));
- // g.setColor(profcolour.findColour(dc[0]).darker());
- g.setColor(profcolour.findColour(dc[0], column, null));
-
- hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
- .getBaselineIndex()]));
-
- g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
+ final String codonTranslation = ResidueProperties
+ .codonTranslate(new String(dc));
+ colour = profcolour.findColour(codonTranslation.charAt(0),
+ column, null);
}
+ else
+ {
+ colour = profcolour.findColour(dc[0], column, null);
+ }
+ g.setColor(colour == Color.white ? Color.lightGray : colour);
+
+ hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
+ .getBaselineIndex()]));
+
+ g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
+ valuesProcessed++;
}
g.setFont(ofont);
}
import java.awt.Image;
import java.awt.image.ImageObserver;
+/**
+ * semi-insulated interface for rendering a faded image whilst a calculation is
+ * in progress on annotation panel. Will need to remove java.awt dependencies
+ * for Android/etc
+ *
+ * @author jprocter
+ *
+ */
public interface AwtRenderPanelI extends ImageObserver
{
/**
boolean offscreenRender = false;
- /**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
- * @param seq
- * DOCUMENT ME!
- * @param sg
- * DOCUMENT ME!
- * @param start
- * DOCUMENT ME!
- * @param end
- * DOCUMENT ME!
- * @param x1
- * DOCUMENT ME!
- * @param y1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
- */
protected SequenceI lastSeq;
char s;
charOffset = (av_charWidth - fm.charWidth(s)) / 2;
g.drawString(String.valueOf(s), charOffset
+ (av_charWidth * (i - start)), pady);
-
}
}
}
charOffset = (av_charWidth - fm.charWidth(s)) / 2;
g.drawString(String.valueOf(s), charOffset
+ (av_charWidth * (i - start)), pady);
-
}
}
}
return initialCol;
}
- final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq
- .getDatasetSequence() : seq;
+ SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
if (seq != lastSeq)
{
lastSeq = seq;
- sequenceFeatures = aseq.getSequenceFeatures();
- if (sequenceFeatures != null)
+ lastSequenceFeatures = sequenceFeatures;
+ if (lastSequenceFeatures != null)
{
- sfSize = sequenceFeatures.length;
+ sfSize = lastSequenceFeatures.length;
}
}
else
{
- if (sequenceFeatures != aseq.getSequenceFeatures())
+ if (lastSequenceFeatures != sequenceFeatures)
{
- sequenceFeatures = aseq.getSequenceFeatures();
- if (sequenceFeatures != null)
+ lastSequenceFeatures = sequenceFeatures;
+ if (lastSequenceFeatures != null)
{
- sfSize = sequenceFeatures.length;
+ sfSize = lastSequenceFeatures.length;
}
}
}
- if (sequenceFeatures == null || sfSize == 0)
+ if (lastSequenceFeatures == null || sfSize == 0)
{
return initialCol;
}
}
- private volatile SequenceFeature[] sequenceFeatures;
+ private volatile SequenceFeature[] lastSequenceFeatures;
int sfSize;
public synchronized void drawSequence(Graphics g, final SequenceI seq,
int start, int end, int y1)
{
- final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq
- .getDatasetSequence() : seq;
- if (aseq.getSequenceFeatures() == null
- || aseq.getSequenceFeatures().length == 0)
+ SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
+ if (sequenceFeatures == null || sequenceFeatures.length == 0)
{
return;
}
updateFeatures();
if (lastSeq == null || seq != lastSeq
- || aseq.getSequenceFeatures() != sequenceFeatures)
+ || sequenceFeatures != lastSequenceFeatures)
{
lastSeq = seq;
- sequenceFeatures = aseq.getSequenceFeatures();
+ lastSequenceFeatures = sequenceFeatures;
}
if (transparency != 1 && g != null)
epos = lastSeq.findPosition(end);
}
- sfSize = sequenceFeatures.length;
+ sfSize = lastSequenceFeatures.length;
String type;
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
{
// current feature to render
for (sfindex = 0; sfindex < sfSize; sfindex++)
{
- if (!sequenceFeatures[sfindex].type.equals(type))
+ final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
+ if (!sequenceFeature.type.equals(type))
{
continue;
}
if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- && sequenceFeatures[sfindex].featureGroup.length() != 0
- && featureGroups
- .containsKey(sequenceFeatures[sfindex].featureGroup)
- && !featureGroups
- .get(sequenceFeatures[sfindex].featureGroup)
+ && sequenceFeature.featureGroup != null
+ && sequenceFeature.featureGroup.length() != 0
+ && featureGroups.containsKey(sequenceFeature.featureGroup)
+ && !featureGroups.get(sequenceFeature.featureGroup)
.booleanValue())
{
continue;
}
if (!offscreenRender
- && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
+ && (sequenceFeature.getBegin() > epos || sequenceFeature
.getEnd() < spos))
{
continue;
if (offscreenRender && offscreenImage == null)
{
- if (sequenceFeatures[sfindex].begin <= start
- && sequenceFeatures[sfindex].end >= start)
+ if (sequenceFeature.begin <= start
+ && sequenceFeature.end >= start)
{
// this is passed out to the overview and other sequence renderers
// (e.g. molecule viewer) to get displayed colour for rendered
// sequence
- currentColour = new Integer(
- getColour(sequenceFeatures[sfindex]).getRGB());
+ currentColour = new Integer(getColour(sequenceFeature).getRGB());
// used to be retreived from av.featuresDisplayed
// currentColour = av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type);
}
}
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+ else if (sequenceFeature.type.equals("disulfide bond"))
{
-
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- getColour(sequenceFeatures[sfindex])
+ renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
+ seq.findIndex(sequenceFeature.begin) - 1,
+ getColour(sequenceFeature)
// new Color(((Integer) av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type)).intValue())
, start, end, y1);
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex])
+ renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1,
+ seq.findIndex(sequenceFeature.end) - 1,
+ getColour(sequenceFeature)
// new Color(((Integer) av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type)).intValue())
, start, end, y1);
}
- else if (showFeature(sequenceFeatures[sfindex]))
+ else if (showFeature(sequenceFeature))
{
if (av_isShowSeqFeatureHeight
- && sequenceFeatures[sfindex].score != Float.NaN)
+ && sequenceFeature.score != Float.NaN)
{
renderScoreFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1,
- normaliseScore(sequenceFeatures[sfindex]));
+ seq.findIndex(sequenceFeature.begin) - 1,
+ seq.findIndex(sequenceFeature.end) - 1,
+ getColour(sequenceFeature), start, end, y1,
+ normaliseScore(sequenceFeature));
}
else
{
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1);
+ renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
+ seq.findIndex(sequenceFeature.end) - 1,
+ getColour(sequenceFeature), start, end, y1);
}
}
*/
package jalview.schemabinding.version2;
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class Viewport implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _conservationSelected.
- */
- private boolean _conservationSelected;
-
- /**
- * keeps track of state for field: _conservationSelected
- */
- private boolean _has_conservationSelected;
-
- /**
- * Field _pidSelected.
- */
- private boolean _pidSelected;
-
- /**
- * keeps track of state for field: _pidSelected
- */
- private boolean _has_pidSelected;
-
- /**
- * Field _bgColour.
- */
- private java.lang.String _bgColour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _showFullId.
- */
- private boolean _showFullId;
-
- /**
- * keeps track of state for field: _showFullId
- */
- private boolean _has_showFullId;
-
- /**
- * Field _rightAlignIds.
- */
- private boolean _rightAlignIds;
-
- /**
- * keeps track of state for field: _rightAlignIds
- */
- private boolean _has_rightAlignIds;
-
- /**
- * Field _showText.
- */
- private boolean _showText;
-
- /**
- * keeps track of state for field: _showText
- */
- private boolean _has_showText;
-
- /**
- * Field _showColourText.
- */
- private boolean _showColourText;
-
- /**
- * keeps track of state for field: _showColourText
- */
- private boolean _has_showColourText;
-
- /**
- * Field _showUnconserved.
- */
- private boolean _showUnconserved = false;
-
- /**
- * keeps track of state for field: _showUnconserved
- */
- private boolean _has_showUnconserved;
-
- /**
- * Field _showBoxes.
- */
- private boolean _showBoxes;
-
- /**
- * keeps track of state for field: _showBoxes
- */
- private boolean _has_showBoxes;
-
- /**
- * Field _wrapAlignment.
- */
- private boolean _wrapAlignment;
-
- /**
- * keeps track of state for field: _wrapAlignment
- */
- private boolean _has_wrapAlignment;
-
- /**
- * Field _renderGaps.
- */
- private boolean _renderGaps;
-
- /**
- * keeps track of state for field: _renderGaps
- */
- private boolean _has_renderGaps;
-
- /**
- * Field _showSequenceFeatures.
- */
- private boolean _showSequenceFeatures;
-
- /**
- * keeps track of state for field: _showSequenceFeatures
- */
- private boolean _has_showSequenceFeatures;
-
- /**
- * Field _showNPfeatureTooltip.
- */
- private boolean _showNPfeatureTooltip;
-
- /**
- * keeps track of state for field: _showNPfeatureTooltip
- */
- private boolean _has_showNPfeatureTooltip;
-
- /**
- * Field _showDbRefTooltip.
- */
- private boolean _showDbRefTooltip;
-
- /**
- * keeps track of state for field: _showDbRefTooltip
- */
- private boolean _has_showDbRefTooltip;
-
- /**
- * Field _followHighlight.
- */
- private boolean _followHighlight = true;
-
- /**
- * keeps track of state for field: _followHighlight
- */
- private boolean _has_followHighlight;
-
- /**
- * Field _followSelection.
- */
- private boolean _followSelection = true;
-
- /**
- * keeps track of state for field: _followSelection
- */
- private boolean _has_followSelection;
-
- /**
- * Field _showAnnotation.
- */
- private boolean _showAnnotation;
-
- /**
- * keeps track of state for field: _showAnnotation
- */
- private boolean _has_showAnnotation;
-
- /**
- * Field _centreColumnLabels.
- */
- private boolean _centreColumnLabels = false;
-
- /**
- * keeps track of state for field: _centreColumnLabels
- */
- private boolean _has_centreColumnLabels;
-
- /**
- * Field _showGroupConservation.
- */
- private boolean _showGroupConservation = false;
-
- /**
- * keeps track of state for field: _showGroupConservation
- */
- private boolean _has_showGroupConservation;
-
- /**
- * Field _showGroupConsensus.
- */
- private boolean _showGroupConsensus = false;
-
- /**
- * keeps track of state for field: _showGroupConsensus
- */
- private boolean _has_showGroupConsensus;
-
- /**
- * Field _showConsensusHistogram.
- */
- private boolean _showConsensusHistogram = true;
-
- /**
- * keeps track of state for field: _showConsensusHistogram
- */
- private boolean _has_showConsensusHistogram;
-
- /**
- * Field _showSequenceLogo.
- */
- private boolean _showSequenceLogo = false;
-
- /**
- * keeps track of state for field: _showSequenceLogo
- */
- private boolean _has_showSequenceLogo;
-
- /**
- * Field _normaliseSequenceLogo.
- */
- private boolean _normaliseSequenceLogo = false;
-
- /**
- * keeps track of state for field: _normaliseSequenceLogo
- */
- private boolean _has_normaliseSequenceLogo;
-
- /**
- * Field _ignoreGapsinConsensus.
- */
- private boolean _ignoreGapsinConsensus = true;
-
- /**
- * keeps track of state for field: _ignoreGapsinConsensus
- */
- private boolean _has_ignoreGapsinConsensus;
-
- /**
- * Field _startRes.
- */
- private int _startRes;
-
- /**
- * keeps track of state for field: _startRes
- */
- private boolean _has_startRes;
-
- /**
- * Field _startSeq.
- */
- private int _startSeq;
-
- /**
- * keeps track of state for field: _startSeq
- */
- private boolean _has_startSeq;
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- /**
- * Field _viewName.
- */
- private java.lang.String _viewName;
-
- /**
- * Field _sequenceSetId.
- */
- private java.lang.String _sequenceSetId;
-
- /**
- * Field _gatheredViews.
- */
- private boolean _gatheredViews;
-
- /**
- * keeps track of state for field: _gatheredViews
- */
- private boolean _has_gatheredViews;
-
- /**
- * Field _textCol1.
- */
- private int _textCol1;
-
- /**
- * keeps track of state for field: _textCol1
- */
- private boolean _has_textCol1;
-
- /**
- * Field _textCol2.
- */
- private int _textCol2;
-
- /**
- * keeps track of state for field: _textCol2
- */
- private boolean _has_textCol2;
-
- /**
- * Field _textColThreshold.
- */
- private int _textColThreshold;
-
- /**
- * keeps track of state for field: _textColThreshold
- */
- private boolean _has_textColThreshold;
-
- /**
- * unique id used by jalview to synchronize between stored and instantiated
- * views
- *
- */
- private java.lang.String _id;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _annotationColours.
- */
- private jalview.schemabinding.version2.AnnotationColours _annotationColours;
-
- /**
- * Field _hiddenColumnsList.
- */
- private java.util.Vector _hiddenColumnsList;
-
- /**
- * Field _calcIdParamList.
- */
- private java.util.Vector _calcIdParamList;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Viewport()
- {
- super();
- this._hiddenColumnsList = new java.util.Vector();
- this._calcIdParamList = new java.util.Vector();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- *
- *
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException
- {
- this._calcIdParamList.addElement(vCalcIdParam);
- }
-
- /**
- *
- *
- * @param index
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addCalcIdParam(final int index,
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException
- {
- this._calcIdParamList.add(index, vCalcIdParam);
- }
-
- /**
- *
- *
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException
- {
- this._hiddenColumnsList.addElement(vHiddenColumns);
- }
-
- /**
- *
- *
- * @param index
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void addHiddenColumns(final int index,
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException
- {
- this._hiddenColumnsList.add(index, vHiddenColumns);
- }
-
- /**
- */
- public void deleteCentreColumnLabels()
- {
- this._has_centreColumnLabels = false;
- }
-
- /**
- */
- public void deleteConsThreshold()
- {
- this._has_consThreshold = false;
- }
-
- /**
- */
- public void deleteConservationSelected()
- {
- this._has_conservationSelected = false;
- }
-
- /**
- */
- public void deleteFollowHighlight()
- {
- this._has_followHighlight = false;
- }
-
- /**
- */
- public void deleteFollowSelection()
- {
- this._has_followSelection = false;
- }
-
- /**
- */
- public void deleteFontSize()
- {
- this._has_fontSize = false;
- }
-
- /**
- */
- public void deleteFontStyle()
- {
- this._has_fontStyle = false;
- }
-
- /**
- */
- public void deleteGatheredViews()
- {
- this._has_gatheredViews = false;
- }
-
- /**
- */
- public void deleteHeight()
- {
- this._has_height = false;
- }
+public class Viewport implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _conservationSelected.
+ */
+ private boolean _conservationSelected;
+
+ /**
+ * keeps track of state for field: _conservationSelected
+ */
+ private boolean _has_conservationSelected;
+
+ /**
+ * Field _pidSelected.
+ */
+ private boolean _pidSelected;
+
+ /**
+ * keeps track of state for field: _pidSelected
+ */
+ private boolean _has_pidSelected;
+
+ /**
+ * Field _bgColour.
+ */
+ private java.lang.String _bgColour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _showFullId.
+ */
+ private boolean _showFullId;
+
+ /**
+ * keeps track of state for field: _showFullId
+ */
+ private boolean _has_showFullId;
+
+ /**
+ * Field _rightAlignIds.
+ */
+ private boolean _rightAlignIds;
+
+ /**
+ * keeps track of state for field: _rightAlignIds
+ */
+ private boolean _has_rightAlignIds;
+
+ /**
+ * Field _showText.
+ */
+ private boolean _showText;
+
+ /**
+ * keeps track of state for field: _showText
+ */
+ private boolean _has_showText;
+
+ /**
+ * Field _showColourText.
+ */
+ private boolean _showColourText;
+
+ /**
+ * keeps track of state for field: _showColourText
+ */
+ private boolean _has_showColourText;
+
+ /**
+ * Field _showUnconserved.
+ */
+ private boolean _showUnconserved = false;
+
+ /**
+ * keeps track of state for field: _showUnconserved
+ */
+ private boolean _has_showUnconserved;
+
+ /**
+ * Field _showBoxes.
+ */
+ private boolean _showBoxes;
+
+ /**
+ * keeps track of state for field: _showBoxes
+ */
+ private boolean _has_showBoxes;
+
+ /**
+ * Field _wrapAlignment.
+ */
+ private boolean _wrapAlignment;
+
+ /**
+ * keeps track of state for field: _wrapAlignment
+ */
+ private boolean _has_wrapAlignment;
+
+ /**
+ * Field _renderGaps.
+ */
+ private boolean _renderGaps;
+
+ /**
+ * keeps track of state for field: _renderGaps
+ */
+ private boolean _has_renderGaps;
+
+ /**
+ * Field _showSequenceFeatures.
+ */
+ private boolean _showSequenceFeatures;
+
+ /**
+ * keeps track of state for field: _showSequenceFeatures
+ */
+ private boolean _has_showSequenceFeatures;
+
+ /**
+ * Field _showNPfeatureTooltip.
+ */
+ private boolean _showNPfeatureTooltip;
+
+ /**
+ * keeps track of state for field: _showNPfeatureTooltip
+ */
+ private boolean _has_showNPfeatureTooltip;
+
+ /**
+ * Field _showDbRefTooltip.
+ */
+ private boolean _showDbRefTooltip;
+
+ /**
+ * keeps track of state for field: _showDbRefTooltip
+ */
+ private boolean _has_showDbRefTooltip;
+
+ /**
+ * Field _followHighlight.
+ */
+ private boolean _followHighlight = true;
+
+ /**
+ * keeps track of state for field: _followHighlight
+ */
+ private boolean _has_followHighlight;
+
+ /**
+ * Field _followSelection.
+ */
+ private boolean _followSelection = true;
+
+ /**
+ * keeps track of state for field: _followSelection
+ */
+ private boolean _has_followSelection;
+
+ /**
+ * Field _showAnnotation.
+ */
+ private boolean _showAnnotation;
+
+ /**
+ * keeps track of state for field: _showAnnotation
+ */
+ private boolean _has_showAnnotation;
+
+ /**
+ * Field _centreColumnLabels.
+ */
+ private boolean _centreColumnLabels = false;
+
+ /**
+ * keeps track of state for field: _centreColumnLabels
+ */
+ private boolean _has_centreColumnLabels;
+
+ /**
+ * Field _showGroupConservation.
+ */
+ private boolean _showGroupConservation = false;
+
+ /**
+ * keeps track of state for field: _showGroupConservation
+ */
+ private boolean _has_showGroupConservation;
+
+ /**
+ * Field _showGroupConsensus.
+ */
+ private boolean _showGroupConsensus = false;
+
+ /**
+ * keeps track of state for field: _showGroupConsensus
+ */
+ private boolean _has_showGroupConsensus;
+
+ /**
+ * Field _showConsensusHistogram.
+ */
+ private boolean _showConsensusHistogram = true;
+
+ /**
+ * keeps track of state for field: _showConsensusHistogram
+ */
+ private boolean _has_showConsensusHistogram;
+
+ /**
+ * Field _showSequenceLogo.
+ */
+ private boolean _showSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _showSequenceLogo
+ */
+ private boolean _has_showSequenceLogo;
+
+ /**
+ * Field _normaliseSequenceLogo.
+ */
+ private boolean _normaliseSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _normaliseSequenceLogo
+ */
+ private boolean _has_normaliseSequenceLogo;
+
+ /**
+ * Field _ignoreGapsinConsensus.
+ */
+ private boolean _ignoreGapsinConsensus = true;
+
+ /**
+ * keeps track of state for field: _ignoreGapsinConsensus
+ */
+ private boolean _has_ignoreGapsinConsensus;
+
+ /**
+ * Field _startRes.
+ */
+ private int _startRes;
+
+ /**
+ * keeps track of state for field: _startRes
+ */
+ private boolean _has_startRes;
+
+ /**
+ * Field _startSeq.
+ */
+ private int _startSeq;
+
+ /**
+ * keeps track of state for field: _startSeq
+ */
+ private boolean _has_startSeq;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _viewName.
+ */
+ private java.lang.String _viewName;
- /**
+ /**
+ * Field _sequenceSetId.
*/
- public void deleteIgnoreGapsinConsensus()
- {
- this._has_ignoreGapsinConsensus = false;
- }
+ private java.lang.String _sequenceSetId;
- /**
+ /**
+ * Field _gatheredViews.
*/
- public void deleteNormaliseSequenceLogo()
- {
- this._has_normaliseSequenceLogo = false;
- }
+ private boolean _gatheredViews;
- /**
+ /**
+ * keeps track of state for field: _gatheredViews
*/
- public void deletePidSelected()
- {
- this._has_pidSelected = false;
- }
+ private boolean _has_gatheredViews;
- /**
+ /**
+ * Field _textCol1.
*/
- public void deletePidThreshold()
- {
- this._has_pidThreshold = false;
- }
+ private int _textCol1;
- /**
+ /**
+ * keeps track of state for field: _textCol1
*/
- public void deleteRenderGaps()
- {
- this._has_renderGaps = false;
- }
+ private boolean _has_textCol1;
- /**
+ /**
+ * Field _textCol2.
*/
- public void deleteRightAlignIds()
- {
- this._has_rightAlignIds = false;
- }
+ private int _textCol2;
- /**
+ /**
+ * keeps track of state for field: _textCol2
*/
- public void deleteShowAnnotation()
- {
- this._has_showAnnotation = false;
- }
+ private boolean _has_textCol2;
- /**
+ /**
+ * Field _textColThreshold.
*/
- public void deleteShowBoxes()
- {
- this._has_showBoxes = false;
- }
+ private int _textColThreshold;
- /**
+ /**
+ * keeps track of state for field: _textColThreshold
*/
- public void deleteShowColourText()
- {
- this._has_showColourText = false;
- }
+ private boolean _has_textColThreshold;
- /**
+ /**
+ * unique id used by jalview to
+ * synchronize between stored and
+ * instantiated views
+ *
*/
- public void deleteShowConsensusHistogram()
- {
- this._has_showConsensusHistogram = false;
- }
+ private java.lang.String _id;
- /**
+ /**
+ * The viewport id of this viewport's (cdna/protein) coding
+ * complement, if any
+ *
*/
- public void deleteShowDbRefTooltip()
- {
- this._has_showDbRefTooltip = false;
- }
+ private java.lang.String _complementId;
- /**
+ /**
+ * Field _width.
*/
- public void deleteShowFullId()
- {
- this._has_showFullId = false;
- }
+ private int _width;
- /**
+ /**
+ * keeps track of state for field: _width
*/
- public void deleteShowGroupConsensus()
- {
- this._has_showGroupConsensus = false;
- }
+ private boolean _has_width;
- /**
+ /**
+ * Field _height.
*/
- public void deleteShowGroupConservation()
- {
- this._has_showGroupConservation = false;
- }
+ private int _height;
- /**
+ /**
+ * keeps track of state for field: _height
*/
- public void deleteShowNPfeatureTooltip()
- {
- this._has_showNPfeatureTooltip = false;
- }
+ private boolean _has_height;
- /**
+ /**
+ * Field _xpos.
*/
- public void deleteShowSequenceFeatures()
- {
- this._has_showSequenceFeatures = false;
- }
+ private int _xpos;
- /**
+ /**
+ * keeps track of state for field: _xpos
*/
- public void deleteShowSequenceLogo()
- {
- this._has_showSequenceLogo = false;
- }
+ private boolean _has_xpos;
- /**
+ /**
+ * Field _ypos.
*/
- public void deleteShowText()
- {
- this._has_showText = false;
- }
+ private int _ypos;
- /**
+ /**
+ * keeps track of state for field: _ypos
*/
- public void deleteShowUnconserved()
- {
- this._has_showUnconserved = false;
- }
+ private boolean _has_ypos;
- /**
+ /**
+ * Field _annotationColours.
*/
- public void deleteStartRes()
- {
- this._has_startRes = false;
- }
-
- /**
- */
- public void deleteStartSeq()
- {
- this._has_startSeq = false;
- }
-
- /**
- */
- public void deleteTextCol1()
- {
- this._has_textCol1 = false;
- }
-
- /**
- */
- public void deleteTextCol2()
- {
- this._has_textCol2 = false;
- }
-
- /**
- */
- public void deleteTextColThreshold()
- {
- this._has_textColThreshold = false;
- }
-
- /**
- */
- public void deleteWidth()
- {
- this._has_width = false;
- }
-
- /**
- */
- public void deleteWrapAlignment()
- {
- this._has_wrapAlignment = false;
- }
-
- /**
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- }
-
- /**
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- }
-
- /**
- * Method enumerateCalcIdParam.
- *
- * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
- * elements
- */
- public java.util.Enumeration enumerateCalcIdParam()
- {
- return this._calcIdParamList.elements();
- }
-
- /**
- * Method enumerateHiddenColumns.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.HiddenColumns elements
- */
- public java.util.Enumeration enumerateHiddenColumns()
- {
- return this._hiddenColumnsList.elements();
- }
-
- /**
- * Returns the value of field 'annotationColours'.
- *
- * @return the value of field 'AnnotationColours'.
- */
- public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
- {
- return this._annotationColours;
- }
-
- /**
- * Returns the value of field 'bgColour'.
- *
- * @return the value of field 'BgColour'.
- */
- public java.lang.String getBgColour()
- {
- return this._bgColour;
- }
-
- /**
- * Method getCalcIdParam.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
- * given index
- */
- public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
- final int index) throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._calcIdParamList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getCalcIdParam",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._calcIdParamList.size() - 1)).toString()
- }));
- }
-
- return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
- .get(index);
- }
-
- /**
- * Method getCalcIdParam.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
- {
- jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
- return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
- .toArray(array);
- }
-
- /**
- * Method getCalcIdParamCount.
- *
- * @return the size of this collection
- */
- public int getCalcIdParamCount()
- {
- return this._calcIdParamList.size();
- }
-
- /**
- * Returns the value of field 'centreColumnLabels'.
- *
- * @return the value of field 'CentreColumnLabels'.
- */
- public boolean getCentreColumnLabels()
- {
- return this._centreColumnLabels;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold()
- {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean getConservationSelected()
- {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'followHighlight'.
- *
- * @return the value of field 'FollowHighlight'.
- */
- public boolean getFollowHighlight()
- {
- return this._followHighlight;
- }
-
- /**
- * Returns the value of field 'followSelection'.
- *
- * @return the value of field 'FollowSelection'.
- */
- public boolean getFollowSelection()
- {
- return this._followSelection;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'gatheredViews'.
- *
- * @return the value of field 'GatheredViews'.
- */
- public boolean getGatheredViews()
- {
- return this._gatheredViews;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight()
- {
- return this._height;
- }
-
- /**
- * Method getHiddenColumns.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- * @return the value of the jalview.schemabinding.version2.HiddenColumns at
- * the given index
- */
- public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
- final int index) throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._hiddenColumnsList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getHiddenColumns",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString()
- }));
- }
-
- return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
- .get(index);
- }
-
- /**
- * Method getHiddenColumns.Returns the contents of the collection in an Array.
- * <p>
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * <i>know</i> that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
- {
- jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
- return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
- .toArray(array);
- }
-
- /**
- * Method getHiddenColumnsCount.
- *
- * @return the size of this collection
- */
- public int getHiddenColumnsCount()
- {
- return this._hiddenColumnsList.size();
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the following
- * description: unique id used by jalview to synchronize between stored and
- * instantiated views
- *
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- }
-
- /**
- * Returns the value of field 'ignoreGapsinConsensus'.
- *
- * @return the value of field 'IgnoreGapsinConsensus'.
- */
- public boolean getIgnoreGapsinConsensus()
- {
- return this._ignoreGapsinConsensus;
- }
-
- /**
- * Returns the value of field 'normaliseSequenceLogo'.
- *
- * @return the value of field 'NormaliseSequenceLogo'.
- */
- public boolean getNormaliseSequenceLogo()
- {
- return this._normaliseSequenceLogo;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean getPidSelected()
- {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold()
- {
- return this._pidThreshold;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean getRenderGaps()
- {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'rightAlignIds'.
- *
- * @return the value of field 'RightAlignIds'.
- */
- public boolean getRightAlignIds()
- {
- return this._rightAlignIds;
- }
-
- /**
- * Returns the value of field 'sequenceSetId'.
- *
- * @return the value of field 'SequenceSetId'.
- */
- public java.lang.String getSequenceSetId()
- {
- return this._sequenceSetId;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean getShowAnnotation()
- {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean getShowBoxes()
- {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean getShowColourText()
- {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConsensusHistogram'.
- *
- * @return the value of field 'ShowConsensusHistogram'.
- */
- public boolean getShowConsensusHistogram()
- {
- return this._showConsensusHistogram;
- }
-
- /**
- * Returns the value of field 'showDbRefTooltip'.
- *
- * @return the value of field 'ShowDbRefTooltip'.
- */
- public boolean getShowDbRefTooltip()
- {
- return this._showDbRefTooltip;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean getShowFullId()
- {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showGroupConsensus'.
- *
- * @return the value of field 'ShowGroupConsensus'.
- */
- public boolean getShowGroupConsensus()
- {
- return this._showGroupConsensus;
- }
-
- /**
- * Returns the value of field 'showGroupConservation'.
- *
- * @return the value of field 'ShowGroupConservation'.
- */
- public boolean getShowGroupConservation()
- {
- return this._showGroupConservation;
- }
-
- /**
- * Returns the value of field 'showNPfeatureTooltip'.
- *
- * @return the value of field 'ShowNPfeatureTooltip'.
- */
- public boolean getShowNPfeatureTooltip()
- {
- return this._showNPfeatureTooltip;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean getShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showSequenceLogo'.
- *
- * @return the value of field 'ShowSequenceLogo'.
- */
- public boolean getShowSequenceLogo()
- {
- return this._showSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean getShowText()
- {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'showUnconserved'.
- *
- * @return the value of field 'ShowUnconserved'.
- */
- public boolean getShowUnconserved()
- {
- return this._showUnconserved;
- }
-
- /**
- * Returns the value of field 'startRes'.
- *
- * @return the value of field 'StartRes'.
- */
- public int getStartRes()
- {
- return this._startRes;
- }
-
- /**
- * Returns the value of field 'startSeq'.
- *
- * @return the value of field 'StartSeq'.
- */
- public int getStartSeq()
- {
- return this._startSeq;
- }
-
- /**
- * Returns the value of field 'textCol1'.
- *
- * @return the value of field 'TextCol1'.
- */
- public int getTextCol1()
- {
- return this._textCol1;
- }
-
- /**
- * Returns the value of field 'textCol2'.
- *
- * @return the value of field 'TextCol2'.
- */
- public int getTextCol2()
- {
- return this._textCol2;
- }
-
- /**
- * Returns the value of field 'textColThreshold'.
- *
- * @return the value of field 'TextColThreshold'.
- */
- public int getTextColThreshold()
- {
- return this._textColThreshold;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- }
-
- /**
- * Returns the value of field 'viewName'.
- *
- * @return the value of field 'ViewName'.
- */
- public java.lang.String getViewName()
- {
- return this._viewName;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth()
- {
- return this._width;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean getWrapAlignment()
- {
- return this._wrapAlignment;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- }
-
- /**
- * Method hasCentreColumnLabels.
- *
- * @return true if at least one CentreColumnLabels has been adde
- */
- public boolean hasCentreColumnLabels()
- {
- return this._has_centreColumnLabels;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold()
- {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasConservationSelected.
- *
- * @return true if at least one ConservationSelected has been added
- */
- public boolean hasConservationSelected()
- {
- return this._has_conservationSelected;
- }
-
- /**
- * Method hasFollowHighlight.
- *
- * @return true if at least one FollowHighlight has been added
- */
- public boolean hasFollowHighlight()
- {
- return this._has_followHighlight;
- }
-
- /**
- * Method hasFollowSelection.
- *
- * @return true if at least one FollowSelection has been added
- */
- public boolean hasFollowSelection()
- {
- return this._has_followSelection;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasGatheredViews.
- *
- * @return true if at least one GatheredViews has been added
- */
- public boolean hasGatheredViews()
- {
- return this._has_gatheredViews;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight()
- {
- return this._has_height;
- }
-
- /**
- * Method hasIgnoreGapsinConsensus.
- *
- * @return true if at least one IgnoreGapsinConsensus has been added
- */
- public boolean hasIgnoreGapsinConsensus()
- {
- return this._has_ignoreGapsinConsensus;
- }
-
- /**
- * Method hasNormaliseSequenceLogo.
- *
- * @return true if at least one NormaliseSequenceLogo has been added
- */
- public boolean hasNormaliseSequenceLogo()
- {
- return this._has_normaliseSequenceLogo;
- }
-
- /**
- * Method hasPidSelected.
- *
- * @return true if at least one PidSelected has been added
- */
- public boolean hasPidSelected()
- {
- return this._has_pidSelected;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold()
- {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasRenderGaps.
- *
- * @return true if at least one RenderGaps has been added
- */
- public boolean hasRenderGaps()
- {
- return this._has_renderGaps;
- }
-
- /**
- * Method hasRightAlignIds.
- *
- * @return true if at least one RightAlignIds has been added
- */
- public boolean hasRightAlignIds()
- {
- return this._has_rightAlignIds;
- }
-
- /**
- * Method hasShowAnnotation.
- *
- * @return true if at least one ShowAnnotation has been added
- */
- public boolean hasShowAnnotation()
- {
- return this._has_showAnnotation;
- }
-
- /**
- * Method hasShowBoxes.
- *
- * @return true if at least one ShowBoxes has been added
- */
- public boolean hasShowBoxes()
- {
- return this._has_showBoxes;
- }
-
- /**
- * Method hasShowColourText.
- *
- * @return true if at least one ShowColourText has been added
- */
- public boolean hasShowColourText()
- {
- return this._has_showColourText;
- }
-
- /**
- * Method hasShowConsensusHistogram.
- *
- * @return true if at least one ShowConsensusHistogram has been added
- */
- public boolean hasShowConsensusHistogram()
- {
- return this._has_showConsensusHistogram;
- }
-
- /**
- * Method hasShowDbRefTooltip.
- *
- * @return true if at least one ShowDbRefTooltip has been added
- */
- public boolean hasShowDbRefTooltip()
- {
- return this._has_showDbRefTooltip;
- }
-
- /**
- * Method hasShowFullId.
- *
- * @return true if at least one ShowFullId has been added
- */
- public boolean hasShowFullId()
- {
- return this._has_showFullId;
- }
-
- /**
- * Method hasShowGroupConsensus.
- *
- * @return true if at least one ShowGroupConsensus has been adde
- */
- public boolean hasShowGroupConsensus()
- {
- return this._has_showGroupConsensus;
- }
-
- /**
- * Method hasShowGroupConservation.
- *
- * @return true if at least one ShowGroupConservation has been added
- */
- public boolean hasShowGroupConservation()
- {
- return this._has_showGroupConservation;
- }
-
- /**
- * Method hasShowNPfeatureTooltip.
- *
- * @return true if at least one ShowNPfeatureTooltip has been added
- */
- public boolean hasShowNPfeatureTooltip()
- {
- return this._has_showNPfeatureTooltip;
- }
-
- /**
- * Method hasShowSequenceFeatures.
- *
- * @return true if at least one ShowSequenceFeatures has been added
- */
- public boolean hasShowSequenceFeatures()
- {
- return this._has_showSequenceFeatures;
- }
-
- /**
- * Method hasShowSequenceLogo.
- *
- * @return true if at least one ShowSequenceLogo has been added
- */
- public boolean hasShowSequenceLogo()
- {
- return this._has_showSequenceLogo;
- }
-
- /**
- * Method hasShowText.
- *
- * @return true if at least one ShowText has been added
- */
- public boolean hasShowText()
- {
- return this._has_showText;
- }
-
- /**
- * Method hasShowUnconserved.
- *
- * @return true if at least one ShowUnconserved has been added
- */
- public boolean hasShowUnconserved()
- {
- return this._has_showUnconserved;
- }
-
- /**
- * Method hasStartRes.
- *
- * @return true if at least one StartRes has been added
- */
- public boolean hasStartRes()
- {
- return this._has_startRes;
- }
-
- /**
- * Method hasStartSeq.
- *
- * @return true if at least one StartSeq has been added
- */
- public boolean hasStartSeq()
- {
- return this._has_startSeq;
- }
-
- /**
- * Method hasTextCol1.
- *
- * @return true if at least one TextCol1 has been added
- */
- public boolean hasTextCol1()
- {
- return this._has_textCol1;
- }
-
- /**
- * Method hasTextCol2.
- *
- * @return true if at least one TextCol2 has been added
- */
- public boolean hasTextCol2()
- {
- return this._has_textCol2;
- }
-
- /**
- * Method hasTextColThreshold.
- *
- * @return true if at least one TextColThreshold has been added
- */
- public boolean hasTextColThreshold()
- {
- return this._has_textColThreshold;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth()
- {
- return this._has_width;
- }
-
- /**
- * Method hasWrapAlignment.
- *
- * @return true if at least one WrapAlignment has been added
- */
- public boolean hasWrapAlignment()
- {
- return this._has_wrapAlignment;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'centreColumnLabels'.
- *
- * @return the value of field 'CentreColumnLabels'.
- */
- public boolean isCentreColumnLabels()
- {
- return this._centreColumnLabels;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean isConservationSelected()
- {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'followHighlight'.
- *
- * @return the value of field 'FollowHighlight'.
- */
- public boolean isFollowHighlight()
- {
- return this._followHighlight;
- }
-
- /**
- * Returns the value of field 'followSelection'.
- *
- * @return the value of field 'FollowSelection'.
- */
- public boolean isFollowSelection()
- {
- return this._followSelection;
- }
-
- /**
- * Returns the value of field 'gatheredViews'.
- *
- * @return the value of field 'GatheredViews'.
- */
- public boolean isGatheredViews()
- {
- return this._gatheredViews;
- }
-
- /**
- * Returns the value of field 'ignoreGapsinConsensus'.
- *
- * @return the value of field 'IgnoreGapsinConsensus'.
- */
- public boolean isIgnoreGapsinConsensus()
- {
- return this._ignoreGapsinConsensus;
- }
-
- /**
- * Returns the value of field 'normaliseSequenceLogo'.
- *
- * @return the value of field 'NormaliseSequenceLogo'.
- */
- public boolean isNormaliseSequenceLogo()
- {
- return this._normaliseSequenceLogo;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean isPidSelected()
- {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean isRenderGaps()
- {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'rightAlignIds'.
- *
- * @return the value of field 'RightAlignIds'.
- */
- public boolean isRightAlignIds()
- {
- return this._rightAlignIds;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean isShowAnnotation()
- {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean isShowBoxes()
- {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean isShowColourText()
- {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConsensusHistogram'.
- *
- * @return the value of field 'ShowConsensusHistogram'.
- */
- public boolean isShowConsensusHistogram()
- {
- return this._showConsensusHistogram;
- }
-
- /**
- * Returns the value of field 'showDbRefTooltip'.
- *
- * @return the value of field 'ShowDbRefTooltip'.
- */
- public boolean isShowDbRefTooltip()
- {
- return this._showDbRefTooltip;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean isShowFullId()
- {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showGroupConsensus'.
- *
- * @return the value of field 'ShowGroupConsensus'.
- */
- public boolean isShowGroupConsensus()
- {
- return this._showGroupConsensus;
- }
-
- /**
- * Returns the value of field 'showGroupConservation'.
- *
- * @return the value of field 'ShowGroupConservation'.
- */
- public boolean isShowGroupConservation()
- {
- return this._showGroupConservation;
- }
-
- /**
- * Returns the value of field 'showNPfeatureTooltip'.
- *
- * @return the value of field 'ShowNPfeatureTooltip'.
- */
- public boolean isShowNPfeatureTooltip()
- {
- return this._showNPfeatureTooltip;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean isShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showSequenceLogo'.
- *
- * @return the value of field 'ShowSequenceLogo'.
- */
- public boolean isShowSequenceLogo()
- {
- return this._showSequenceLogo;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean isShowText()
- {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'showUnconserved'.
- *
- * @return the value of field 'ShowUnconserved'.
- */
- public boolean isShowUnconserved()
- {
- return this._showUnconserved;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean isWrapAlignment()
- {
- return this._wrapAlignment;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllCalcIdParam()
- {
- this._calcIdParamList.clear();
- }
-
- /**
- */
- public void removeAllHiddenColumns()
- {
- this._hiddenColumnsList.clear();
- }
-
- /**
- * Method removeCalcIdParam.
- *
- * @param vCalcIdParam
- * @return true if the object was removed from the collection.
- */
- public boolean removeCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- {
- boolean removed = _calcIdParamList.remove(vCalcIdParam);
- return removed;
- }
-
- /**
- * Method removeCalcIdParamAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
- final int index)
- {
- java.lang.Object obj = this._calcIdParamList.remove(index);
- return (jalview.schemabinding.version2.CalcIdParam) obj;
- }
-
- /**
- * Method removeHiddenColumns.
- *
- * @param vHiddenColumns
- * @return true if the object was removed from the collection.
- */
- public boolean removeHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- {
- boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
- return removed;
- }
-
- /**
- * Method removeHiddenColumnsAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
- final int index)
- {
- java.lang.Object obj = this._hiddenColumnsList.remove(index);
- return (jalview.schemabinding.version2.HiddenColumns) obj;
- }
-
- /**
- * Sets the value of field 'annotationColours'.
- *
- * @param annotationColours
- * the value of field 'annotationColours'.
- */
- public void setAnnotationColours(
- final jalview.schemabinding.version2.AnnotationColours annotationColours)
- {
- this._annotationColours = annotationColours;
- }
-
- /**
- * Sets the value of field 'bgColour'.
- *
- * @param bgColour
- * the value of field 'bgColour'.
- */
- public void setBgColour(final java.lang.String bgColour)
- {
- this._bgColour = bgColour;
- }
-
- /**
- *
- *
- * @param index
- * @param vCalcIdParam
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setCalcIdParam(final int index,
- final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._calcIdParamList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setCalcIdParam",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._calcIdParamList.size() - 1)).toString()
- }));
- }
-
- this._calcIdParamList.set(index, vCalcIdParam);
- }
-
- /**
- *
- *
- * @param vCalcIdParamArray
- */
- public void setCalcIdParam(
- final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
- {
- // -- copy array
- _calcIdParamList.clear();
-
- for (int i = 0; i < vCalcIdParamArray.length; i++)
- {
- this._calcIdParamList.add(vCalcIdParamArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'centreColumnLabels'.
- *
- * @param centreColumnLabels
- * the value of field 'centreColumnLabels'.
- */
- public void setCentreColumnLabels(final boolean centreColumnLabels)
- {
- this._centreColumnLabels = centreColumnLabels;
- this._has_centreColumnLabels = true;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold
- * the value of field 'consThreshold'.
- */
- public void setConsThreshold(final int consThreshold)
- {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'conservationSelected'.
- *
- * @param conservationSelected
- * the value of field 'conservationSelected'.
- */
- public void setConservationSelected(final boolean conservationSelected)
- {
- this._conservationSelected = conservationSelected;
- this._has_conservationSelected = true;
- }
-
- /**
- * Sets the value of field 'followHighlight'.
- *
- * @param followHighlight
- * the value of field 'followHighlight'.
- */
- public void setFollowHighlight(final boolean followHighlight)
- {
- this._followHighlight = followHighlight;
- this._has_followHighlight = true;
- }
-
- /**
- * Sets the value of field 'followSelection'.
- *
- * @param followSelection
- * the value of field 'followSelection'.
- */
- public void setFollowSelection(final boolean followSelection)
- {
- this._followSelection = followSelection;
- this._has_followSelection = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName
- * the value of field 'fontName'.
- */
- public void setFontName(final java.lang.String fontName)
- {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize
- * the value of field 'fontSize'.
- */
- public void setFontSize(final int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle
- * the value of field 'fontStyle'.
- */
- public void setFontStyle(final int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'gatheredViews'.
- *
- * @param gatheredViews
- * the value of field 'gatheredViews'.
- */
- public void setGatheredViews(final boolean gatheredViews)
- {
- this._gatheredViews = gatheredViews;
- this._has_gatheredViews = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height
- * the value of field 'height'.
- */
- public void setHeight(final int height)
- {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vHiddenColumns
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setHiddenColumns(final int index,
- final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._hiddenColumnsList.size())
- {
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setHiddenColumns",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString()
- }));
- }
-
- this._hiddenColumnsList.set(index, vHiddenColumns);
- }
-
- /**
- *
- *
- * @param vHiddenColumnsArray
- */
- public void setHiddenColumns(
- final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
- {
- // -- copy array
- _hiddenColumnsList.clear();
-
- for (int i = 0; i < vHiddenColumnsArray.length; i++)
- {
- this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'id'. The field 'id' has the following description:
- * unique id used by jalview to synchronize between stored and instantiated
- * views
- *
- *
- * @param id
- * the value of field 'id'.
- */
- public void setId(final java.lang.String id)
- {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'ignoreGapsinConsensus'.
- *
- * @param ignoreGapsinConsensus
- * the value of field 'ignoreGapsinConsensus'.
- */
- public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
- {
- this._ignoreGapsinConsensus = ignoreGapsinConsensus;
- this._has_ignoreGapsinConsensus = true;
- }
-
- /**
- * Sets the value of field 'normaliseSequenceLogo'.
- *
- * @param normaliseSequenceLogo
- * the value of field 'normaliseSequenceLogo'.
- */
- public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
- {
- this._normaliseSequenceLogo = normaliseSequenceLogo;
- this._has_normaliseSequenceLogo = true;
- }
-
- /**
- * Sets the value of field 'pidSelected'.
- *
- * @param pidSelected
- * the value of field 'pidSelected'.
- */
- public void setPidSelected(final boolean pidSelected)
- {
- this._pidSelected = pidSelected;
- this._has_pidSelected = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold
- * the value of field 'pidThreshold'.
- */
- public void setPidThreshold(final int pidThreshold)
- {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- * Sets the value of field 'renderGaps'.
- *
- * @param renderGaps
- * the value of field 'renderGaps'.
- */
- public void setRenderGaps(final boolean renderGaps)
- {
- this._renderGaps = renderGaps;
- this._has_renderGaps = true;
- }
-
- /**
- * Sets the value of field 'rightAlignIds'.
- *
- * @param rightAlignIds
- * the value of field 'rightAlignIds'.
- */
- public void setRightAlignIds(final boolean rightAlignIds)
- {
- this._rightAlignIds = rightAlignIds;
- this._has_rightAlignIds = true;
- }
-
- /**
- * Sets the value of field 'sequenceSetId'.
- *
- * @param sequenceSetId
- * the value of field 'sequenceSetId'.
- */
- public void setSequenceSetId(final java.lang.String sequenceSetId)
- {
- this._sequenceSetId = sequenceSetId;
- }
-
- /**
- * Sets the value of field 'showAnnotation'.
- *
- * @param showAnnotation
- * the value of field 'showAnnotation'.
- */
- public void setShowAnnotation(final boolean showAnnotation)
- {
- this._showAnnotation = showAnnotation;
- this._has_showAnnotation = true;
- }
-
- /**
- * Sets the value of field 'showBoxes'.
- *
- * @param showBoxes
- * the value of field 'showBoxes'.
- */
- public void setShowBoxes(final boolean showBoxes)
- {
- this._showBoxes = showBoxes;
- this._has_showBoxes = true;
- }
-
- /**
- * Sets the value of field 'showColourText'.
- *
- * @param showColourText
- * the value of field 'showColourText'.
- */
- public void setShowColourText(final boolean showColourText)
- {
- this._showColourText = showColourText;
- this._has_showColourText = true;
- }
-
- /**
- * Sets the value of field 'showConsensusHistogram'.
- *
- * @param showConsensusHistogram
- * the value of field 'showConsensusHistogram'.
- */
- public void setShowConsensusHistogram(final boolean showConsensusHistogram)
- {
- this._showConsensusHistogram = showConsensusHistogram;
- this._has_showConsensusHistogram = true;
- }
-
- /**
- * Sets the value of field 'showDbRefTooltip'.
- *
- * @param showDbRefTooltip
- * the value of field 'showDbRefTooltip'
- */
- public void setShowDbRefTooltip(final boolean showDbRefTooltip)
- {
- this._showDbRefTooltip = showDbRefTooltip;
- this._has_showDbRefTooltip = true;
- }
-
- /**
- * Sets the value of field 'showFullId'.
- *
- * @param showFullId
- * the value of field 'showFullId'.
- */
- public void setShowFullId(final boolean showFullId)
- {
- this._showFullId = showFullId;
- this._has_showFullId = true;
- }
-
- /**
- * Sets the value of field 'showGroupConsensus'.
- *
- * @param showGroupConsensus
- * the value of field 'showGroupConsensus'.
- */
- public void setShowGroupConsensus(final boolean showGroupConsensus)
- {
- this._showGroupConsensus = showGroupConsensus;
- this._has_showGroupConsensus = true;
- }
-
- /**
- * Sets the value of field 'showGroupConservation'.
- *
- * @param showGroupConservation
- * the value of field 'showGroupConservation'.
- */
- public void setShowGroupConservation(final boolean showGroupConservation)
- {
- this._showGroupConservation = showGroupConservation;
- this._has_showGroupConservation = true;
- }
-
- /**
- * Sets the value of field 'showNPfeatureTooltip'.
- *
- * @param showNPfeatureTooltip
- * the value of field 'showNPfeatureTooltip'.
- */
- public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
- {
- this._showNPfeatureTooltip = showNPfeatureTooltip;
- this._has_showNPfeatureTooltip = true;
- }
-
- /**
- * Sets the value of field 'showSequenceFeatures'.
- *
- * @param showSequenceFeatures
- * the value of field 'showSequenceFeatures'.
- */
- public void setShowSequenceFeatures(final boolean showSequenceFeatures)
- {
- this._showSequenceFeatures = showSequenceFeatures;
- this._has_showSequenceFeatures = true;
- }
-
- /**
- * Sets the value of field 'showSequenceLogo'.
- *
- * @param showSequenceLogo
- * the value of field 'showSequenceLogo'
- */
- public void setShowSequenceLogo(final boolean showSequenceLogo)
- {
- this._showSequenceLogo = showSequenceLogo;
- this._has_showSequenceLogo = true;
- }
-
- /**
- * Sets the value of field 'showText'.
- *
- * @param showText
- * the value of field 'showText'.
- */
- public void setShowText(final boolean showText)
- {
- this._showText = showText;
- this._has_showText = true;
- }
-
- /**
- * Sets the value of field 'showUnconserved'.
- *
- * @param showUnconserved
- * the value of field 'showUnconserved'.
- */
- public void setShowUnconserved(final boolean showUnconserved)
- {
- this._showUnconserved = showUnconserved;
- this._has_showUnconserved = true;
- }
-
- /**
- * Sets the value of field 'startRes'.
- *
- * @param startRes
- * the value of field 'startRes'.
- */
- public void setStartRes(final int startRes)
- {
- this._startRes = startRes;
- this._has_startRes = true;
- }
-
- /**
- * Sets the value of field 'startSeq'.
- *
- * @param startSeq
- * the value of field 'startSeq'.
- */
- public void setStartSeq(final int startSeq)
- {
- this._startSeq = startSeq;
- this._has_startSeq = true;
- }
-
- /**
- * Sets the value of field 'textCol1'.
- *
- * @param textCol1
- * the value of field 'textCol1'.
- */
- public void setTextCol1(final int textCol1)
- {
- this._textCol1 = textCol1;
- this._has_textCol1 = true;
- }
-
- /**
- * Sets the value of field 'textCol2'.
- *
- * @param textCol2
- * the value of field 'textCol2'.
- */
- public void setTextCol2(final int textCol2)
- {
- this._textCol2 = textCol2;
- this._has_textCol2 = true;
- }
-
- /**
- * Sets the value of field 'textColThreshold'.
- *
- * @param textColThreshold
- * the value of field 'textColThreshold'
- */
- public void setTextColThreshold(final int textColThreshold)
- {
- this._textColThreshold = textColThreshold;
- this._has_textColThreshold = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title
- * the value of field 'title'.
- */
- public void setTitle(final java.lang.String title)
- {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'viewName'.
- *
- * @param viewName
- * the value of field 'viewName'.
- */
- public void setViewName(final java.lang.String viewName)
- {
- this._viewName = viewName;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width
- * the value of field 'width'.
- */
- public void setWidth(final int width)
- {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'wrapAlignment'.
- *
- * @param wrapAlignment
- * the value of field 'wrapAlignment'.
- */
- public void setWrapAlignment(final boolean wrapAlignment)
- {
- this._wrapAlignment = wrapAlignment;
- this._has_wrapAlignment = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos
- * the value of field 'xpos'.
- */
- public void setXpos(final int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos
- * the value of field 'ypos'.
- */
- public void setYpos(final int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.schemabinding.version2.Viewport
- */
- public static jalview.schemabinding.version2.Viewport unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.schemabinding.version2.Viewport) Unmarshaller
- .unmarshal(jalview.schemabinding.version2.Viewport.class,
- reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+ /**
+ * Field _hiddenColumnsList.
+ */
+ private java.util.Vector _hiddenColumnsList;
+
+ /**
+ * Field _calcIdParamList.
+ */
+ private java.util.Vector _calcIdParamList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Viewport() {
+ super();
+ this._hiddenColumnsList = new java.util.Vector();
+ this._calcIdParamList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ this._calcIdParamList.addElement(vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ this._calcIdParamList.add(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException {
+ this._hiddenColumnsList.addElement(vHiddenColumns);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addHiddenColumns(
+ final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException {
+ this._hiddenColumnsList.add(index, vHiddenColumns);
+ }
+
+ /**
+ */
+ public void deleteCentreColumnLabels(
+ ) {
+ this._has_centreColumnLabels= false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold(
+ ) {
+ this._has_consThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteConservationSelected(
+ ) {
+ this._has_conservationSelected= false;
+ }
+
+ /**
+ */
+ public void deleteFollowHighlight(
+ ) {
+ this._has_followHighlight= false;
+ }
+
+ /**
+ */
+ public void deleteFollowSelection(
+ ) {
+ this._has_followSelection= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteGatheredViews(
+ ) {
+ this._has_gatheredViews= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteIgnoreGapsinConsensus(
+ ) {
+ this._has_ignoreGapsinConsensus= false;
+ }
+
+ /**
+ */
+ public void deleteNormaliseSequenceLogo(
+ ) {
+ this._has_normaliseSequenceLogo= false;
+ }
+
+ /**
+ */
+ public void deletePidSelected(
+ ) {
+ this._has_pidSelected= false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold(
+ ) {
+ this._has_pidThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteRenderGaps(
+ ) {
+ this._has_renderGaps= false;
+ }
+
+ /**
+ */
+ public void deleteRightAlignIds(
+ ) {
+ this._has_rightAlignIds= false;
+ }
+
+ /**
+ */
+ public void deleteShowAnnotation(
+ ) {
+ this._has_showAnnotation= false;
+ }
+
+ /**
+ */
+ public void deleteShowBoxes(
+ ) {
+ this._has_showBoxes= false;
+ }
+
+ /**
+ */
+ public void deleteShowColourText(
+ ) {
+ this._has_showColourText= false;
+ }
+
+ /**
+ */
+ public void deleteShowConsensusHistogram(
+ ) {
+ this._has_showConsensusHistogram= false;
+ }
+
+ /**
+ */
+ public void deleteShowDbRefTooltip(
+ ) {
+ this._has_showDbRefTooltip= false;
+ }
+
+ /**
+ */
+ public void deleteShowFullId(
+ ) {
+ this._has_showFullId= false;
+ }
+
+ /**
+ */
+ public void deleteShowGroupConsensus(
+ ) {
+ this._has_showGroupConsensus= false;
+ }
+
+ /**
+ */
+ public void deleteShowGroupConservation(
+ ) {
+ this._has_showGroupConservation= false;
+ }
+
+ /**
+ */
+ public void deleteShowNPfeatureTooltip(
+ ) {
+ this._has_showNPfeatureTooltip= false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceFeatures(
+ ) {
+ this._has_showSequenceFeatures= false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceLogo(
+ ) {
+ this._has_showSequenceLogo= false;
+ }
+
+ /**
+ */
+ public void deleteShowText(
+ ) {
+ this._has_showText= false;
+ }
+
+ /**
+ */
+ public void deleteShowUnconserved(
+ ) {
+ this._has_showUnconserved= false;
+ }
+
+ /**
+ */
+ public void deleteStartRes(
+ ) {
+ this._has_startRes= false;
+ }
+
+ /**
+ */
+ public void deleteStartSeq(
+ ) {
+ this._has_startSeq= false;
+ }
+
+ /**
+ */
+ public void deleteTextCol1(
+ ) {
+ this._has_textCol1= false;
+ }
+
+ /**
+ */
+ public void deleteTextCol2(
+ ) {
+ this._has_textCol2= false;
+ }
+
+ /**
+ */
+ public void deleteTextColThreshold(
+ ) {
+ this._has_textColThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteWrapAlignment(
+ ) {
+ this._has_wrapAlignment= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Method enumerateCalcIdParam.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.CalcIdParam elements
+ */
+ public java.util.Enumeration enumerateCalcIdParam(
+ ) {
+ return this._calcIdParamList.elements();
+ }
+
+ /**
+ * Method enumerateHiddenColumns.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.HiddenColumns elements
+ */
+ public java.util.Enumeration enumerateHiddenColumns(
+ ) {
+ return this._hiddenColumnsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
+ ) {
+ return this._annotationColours;
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public java.lang.String getBgColour(
+ ) {
+ return this._bgColour;
+ }
+
+ /**
+ * Method getCalcIdParam.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.CalcIdParam at the given index
+ */
+ public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size()) {
+ throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
+ }
+
+ /**
+ * Method getCalcIdParam.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
+ ) {
+ jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
+ return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
+ }
+
+ /**
+ * Method getCalcIdParamCount.
+ *
+ * @return the size of this collection
+ */
+ public int getCalcIdParamCount(
+ ) {
+ return this._calcIdParamList.size();
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean getCentreColumnLabels(
+ ) {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'complementId'. The field
+ * 'complementId' has the following description: The viewport
+ * id of this viewport's (cdna/protein) coding complement, if
+ * any
+ *
+ *
+ * @return the value of field 'ComplementId'.
+ */
+ public java.lang.String getComplementId(
+ ) {
+ return this._complementId;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold(
+ ) {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean getConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean getFollowHighlight(
+ ) {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean getFollowSelection(
+ ) {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName(
+ ) {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize(
+ ) {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle(
+ ) {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean getGatheredViews(
+ ) {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Method getHiddenColumns.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.HiddenColumns at the given
+ * index
+ */
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size()) {
+ throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
+ }
+
+ /**
+ * Method getHiddenColumns.Returns the contents of the
+ * collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
+ ) {
+ jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
+ return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
+ }
+
+ /**
+ * Method getHiddenColumnsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getHiddenColumnsCount(
+ ) {
+ return this._hiddenColumnsList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: unique id used by jalview to
+ * synchronize between stored and
+ * instantiated views
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean getIgnoreGapsinConsensus(
+ ) {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean getNormaliseSequenceLogo(
+ ) {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold(
+ ) {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean getRightAlignIds(
+ ) {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSetId'.
+ *
+ * @return the value of field 'SequenceSetId'.
+ */
+ public java.lang.String getSequenceSetId(
+ ) {
+ return this._sequenceSetId;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean getShowConsensusHistogram(
+ ) {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean getShowDbRefTooltip(
+ ) {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean getShowGroupConsensus(
+ ) {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean getShowGroupConservation(
+ ) {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean getShowNPfeatureTooltip(
+ ) {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean getShowSequenceLogo(
+ ) {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean getShowUnconserved(
+ ) {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes(
+ ) {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq(
+ ) {
+ return this._startSeq;
+ }
+
+ /**
+ * Returns the value of field 'textCol1'.
+ *
+ * @return the value of field 'TextCol1'.
+ */
+ public int getTextCol1(
+ ) {
+ return this._textCol1;
+ }
+
+ /**
+ * Returns the value of field 'textCol2'.
+ *
+ * @return the value of field 'TextCol2'.
+ */
+ public int getTextCol2(
+ ) {
+ return this._textCol2;
+ }
+
+ /**
+ * Returns the value of field 'textColThreshold'.
+ *
+ * @return the value of field 'TextColThreshold'.
+ */
+ public int getTextColThreshold(
+ ) {
+ return this._textColThreshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'viewName'.
+ *
+ * @return the value of field 'ViewName'.
+ */
+ public java.lang.String getViewName(
+ ) {
+ return this._viewName;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCentreColumnLabels.
+ *
+ * @return true if at least one CentreColumnLabels has been adde
+ */
+ public boolean hasCentreColumnLabels(
+ ) {
+ return this._has_centreColumnLabels;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold(
+ ) {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been
+ * added
+ */
+ public boolean hasConservationSelected(
+ ) {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFollowHighlight.
+ *
+ * @return true if at least one FollowHighlight has been added
+ */
+ public boolean hasFollowHighlight(
+ ) {
+ return this._has_followHighlight;
+ }
+
+ /**
+ * Method hasFollowSelection.
+ *
+ * @return true if at least one FollowSelection has been added
+ */
+ public boolean hasFollowSelection(
+ ) {
+ return this._has_followSelection;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasGatheredViews.
+ *
+ * @return true if at least one GatheredViews has been added
+ */
+ public boolean hasGatheredViews(
+ ) {
+ return this._has_gatheredViews;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasIgnoreGapsinConsensus.
+ *
+ * @return true if at least one IgnoreGapsinConsensus has been
+ * added
+ */
+ public boolean hasIgnoreGapsinConsensus(
+ ) {
+ return this._has_ignoreGapsinConsensus;
+ }
+
+ /**
+ * Method hasNormaliseSequenceLogo.
+ *
+ * @return true if at least one NormaliseSequenceLogo has been
+ * added
+ */
+ public boolean hasNormaliseSequenceLogo(
+ ) {
+ return this._has_normaliseSequenceLogo;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected(
+ ) {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold(
+ ) {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps(
+ ) {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasRightAlignIds.
+ *
+ * @return true if at least one RightAlignIds has been added
+ */
+ public boolean hasRightAlignIds(
+ ) {
+ return this._has_rightAlignIds;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation(
+ ) {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes(
+ ) {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText(
+ ) {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConsensusHistogram.
+ *
+ * @return true if at least one ShowConsensusHistogram has been
+ * added
+ */
+ public boolean hasShowConsensusHistogram(
+ ) {
+ return this._has_showConsensusHistogram;
+ }
+
+ /**
+ * Method hasShowDbRefTooltip.
+ *
+ * @return true if at least one ShowDbRefTooltip has been added
+ */
+ public boolean hasShowDbRefTooltip(
+ ) {
+ return this._has_showDbRefTooltip;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId(
+ ) {
+ return this._has_showFullId;
+ }
+
+ /**
+ * Method hasShowGroupConsensus.
+ *
+ * @return true if at least one ShowGroupConsensus has been adde
+ */
+ public boolean hasShowGroupConsensus(
+ ) {
+ return this._has_showGroupConsensus;
+ }
+
+ /**
+ * Method hasShowGroupConservation.
+ *
+ * @return true if at least one ShowGroupConservation has been
+ * added
+ */
+ public boolean hasShowGroupConservation(
+ ) {
+ return this._has_showGroupConservation;
+ }
+
+ /**
+ * Method hasShowNPfeatureTooltip.
+ *
+ * @return true if at least one ShowNPfeatureTooltip has been
+ * added
+ */
+ public boolean hasShowNPfeatureTooltip(
+ ) {
+ return this._has_showNPfeatureTooltip;
+ }
+
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been
+ * added
+ */
+ public boolean hasShowSequenceFeatures(
+ ) {
+ return this._has_showSequenceFeatures;
+ }
+
+ /**
+ * Method hasShowSequenceLogo.
+ *
+ * @return true if at least one ShowSequenceLogo has been added
+ */
+ public boolean hasShowSequenceLogo(
+ ) {
+ return this._has_showSequenceLogo;
+ }
+
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
+ */
+ public boolean hasShowText(
+ ) {
+ return this._has_showText;
+ }
+
+ /**
+ * Method hasShowUnconserved.
+ *
+ * @return true if at least one ShowUnconserved has been added
+ */
+ public boolean hasShowUnconserved(
+ ) {
+ return this._has_showUnconserved;
+ }
+
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
+ */
+ public boolean hasStartRes(
+ ) {
+ return this._has_startRes;
+ }
+
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
+ */
+ public boolean hasStartSeq(
+ ) {
+ return this._has_startSeq;
+ }
+
+ /**
+ * Method hasTextCol1.
+ *
+ * @return true if at least one TextCol1 has been added
+ */
+ public boolean hasTextCol1(
+ ) {
+ return this._has_textCol1;
+ }
+
+ /**
+ * Method hasTextCol2.
+ *
+ * @return true if at least one TextCol2 has been added
+ */
+ public boolean hasTextCol2(
+ ) {
+ return this._has_textCol2;
+ }
+
+ /**
+ * Method hasTextColThreshold.
+ *
+ * @return true if at least one TextColThreshold has been added
+ */
+ public boolean hasTextColThreshold(
+ ) {
+ return this._has_textColThreshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
+ */
+ public boolean hasWrapAlignment(
+ ) {
+ return this._has_wrapAlignment;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'centreColumnLabels'.
+ *
+ * @return the value of field 'CentreColumnLabels'.
+ */
+ public boolean isCentreColumnLabels(
+ ) {
+ return this._centreColumnLabels;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean isConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'followHighlight'.
+ *
+ * @return the value of field 'FollowHighlight'.
+ */
+ public boolean isFollowHighlight(
+ ) {
+ return this._followHighlight;
+ }
+
+ /**
+ * Returns the value of field 'followSelection'.
+ *
+ * @return the value of field 'FollowSelection'.
+ */
+ public boolean isFollowSelection(
+ ) {
+ return this._followSelection;
+ }
+
+ /**
+ * Returns the value of field 'gatheredViews'.
+ *
+ * @return the value of field 'GatheredViews'.
+ */
+ public boolean isGatheredViews(
+ ) {
+ return this._gatheredViews;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean isIgnoreGapsinConsensus(
+ ) {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean isNormaliseSequenceLogo(
+ ) {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean isPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean isRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'rightAlignIds'.
+ *
+ * @return the value of field 'RightAlignIds'.
+ */
+ public boolean isRightAlignIds(
+ ) {
+ return this._rightAlignIds;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean isShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean isShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean isShowConsensusHistogram(
+ ) {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showDbRefTooltip'.
+ *
+ * @return the value of field 'ShowDbRefTooltip'.
+ */
+ public boolean isShowDbRefTooltip(
+ ) {
+ return this._showDbRefTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConsensus'.
+ *
+ * @return the value of field 'ShowGroupConsensus'.
+ */
+ public boolean isShowGroupConsensus(
+ ) {
+ return this._showGroupConsensus;
+ }
+
+ /**
+ * Returns the value of field 'showGroupConservation'.
+ *
+ * @return the value of field 'ShowGroupConservation'.
+ */
+ public boolean isShowGroupConservation(
+ ) {
+ return this._showGroupConservation;
+ }
+
+ /**
+ * Returns the value of field 'showNPfeatureTooltip'.
+ *
+ * @return the value of field 'ShowNPfeatureTooltip'.
+ */
+ public boolean isShowNPfeatureTooltip(
+ ) {
+ return this._showNPfeatureTooltip;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean isShowSequenceLogo(
+ ) {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean isShowUnconserved(
+ ) {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllCalcIdParam(
+ ) {
+ this._calcIdParamList.clear();
+ }
+
+ /**
+ */
+ public void removeAllHiddenColumns(
+ ) {
+ this._hiddenColumnsList.clear();
+ }
+
+ /**
+ * Method removeCalcIdParam.
+ *
+ * @param vCalcIdParam
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
+ boolean removed = _calcIdParamList.remove(vCalcIdParam);
+ return removed;
+ }
+
+ /**
+ * Method removeCalcIdParamAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
+ final int index) {
+ java.lang.Object obj = this._calcIdParamList.remove(index);
+ return (jalview.schemabinding.version2.CalcIdParam) obj;
+ }
+
+ /**
+ * Method removeHiddenColumns.
+ *
+ * @param vHiddenColumns
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
+ boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
+ return removed;
+ }
+
+ /**
+ * Method removeHiddenColumnsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
+ final int index) {
+ java.lang.Object obj = this._hiddenColumnsList.remove(index);
+ return (jalview.schemabinding.version2.HiddenColumns) obj;
+ }
+
+ /**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours the value of field
+ * 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours) {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour the value of field 'bgColour'.
+ */
+ public void setBgColour(
+ final java.lang.String bgColour) {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setCalcIdParam(
+ final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size()) {
+ throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ this._calcIdParamList.set(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vCalcIdParamArray
+ */
+ public void setCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
+ //-- copy array
+ _calcIdParamList.clear();
+
+ for (int i = 0; i < vCalcIdParamArray.length; i++) {
+ this._calcIdParamList.add(vCalcIdParamArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'centreColumnLabels'.
+ *
+ * @param centreColumnLabels the value of field
+ * 'centreColumnLabels'.
+ */
+ public void setCentreColumnLabels(
+ final boolean centreColumnLabels) {
+ this._centreColumnLabels = centreColumnLabels;
+ this._has_centreColumnLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'complementId'. The field
+ * 'complementId' has the following description: The viewport
+ * id of this viewport's (cdna/protein) coding complement, if
+ * any
+ *
+ *
+ * @param complementId the value of field 'complementId'.
+ */
+ public void setComplementId(
+ final java.lang.String complementId) {
+ this._complementId = complementId;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(
+ final int consThreshold) {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected the value of field
+ * 'conservationSelected'.
+ */
+ public void setConservationSelected(
+ final boolean conservationSelected) {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'followHighlight'.
+ *
+ * @param followHighlight the value of field 'followHighlight'.
+ */
+ public void setFollowHighlight(
+ final boolean followHighlight) {
+ this._followHighlight = followHighlight;
+ this._has_followHighlight = true;
+ }
+
+ /**
+ * Sets the value of field 'followSelection'.
+ *
+ * @param followSelection the value of field 'followSelection'.
+ */
+ public void setFollowSelection(
+ final boolean followSelection) {
+ this._followSelection = followSelection;
+ this._has_followSelection = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'gatheredViews'.
+ *
+ * @param gatheredViews the value of field 'gatheredViews'.
+ */
+ public void setGatheredViews(
+ final boolean gatheredViews) {
+ this._gatheredViews = gatheredViews;
+ this._has_gatheredViews = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenColumns
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setHiddenColumns(
+ final int index,
+ final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenColumnsList.size()) {
+ throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
+ }
+
+ this._hiddenColumnsList.set(index, vHiddenColumns);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenColumnsArray
+ */
+ public void setHiddenColumns(
+ final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
+ //-- copy array
+ _hiddenColumnsList.clear();
+
+ for (int i = 0; i < vHiddenColumnsArray.length; i++) {
+ this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: unique id used by jalview to
+ * synchronize between stored and
+ * instantiated views
+ *
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'ignoreGapsinConsensus'.
+ *
+ * @param ignoreGapsinConsensus the value of field
+ * 'ignoreGapsinConsensus'.
+ */
+ public void setIgnoreGapsinConsensus(
+ final boolean ignoreGapsinConsensus) {
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+ this._has_ignoreGapsinConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'normaliseSequenceLogo'.
+ *
+ * @param normaliseSequenceLogo the value of field
+ * 'normaliseSequenceLogo'.
+ */
+ public void setNormaliseSequenceLogo(
+ final boolean normaliseSequenceLogo) {
+ this._normaliseSequenceLogo = normaliseSequenceLogo;
+ this._has_normaliseSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected the value of field 'pidSelected'.
+ */
+ public void setPidSelected(
+ final boolean pidSelected) {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(
+ final int pidThreshold) {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(
+ final boolean renderGaps) {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'rightAlignIds'.
+ *
+ * @param rightAlignIds the value of field 'rightAlignIds'.
+ */
+ public void setRightAlignIds(
+ final boolean rightAlignIds) {
+ this._rightAlignIds = rightAlignIds;
+ this._has_rightAlignIds = true;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSetId'.
+ *
+ * @param sequenceSetId the value of field 'sequenceSetId'.
+ */
+ public void setSequenceSetId(
+ final java.lang.String sequenceSetId) {
+ this._sequenceSetId = sequenceSetId;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(
+ final boolean showAnnotation) {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(
+ final boolean showBoxes) {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText the value of field 'showColourText'.
+ */
+ public void setShowColourText(
+ final boolean showColourText) {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConsensusHistogram'.
+ *
+ * @param showConsensusHistogram the value of field
+ * 'showConsensusHistogram'.
+ */
+ public void setShowConsensusHistogram(
+ final boolean showConsensusHistogram) {
+ this._showConsensusHistogram = showConsensusHistogram;
+ this._has_showConsensusHistogram = true;
+ }
+
+ /**
+ * Sets the value of field 'showDbRefTooltip'.
+ *
+ * @param showDbRefTooltip the value of field 'showDbRefTooltip'
+ */
+ public void setShowDbRefTooltip(
+ final boolean showDbRefTooltip) {
+ this._showDbRefTooltip = showDbRefTooltip;
+ this._has_showDbRefTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId the value of field 'showFullId'.
+ */
+ public void setShowFullId(
+ final boolean showFullId) {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConsensus'.
+ *
+ * @param showGroupConsensus the value of field
+ * 'showGroupConsensus'.
+ */
+ public void setShowGroupConsensus(
+ final boolean showGroupConsensus) {
+ this._showGroupConsensus = showGroupConsensus;
+ this._has_showGroupConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'showGroupConservation'.
+ *
+ * @param showGroupConservation the value of field
+ * 'showGroupConservation'.
+ */
+ public void setShowGroupConservation(
+ final boolean showGroupConservation) {
+ this._showGroupConservation = showGroupConservation;
+ this._has_showGroupConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showNPfeatureTooltip'.
+ *
+ * @param showNPfeatureTooltip the value of field
+ * 'showNPfeatureTooltip'.
+ */
+ public void setShowNPfeatureTooltip(
+ final boolean showNPfeatureTooltip) {
+ this._showNPfeatureTooltip = showNPfeatureTooltip;
+ this._has_showNPfeatureTooltip = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures the value of field
+ * 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(
+ final boolean showSequenceFeatures) {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceLogo'.
+ *
+ * @param showSequenceLogo the value of field 'showSequenceLogo'
+ */
+ public void setShowSequenceLogo(
+ final boolean showSequenceLogo) {
+ this._showSequenceLogo = showSequenceLogo;
+ this._has_showSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText the value of field 'showText'.
+ */
+ public void setShowText(
+ final boolean showText) {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'showUnconserved'.
+ *
+ * @param showUnconserved the value of field 'showUnconserved'.
+ */
+ public void setShowUnconserved(
+ final boolean showUnconserved) {
+ this._showUnconserved = showUnconserved;
+ this._has_showUnconserved = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes the value of field 'startRes'.
+ */
+ public void setStartRes(
+ final int startRes) {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq the value of field 'startSeq'.
+ */
+ public void setStartSeq(
+ final int startSeq) {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol1'.
+ *
+ * @param textCol1 the value of field 'textCol1'.
+ */
+ public void setTextCol1(
+ final int textCol1) {
+ this._textCol1 = textCol1;
+ this._has_textCol1 = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol2'.
+ *
+ * @param textCol2 the value of field 'textCol2'.
+ */
+ public void setTextCol2(
+ final int textCol2) {
+ this._textCol2 = textCol2;
+ this._has_textCol2 = true;
+ }
+
+ /**
+ * Sets the value of field 'textColThreshold'.
+ *
+ * @param textColThreshold the value of field 'textColThreshold'
+ */
+ public void setTextColThreshold(
+ final int textColThreshold) {
+ this._textColThreshold = textColThreshold;
+ this._has_textColThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'viewName'.
+ *
+ * @param viewName the value of field 'viewName'.
+ */
+ public void setViewName(
+ final java.lang.String viewName) {
+ this._viewName = viewName;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(
+ final boolean wrapAlignment) {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.Viewport
+ */
+ public static jalview.schemabinding.version2.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
*/
package jalview.schemabinding.version2.descriptors;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Viewport;
*
* @version $Revision$ $Date$
*/
-public class ViewportDescriptor extends
- org.exolab.castor.xml.util.XMLClassDescriptorImpl
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public ViewportDescriptor()
- {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "Viewport";
- _elementDefinition = true;
-
- // -- set grouping compositor
- setCompositorAsSequence();
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- // -- initialize attribute descriptors
-
- // -- _conservationSelected
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_conservationSelected",
- "conservationSelected",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasConservationSelected())
- {
- return null;
- }
- return (target.getConservationSelected() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteConservationSelected();
- return;
- }
- target.setConservationSelected(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _conservationSelected
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public ViewportDescriptor() {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "Viewport";
+ _elementDefinition = true;
+
+ //-- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ //-- initialize attribute descriptors
+
+ //-- _conservationSelected
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasConservationSelected()) { return null; }
+ return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteConservationSelected();
+ return;
+ }
+ target.setConservationSelected( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _conservationSelected
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _pidSelected
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasPidSelected()) { return null; }
+ return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deletePidSelected();
+ return;
+ }
+ target.setPidSelected( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _pidSelected
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _bgColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getBgColour();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.setBgColour( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _bgColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ //-- _consThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasConsThreshold()) { return null; }
+ return new java.lang.Integer(target.getConsThreshold());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteConsThreshold();
+ return;
+ }
+ target.setConsThreshold( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _consThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _pidThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasPidThreshold()) { return null; }
+ return new java.lang.Integer(target.getPidThreshold());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deletePidThreshold();
+ return;
+ }
+ target.setPidThreshold( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _pidThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getTitle();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.setTitle( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showFullId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowFullId()) { return null; }
+ return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowFullId();
+ return;
+ }
+ target.setShowFullId( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showFullId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _rightAlignIds
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasRightAlignIds()) { return null; }
+ return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteRightAlignIds();
+ return;
+ }
+ target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _rightAlignIds
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showText
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowText()) { return null; }
+ return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowText();
+ return;
+ }
+ target.setShowText( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showText
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showColourText
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowColourText()) { return null; }
+ return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowColourText();
+ return;
+ }
+ target.setShowColourText( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showColourText
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showUnconserved
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowUnconserved()) { return null; }
+ return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowUnconserved();
+ return;
+ }
+ target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showUnconserved
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showBoxes
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowBoxes()) { return null; }
+ return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowBoxes();
+ return;
+ }
+ target.setShowBoxes( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showBoxes
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _wrapAlignment
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasWrapAlignment()) { return null; }
+ return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteWrapAlignment();
+ return;
+ }
+ target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _wrapAlignment
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _renderGaps
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasRenderGaps()) { return null; }
+ return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteRenderGaps();
+ return;
+ }
+ target.setRenderGaps( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _renderGaps
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showSequenceFeatures
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowSequenceFeatures()) { return null; }
+ return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowSequenceFeatures();
+ return;
+ }
+ target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showSequenceFeatures
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showNPfeatureTooltip
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showNPfeatureTooltip", "showNPfeatureTooltip", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowNPfeatureTooltip()) { return null; }
+ return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowNPfeatureTooltip();
+ return;
+ }
+ target.setShowNPfeatureTooltip( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showNPfeatureTooltip
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showDbRefTooltip
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDbRefTooltip", "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowDbRefTooltip()) { return null; }
+ return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowDbRefTooltip();
+ return;
+ }
+ target.setShowDbRefTooltip( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showDbRefTooltip
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _followHighlight
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasFollowHighlight()) { return null; }
+ return (target.getFollowHighlight() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteFollowHighlight();
+ return;
+ }
+ target.setFollowHighlight( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _followHighlight
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _followSelection
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followSelection", "followSelection", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasFollowSelection()) { return null; }
+ return (target.getFollowSelection() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteFollowSelection();
+ return;
+ }
+ target.setFollowSelection( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _followSelection
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showAnnotation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowAnnotation()) { return null; }
+ return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowAnnotation();
+ return;
+ }
+ target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showAnnotation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _centreColumnLabels
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColumnLabels", "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasCentreColumnLabels()) { return null; }
+ return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteCentreColumnLabels();
+ return;
+ }
+ target.setCentreColumnLabels( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _centreColumnLabels
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showGroupConservation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConservation", "showGroupConservation", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowGroupConservation()) { return null; }
+ return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowGroupConservation();
+ return;
+ }
+ target.setShowGroupConservation( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showGroupConservation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showGroupConsensus
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConsensus", "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowGroupConsensus()) { return null; }
+ return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowGroupConsensus();
+ return;
+ }
+ target.setShowGroupConsensus( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showGroupConsensus
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showConsensusHistogram
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowConsensusHistogram()) { return null; }
+ return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowConsensusHistogram();
+ return;
+ }
+ target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showConsensusHistogram
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _showSequenceLogo
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasShowSequenceLogo()) { return null; }
+ return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowSequenceLogo();
+ return;
+ }
+ target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _showSequenceLogo
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _normaliseSequenceLogo
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_normaliseSequenceLogo", "normaliseSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasNormaliseSequenceLogo()) { return null; }
+ return (target.getNormaliseSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteNormaliseSequenceLogo();
+ return;
+ }
+ target.setNormaliseSequenceLogo( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _normaliseSequenceLogo
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _ignoreGapsinConsensus
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasIgnoreGapsinConsensus()) { return null; }
+ return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteIgnoreGapsinConsensus();
+ return;
+ }
+ target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _ignoreGapsinConsensus
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _startRes
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasStartRes()) { return null; }
+ return new java.lang.Integer(target.getStartRes());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteStartRes();
+ return;
+ }
+ target.setStartRes( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _startRes
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _startSeq
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasStartSeq()) { return null; }
+ return new java.lang.Integer(target.getStartSeq());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteStartSeq();
+ return;
+ }
+ target.setStartSeq( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _startSeq
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _fontName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getFontName();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.setFontName( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _fontName
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ //-- _fontSize
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasFontSize()) { return null; }
+ return new java.lang.Integer(target.getFontSize());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteFontSize();
+ return;
+ }
+ target.setFontSize( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _fontSize
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _fontStyle
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasFontStyle()) { return null; }
+ return new java.lang.Integer(target.getFontStyle());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteFontStyle();
+ return;
+ }
+ target.setFontStyle( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _fontStyle
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _viewName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getViewName();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.setViewName( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _viewName
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ //-- _sequenceSetId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getSequenceSetId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.setSequenceSetId( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _sequenceSetId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ //-- _gatheredViews
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasGatheredViews()) { return null; }
+ return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteGatheredViews();
+ return;
+ }
+ target.setGatheredViews( ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _gatheredViews
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _textCol1
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasTextCol1()) { return null; }
+ return new java.lang.Integer(target.getTextCol1());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteTextCol1();
+ return;
+ }
+ target.setTextCol1( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _textCol1
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _textCol2
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasTextCol2()) { return null; }
+ return new java.lang.Integer(target.getTextCol2());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteTextCol2();
+ return;
+ }
+ target.setTextCol2( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _textCol2
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _textColThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasTextColThreshold()) { return null; }
+ return new java.lang.Integer(target.getTextColThreshold());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteTextColThreshold();
+ return;
+ }
+ target.setTextColThreshold( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _textColThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ super.setIdentity(desc);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.setId( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IdValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IdValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _complementId
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_complementId", "complementId", org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getComplementId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.setComplementId( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _complementId
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ //-- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasWidth()) { return null; }
+ return new java.lang.Integer(target.getWidth());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasHeight()) { return null; }
+ return new java.lang.Integer(target.getHeight());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasXpos()) { return null; }
+ return new java.lang.Integer(target.getXpos());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ if (!target.hasYpos()) { return null; }
+ return new java.lang.Integer(target.getYpos());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos( ((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ //-- _annotationColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getAnnotationColours();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new jalview.schemabinding.version2.AnnotationColours();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _annotationColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _hiddenColumnsList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getHiddenColumns();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+ try {
+ Viewport target = (Viewport) object;
+ target.removeAllHiddenColumns();
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new jalview.schemabinding.version2.HiddenColumns();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _hiddenColumnsList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
+ //-- _calcIdParamList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.CalcIdParam.class, "_calcIdParamList", "calcIdParam", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Viewport target = (Viewport) object;
+ return target.getCalcIdParam();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Viewport target = (Viewport) object;
+ target.addCalcIdParam( (jalview.schemabinding.version2.CalcIdParam) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+ try {
+ Viewport target = (Viewport) object;
+ target.removeAllCalcIdParam();
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new jalview.schemabinding.version2.CalcIdParam();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _calcIdParamList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { //-- local scope
+ }
+ desc.setValidator(fieldValidator);
}
- desc.setValidator(fieldValidator);
- // -- _pidSelected
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_pidSelected", "pidSelected",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasPidSelected())
- {
- return null;
- }
- return (target.getPidSelected() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deletePidSelected();
- return;
- }
- target.setPidSelected(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
- // -- validation code for: _pidSelected
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _bgColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_bgColour", "bgColour",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getBgColour();
- }
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.setBgColour((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
+ //-----------/
+ //- Methods -/
+ //-----------/
- public java.lang.Object newInstance(java.lang.Object parent)
- {
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode(
+ ) {
return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _bgColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
}
- desc.setValidator(fieldValidator);
- // -- _consThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_consThreshold", "consThreshold",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasConsThreshold())
- {
- return null;
- }
- return new java.lang.Integer(target.getConsThreshold());
- }
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteConsThreshold();
- return;
- }
- target.setConsThreshold(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _consThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no
+ * identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+ ) {
+ return super.getIdentity();
}
- desc.setValidator(fieldValidator);
- // -- _pidThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasPidThreshold())
- {
- return null;
- }
- return new java.lang.Integer(target.getPidThreshold());
- }
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deletePidThreshold();
- return;
- }
- target.setPidThreshold(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _pidThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass(
+ ) {
+ return jalview.schemabinding.version2.Viewport.class;
}
- desc.setValidator(fieldValidator);
- // -- _title
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_title", "title",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getTitle();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.setTitle((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
- // -- validation code for: _title
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix(
+ ) {
+ return _nsPrefix;
}
- desc.setValidator(fieldValidator);
- // -- _showFullId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showFullId", "showFullId",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowFullId())
- {
- return null;
- }
- return (target.getShowFullId() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowFullId();
- return;
- }
- target.setShowFullId(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showFullId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _rightAlignIds
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasRightAlignIds())
- {
- return null;
- }
- return (target.getRightAlignIds() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteRightAlignIds();
- return;
- }
- target.setRightAlignIds(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _rightAlignIds
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and
+ * unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI(
+ ) {
+ return _nsURI;
}
- desc.setValidator(fieldValidator);
- // -- _showText
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showText", "showText",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowText())
- {
- return null;
- }
- return (target.getShowText() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowText();
- return;
- }
- target.setShowText(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
- // -- validation code for: _showText
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator(
+ ) {
+ return this;
}
- desc.setValidator(fieldValidator);
- // -- _showColourText
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showColourText", "showColourText",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowColourText())
- {
- return null;
- }
- return (target.getShowColourText() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowColourText();
- return;
- }
- target.setShowColourText(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
- // -- validation code for: _showColourText
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName(
+ ) {
+ return _xmlName;
}
- desc.setValidator(fieldValidator);
- // -- _showUnconserved
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowUnconserved())
- {
- return null;
- }
- return (target.getShowUnconserved() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowUnconserved();
- return;
- }
- target.setShowUnconserved(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showUnconserved
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showBoxes
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showBoxes", "showBoxes",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowBoxes())
- {
- return null;
- }
- return (target.getShowBoxes() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowBoxes();
- return;
- }
- target.setShowBoxes(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showBoxes
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _wrapAlignment
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasWrapAlignment())
- {
- return null;
- }
- return (target.getWrapAlignment() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteWrapAlignment();
- return;
- }
- target.setWrapAlignment(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
- // -- validation code for: _wrapAlignment
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that
+ * of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition(
+ ) {
+ return _elementDefinition;
}
- desc.setValidator(fieldValidator);
- // -- _renderGaps
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_renderGaps", "renderGaps",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasRenderGaps())
- {
- return null;
- }
- return (target.getRenderGaps() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteRenderGaps();
- return;
- }
- target.setRenderGaps(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _renderGaps
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showSequenceFeatures
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showSequenceFeatures",
- "showSequenceFeatures",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowSequenceFeatures())
- {
- return null;
- }
- return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowSequenceFeatures();
- return;
- }
- target.setShowSequenceFeatures(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showSequenceFeatures
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showNPfeatureTooltip
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showNPfeatureTooltip",
- "showNPfeatureTooltip",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowNPfeatureTooltip())
- {
- return null;
- }
- return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowNPfeatureTooltip();
- return;
- }
- target.setShowNPfeatureTooltip(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showNPfeatureTooltip
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showDbRefTooltip
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showDbRefTooltip",
- "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowDbRefTooltip())
- {
- return null;
- }
- return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowDbRefTooltip();
- return;
- }
- target.setShowDbRefTooltip(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showDbRefTooltip
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _followHighlight
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_followHighlight", "followHighlight",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasFollowHighlight())
- {
- return null;
- }
- return (target.getFollowHighlight() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteFollowHighlight();
- return;
- }
- target.setFollowHighlight(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _followHighlight
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _followSelection
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_followSelection", "followSelection",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasFollowSelection())
- {
- return null;
- }
- return (target.getFollowSelection() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteFollowSelection();
- return;
- }
- target.setFollowSelection(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _followSelection
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showAnnotation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowAnnotation())
- {
- return null;
- }
- return (target.getShowAnnotation() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowAnnotation();
- return;
- }
- target.setShowAnnotation(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showAnnotation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _centreColumnLabels
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_centreColumnLabels",
- "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasCentreColumnLabels())
- {
- return null;
- }
- return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteCentreColumnLabels();
- return;
- }
- target.setCentreColumnLabels(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _centreColumnLabels
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showGroupConservation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showGroupConservation",
- "showGroupConservation",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowGroupConservation())
- {
- return null;
- }
- return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowGroupConservation();
- return;
- }
- target.setShowGroupConservation(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showGroupConservation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showGroupConsensus
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showGroupConsensus",
- "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowGroupConsensus())
- {
- return null;
- }
- return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowGroupConsensus();
- return;
- }
- target.setShowGroupConsensus(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showGroupConsensus
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showConsensusHistogram
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showConsensusHistogram",
- "showConsensusHistogram",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowConsensusHistogram())
- {
- return null;
- }
- return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowConsensusHistogram();
- return;
- }
- target.setShowConsensusHistogram(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showConsensusHistogram
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _showSequenceLogo
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showSequenceLogo",
- "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasShowSequenceLogo())
- {
- return null;
- }
- return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowSequenceLogo();
- return;
- }
- target.setShowSequenceLogo(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showSequenceLogo
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _normaliseSequenceLogo
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_normaliseSequenceLogo",
- "normaliseSequenceLogo",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasNormaliseSequenceLogo())
- {
- return null;
- }
- return (target.getNormaliseSequenceLogo() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteNormaliseSequenceLogo();
- return;
- }
- target.setNormaliseSequenceLogo(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _normaliseSequenceLogo
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _ignoreGapsinConsensus
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_ignoreGapsinConsensus",
- "ignoreGapsinConsensus",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasIgnoreGapsinConsensus())
- {
- return null;
- }
- return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteIgnoreGapsinConsensus();
- return;
- }
- target.setIgnoreGapsinConsensus(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _ignoreGapsinConsensus
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _startRes
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_startRes", "startRes",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasStartRes())
- {
- return null;
- }
- return new java.lang.Integer(target.getStartRes());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteStartRes();
- return;
- }
- target.setStartRes(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _startRes
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _startSeq
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_startSeq", "startSeq",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasStartSeq())
- {
- return null;
- }
- return new java.lang.Integer(target.getStartSeq());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteStartSeq();
- return;
- }
- target.setStartSeq(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _startSeq
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _fontName
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_fontName", "fontName",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getFontName();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.setFontName((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _fontName
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- _fontSize
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_fontSize", "fontSize",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasFontSize())
- {
- return null;
- }
- return new java.lang.Integer(target.getFontSize());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteFontSize();
- return;
- }
- target.setFontSize(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _fontSize
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _fontStyle
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasFontStyle())
- {
- return null;
- }
- return new java.lang.Integer(target.getFontStyle());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteFontStyle();
- return;
- }
- target.setFontStyle(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _fontStyle
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _viewName
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_viewName", "viewName",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getViewName();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.setViewName((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _viewName
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- _sequenceSetId
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_sequenceSetId", "sequenceSetId",
- org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getSequenceSetId();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.setSequenceSetId((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _sequenceSetId
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- // -- _gatheredViews
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasGatheredViews())
- {
- return null;
- }
- return (target.getGatheredViews() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteGatheredViews();
- return;
- }
- target.setGatheredViews(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _gatheredViews
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _textCol1
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_textCol1", "textCol1",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasTextCol1())
- {
- return null;
- }
- return new java.lang.Integer(target.getTextCol1());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteTextCol1();
- return;
- }
- target.setTextCol1(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _textCol1
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _textCol2
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_textCol2", "textCol2",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasTextCol2())
- {
- return null;
- }
- return new java.lang.Integer(target.getTextCol2());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteTextCol2();
- return;
- }
- target.setTextCol2(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _textCol2
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _textColThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_textColThreshold",
- "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasTextColThreshold())
- {
- return null;
- }
- return new java.lang.Integer(target.getTextColThreshold());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteTextColThreshold();
- return;
- }
- target.setTextColThreshold(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _textColThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_id", "id",
- org.exolab.castor.xml.NodeType.Attribute);
- super.setIdentity(desc);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getId();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.setId((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IdValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IdValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- // -- _width
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_width", "width",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasWidth())
- {
- return null;
- }
- return new java.lang.Integer(target.getWidth());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteWidth();
- return;
- }
- target.setWidth(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _width
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _height
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_height", "height",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasHeight())
- {
- return null;
- }
- return new java.lang.Integer(target.getHeight());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteHeight();
- return;
- }
- target.setHeight(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _height
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _xpos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_xpos", "xpos",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasXpos())
- {
- return null;
- }
- return new java.lang.Integer(target.getXpos());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteXpos();
- return;
- }
- target.setXpos(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _xpos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- _ypos
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_ypos", "ypos",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- if (!target.hasYpos())
- {
- return null;
- }
- return new java.lang.Integer(target.getYpos());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteYpos();
- return;
- }
- target.setYpos(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _ypos
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- // -- initialize element descriptors
-
- // -- _annotationColours
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- jalview.schemabinding.version2.AnnotationColours.class,
- "_annotationColours", "AnnotationColours",
- org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getAnnotationColours();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return new jalview.schemabinding.version2.AnnotationColours();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _annotationColours
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- }
- desc.setValidator(fieldValidator);
- // -- _hiddenColumnsList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- jalview.schemabinding.version2.HiddenColumns.class,
- "_hiddenColumnsList", "hiddenColumns",
- org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getHiddenColumns();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.addHiddenColumns((jalview.schemabinding.version2.HiddenColumns) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.removeAllHiddenColumns();
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return new jalview.schemabinding.version2.HiddenColumns();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- // -- validation code for: _hiddenColumnsList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { // -- local scope
- }
- desc.setValidator(fieldValidator);
- // -- _calcIdParamList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- jalview.schemabinding.version2.CalcIdParam.class,
- "_calcIdParamList", "calcIdParam",
- org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Viewport target = (Viewport) object;
- return target.getCalcIdParam();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.addCalcIdParam((jalview.schemabinding.version2.CalcIdParam) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
- {
- try
- {
- Viewport target = (Viewport) object;
- target.removeAllCalcIdParam();
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return new jalview.schemabinding.version2.CalcIdParam();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("www.jalview.org");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- // -- validation code for: _calcIdParamList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { // -- local scope
- }
- desc.setValidator(fieldValidator);
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode()
- {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()
- {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass()
- {
- return jalview.schemabinding.version2.Viewport.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix()
- {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI()
- {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator()
- {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName()
- {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition()
- {
- return _elementDefinition;
- }
}
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Vector;
-public class ClustalxColourScheme extends ResidueColourScheme // implements
-// IParameterizable
+public class ClustalxColourScheme extends ResidueColourScheme
{
- public static Hashtable colhash = new Hashtable();
+ private static final int EIGHTY_FIVE = 85;
- Hashtable[] cons;
+ private static final int FIFTY = 50;
- int[][] cons2;
+ private static final int EIGHTY = 80;
- ConsensusColour[] colours;
+ private static final int SIXTY = 60;
- ConsensusColour[] ResidueColour;
+ /*
+ * Map from conventional colour names to Clustal version of the same
+ */
+ private static Map<Color, Color> colhash = new HashMap<Color, Color>();
+
+ private int[][] cons2;
+
+ private ConsensusColour[] colours;
- int size;
+ private ConsensusColour[] residueColour;
- Consensus[] conses = new Consensus[32];
+ private int size;
- Vector colourTable = new Vector();
+ private Consensus[] conses = new Consensus[32];
private boolean includeGaps = true;
+ static
{
- colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
- colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
- colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
- colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
- colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
- colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
- colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
- colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
+ colhash.put(Color.RED, new Color(0.9f, 0.2f, 0.1f));
+ colhash.put(Color.BLUE, new Color(0.5f, 0.7f, 0.9f));
+ colhash.put(Color.GREEN, new Color(0.1f, 0.8f, 0.1f));
+ colhash.put(Color.ORANGE, new Color(0.9f, 0.6f, 0.3f));
+ colhash.put(Color.CYAN, new Color(0.1f, 0.7f, 0.7f));
+ colhash.put(Color.PINK, new Color(0.9f, 0.5f, 0.5f));
+ colhash.put(Color.MAGENTA, new Color(0.8f, 0.3f, 0.8f));
+ colhash.put(Color.YELLOW, new Color(0.8f, 0.8f, 0.0f));
}
public ClustalxColourScheme(AnnotatedCollectionI alignment,
public void makeColours()
{
- conses[0] = new Consensus("WLVIMAFCYHP", 60);
- conses[1] = new Consensus("WLVIMAFCYHP", 80);
- conses[2] = new Consensus("ED", 50);
- conses[3] = new Consensus("KR", 60);
- conses[4] = new Consensus("G", 50);
- conses[5] = new Consensus("N", 50);
- conses[6] = new Consensus("QE", 50);
- conses[7] = new Consensus("P", 50);
- conses[8] = new Consensus("TS", 50);
-
- conses[26] = new Consensus("A", 85);
- conses[27] = new Consensus("C", 85);
- conses[10] = new Consensus("E", 85);
- conses[11] = new Consensus("F", 85);
- conses[12] = new Consensus("G", 85);
- conses[13] = new Consensus("H", 85);
- conses[14] = new Consensus("I", 85);
- conses[15] = new Consensus("L", 85);
- conses[16] = new Consensus("M", 85);
- conses[17] = new Consensus("N", 85);
- conses[18] = new Consensus("P", 85);
- conses[19] = new Consensus("Q", 85);
- conses[20] = new Consensus("R", 85);
- conses[21] = new Consensus("S", 85);
- conses[22] = new Consensus("T", 85);
- conses[23] = new Consensus("V", 85);
- conses[24] = new Consensus("W", 85);
- conses[25] = new Consensus("Y", 85);
- conses[28] = new Consensus("K", 85);
- conses[29] = new Consensus("D", 85);
+ conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
+ conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
+ conses[2] = new Consensus("ED", FIFTY);
+ conses[3] = new Consensus("KR", SIXTY);
+ conses[4] = new Consensus("G", FIFTY);
+ conses[5] = new Consensus("N", FIFTY);
+ conses[6] = new Consensus("QE", FIFTY);
+ conses[7] = new Consensus("P", FIFTY);
+ conses[8] = new Consensus("TS", FIFTY);
+
+ conses[26] = new Consensus("A", EIGHTY_FIVE);
+ conses[27] = new Consensus("C", EIGHTY_FIVE);
+ conses[10] = new Consensus("E", EIGHTY_FIVE);
+ conses[11] = new Consensus("F", EIGHTY_FIVE);
+ conses[12] = new Consensus("G", EIGHTY_FIVE);
+ conses[13] = new Consensus("H", EIGHTY_FIVE);
+ conses[14] = new Consensus("I", EIGHTY_FIVE);
+ conses[15] = new Consensus("L", EIGHTY_FIVE);
+ conses[16] = new Consensus("M", EIGHTY_FIVE);
+ conses[17] = new Consensus("N", EIGHTY_FIVE);
+ conses[18] = new Consensus("P", EIGHTY_FIVE);
+ conses[19] = new Consensus("Q", EIGHTY_FIVE);
+ conses[20] = new Consensus("R", EIGHTY_FIVE);
+ conses[21] = new Consensus("S", EIGHTY_FIVE);
+ conses[22] = new Consensus("T", EIGHTY_FIVE);
+ conses[23] = new Consensus("V", EIGHTY_FIVE);
+ conses[24] = new Consensus("W", EIGHTY_FIVE);
+ conses[25] = new Consensus("Y", EIGHTY_FIVE);
+ conses[28] = new Consensus("K", EIGHTY_FIVE);
+ conses[29] = new Consensus("D", EIGHTY_FIVE);
conses[30] = new Consensus("G", 0);
conses[31] = new Consensus("P", 0);
Consensus[] tmp8 = new Consensus[1];
tmp8[0] = conses[30]; // G
- colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
+ colours[7] = new ConsensusColour(colhash.get(Color.ORANGE), tmp8);
Consensus[] tmp9 = new Consensus[1];
tmp9[0] = conses[31]; // P
- colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
+ colours[8] = new ConsensusColour(colhash.get(Color.YELLOW), tmp9);
Consensus[] tmp10 = new Consensus[1];
tmp10[0] = conses[27]; // C
- colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
+ colours[9] = new ConsensusColour(colhash.get(Color.PINK), tmp8);
Consensus[] tmp1 = new Consensus[14];
tmp1[0] = conses[0]; // %
tmp1[11] = conses[25]; // Y
tmp1[12] = conses[18]; // P
tmp1[13] = conses[19]; // p
- colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
+ colours[0] = new ConsensusColour(colhash.get(Color.BLUE), tmp1);
- colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
+ colours[10] = new ConsensusColour(colhash.get(Color.CYAN), tmp1);
Consensus[] tmp2 = new Consensus[5];
tmp2[0] = conses[8]; // t
tmp2[2] = conses[22]; // T
tmp2[3] = conses[0]; // %
tmp2[4] = conses[1]; // #
- colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
+ colours[1] = new ConsensusColour(colhash.get(Color.GREEN), tmp2);
Consensus[] tmp3 = new Consensus[3];
tmp3[0] = conses[17]; // N
tmp3[1] = conses[29]; // D
tmp3[2] = conses[5]; // n
- colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
+ colours[2] = new ConsensusColour(colhash.get(Color.GREEN), tmp3);
Consensus[] tmp4 = new Consensus[6];
tmp4[0] = conses[6]; // q = QE
tmp4[3] = conses[3]; // +
tmp4[4] = conses[28]; // K
tmp4[5] = conses[20]; // R
- colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
+ colours[3] = new ConsensusColour(colhash.get(Color.GREEN), tmp4);
Consensus[] tmp5 = new Consensus[4];
tmp5[0] = conses[3]; // +
tmp5[1] = conses[28]; // K
tmp5[2] = conses[20]; // R
tmp5[3] = conses[19]; // Q
- colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
+ colours[4] = new ConsensusColour(colhash.get(Color.RED), tmp5);
Consensus[] tmp6 = new Consensus[6];
tmp6[0] = conses[3]; // -
tmp6[3] = conses[6]; // QE
tmp6[4] = conses[19]; // Q
tmp6[5] = conses[2]; // DE
- colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
+ colours[5] = new ConsensusColour(colhash.get(Color.MAGENTA), tmp6);
Consensus[] tmp7 = new Consensus[5];
tmp7[0] = conses[3]; // -
tmp7[2] = conses[10]; // E
tmp7[3] = conses[17]; // N
tmp7[4] = conses[2]; // DE
- colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
+ colours[6] = new ConsensusColour(colhash.get(Color.MAGENTA), tmp7);
// Now attach the ConsensusColours to the residue letters
- ResidueColour = new ConsensusColour[20];
- ResidueColour[0] = colours[0]; // A
- ResidueColour[1] = colours[4]; // R
- ResidueColour[2] = colours[2]; // N
- ResidueColour[3] = colours[6]; // D
- ResidueColour[4] = colours[0]; // C
- ResidueColour[5] = colours[3]; // Q
- ResidueColour[6] = colours[5]; // E
- ResidueColour[7] = colours[7]; // G
- ResidueColour[8] = colours[10]; // H
- ResidueColour[9] = colours[0]; // I
- ResidueColour[10] = colours[0]; // L
- ResidueColour[11] = colours[4]; // K
- ResidueColour[12] = colours[0]; // M
- ResidueColour[13] = colours[0]; // F
- ResidueColour[14] = colours[8]; // P
- ResidueColour[15] = colours[1]; // S
- ResidueColour[16] = colours[1]; // T
- ResidueColour[17] = colours[0]; // W
- ResidueColour[18] = colours[10]; // Y
- ResidueColour[19] = colours[0]; // V
+ residueColour = new ConsensusColour[20];
+ residueColour[0] = colours[0]; // A
+ residueColour[1] = colours[4]; // R
+ residueColour[2] = colours[2]; // N
+ residueColour[3] = colours[6]; // D
+ residueColour[4] = colours[0]; // C
+ residueColour[5] = colours[3]; // Q
+ residueColour[6] = colours[5]; // E
+ residueColour[7] = colours[7]; // G
+ residueColour[8] = colours[10]; // H
+ residueColour[9] = colours[0]; // I
+ residueColour[10] = colours[0]; // L
+ residueColour[11] = colours[4]; // K
+ residueColour[12] = colours[0]; // M
+ residueColour[13] = colours[0]; // F
+ residueColour[14] = colours[8]; // P
+ residueColour[15] = colours[1]; // S
+ residueColour[16] = colours[1]; // T
+ residueColour[17] = colours[0]; // W
+ residueColour[18] = colours[10]; // Y
+ residueColour[19] = colours[0]; // V
}
@Override
return currentColour;
}
- for (int k = 0; k < ResidueColour[i].conses.length; k++)
+ for (int k = 0; k < residueColour[i].conses.length; k++)
{
- if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
+ if (residueColour[i].conses[k].isConserved(cons2, j, size,
includeGaps))
{
- currentColour = ResidueColour[i].c;
+ currentColour = residueColour[i].c;
}
}
{
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
- currentColour = (Color) colhash.get("PINK");
+ currentColour = colhash.get(Color.PINK);
}
}
import java.awt.Color;
import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
public static final int[] purinepyrimidineIndex;
- public static final Hashtable aa3Hash = new Hashtable();
+ public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
- public static final Hashtable aa2Triplet = new Hashtable();
+ public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
- public static final Hashtable nucleotideName = new Hashtable();
+ public static final Map<String, String> nucleotideName = new HashMap<String, String>();
static
{
public static final float[] pidThresholds =
{ 80, 60, 40, };
- public static Hashtable codonHash = new Hashtable();
+ public static Map<String, List<String>> codonHash = new HashMap<String, List<String>>();
- public static Vector Lys = new Vector();
+ private static List<String> Lys = new ArrayList<String>();
- public static Vector Asn = new Vector();
+ private static List<String> Asn = new ArrayList<String>();
- public static Vector Gln = new Vector();
+ private static List<String> Gln = new ArrayList<String>();
- public static Vector His = new Vector();
+ private static List<String> His = new ArrayList<String>();
- public static Vector Glu = new Vector();
+ private static List<String> Glu = new ArrayList<String>();
- public static Vector Asp = new Vector();
+ private static List<String> Asp = new ArrayList<String>();
- public static Vector Tyr = new Vector();
+ private static List<String> Tyr = new ArrayList<String>();
- public static Vector Thr = new Vector();
+ private static List<String> Thr = new ArrayList<String>();
- public static Vector Pro = new Vector();
+ private static List<String> Pro = new ArrayList<String>();
- public static Vector Ala = new Vector();
+ private static List<String> Ala = new ArrayList<String>();
- public static Vector Ser = new Vector();
+ private static List<String> Ser = new ArrayList<String>();
- public static Vector Arg = new Vector();
+ private static List<String> Arg = new ArrayList<String>();
- public static Vector Gly = new Vector();
+ private static List<String> Gly = new ArrayList<String>();
- public static Vector Trp = new Vector();
+ private static List<String> Trp = new ArrayList<String>();
- public static Vector Cys = new Vector();
+ private static List<String> Cys = new ArrayList<String>();
- public static Vector Ile = new Vector();
+ private static List<String> Ile = new ArrayList<String>();
- public static Vector Met = new Vector();
+ private static List<String> Met = new ArrayList<String>();
- public static Vector Leu = new Vector();
+ private static List<String> Leu = new ArrayList<String>();
- public static Vector Val = new Vector();
+ private static List<String> Val = new ArrayList<String>();
- public static Vector Phe = new Vector();
+ private static List<String> Phe = new ArrayList<String>();
- public static Vector STOP = new Vector();
+ public static List<String> STOP = new ArrayList<String>();
+
+ public static String START = "ATG";
static
{
/**
* Nucleotide Ambiguity Codes
*/
- public static final Hashtable<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+ public static final Map<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
/**
* Codon triplets with additional symbols for unambiguous codons that include
static
{
- /**
- * 3.2. Purine (adenine or guanine): R
- *
- * R is the symbol previously recommended [1].
+ /*
+ * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
*/
ambiguityCodes.put("R", new String[]
{ "A", "G" });
-
- /**
- * 3.3. Pyrimidine (thymine or cytosine): Y
- *
- * Y is the symbol previously recommended [1].
- */
ambiguityCodes.put("Y", new String[]
{ "T", "C" });
- /**
- * 3.4. Adenine or thymine: W
- *
- * Although several diverse symbols have been used for this pair, (and for
- * the reciprocal pair G+C), only two symbols have a rational basis, L and
- * W: L derives from DNA density (light; G+C - heavy - would thus be H); W
- * derives from the strength of the hydrogen bonding interaction between the
- * base pairs (weak for A+T: G +C - strong - would thus be S). However, the
- * system recommended for the three-base series (not-A = B, etc., see below,
- * section 3.8) rules out H as this would be not-G. W is thus recommended.
- */
ambiguityCodes.put("W", new String[]
{ "A", "T" });
- /**
- * 3.5. Guanine or cytosine: S
- *
- * The choice of this symbol is discussed above in section 3.4.
- */
ambiguityCodes.put("S", new String[]
{ "G", "C" });
- /**
- * 3.6. Adenine or cytosine: M
- *
- * There are few common features between A and C. The presence of an NH2
- * group in similar positions on both bases (Fig. 1) makes possible a
- * logically derived symbol. A and N being ruled out, M (from aMino) is
- * recommended.
- *
- *
- * Fig. 1. Origin of the symbols M and K The four bases are drawn so as to
- * show the relationship between adenine and cytosine on the one hand, which
- * both have aMino groups at the ring position most distant from the point
- * of attachment to the sugar, and between guanine and thymine on the other,
- * which both have Keto groups at the corresponding position. The ring atoms
- * are numbered as recommended [24-26], although for the present purpose
- * this has the disadvantage of giving discordant numbers to the
- * corresponding positions.
- */
ambiguityCodes.put("M", new String[]
{ "A", "C" });
- /**
- * 3.7. Guanine or thymine: K By analogy with A and C (section 3.6), both G
- * and T have Keto groups in similar positions (Fig. 1).
- */
ambiguityCodes.put("K", new String[]
{ "G", "T" });
- /**
- * 3.8. Adenine or thymine or cytosine: H
- *
- * Not-G is the most simple means of memorising this combination and symbols
- * logically related to G were examined. F and H would both be suitable, as
- * the letters before and after G in the alphabet, but A would have no
- * equivalent to F. The use of H has historical precedence [2].
- */
ambiguityCodes.put("H", new String[]
{ "A", "T", "C" });
- /**
- * 3.9. Guanine or cytosine or thymine: B
- *
- * Not-A as above (section 3.8).
- */
ambiguityCodes.put("B", new String[]
{ "G", "T", "C" });
- /**
- * 3.10. Guanine or adenine or cytosine: V
- *
- * Not-T by analogy with not-G (section 3.8) would be U but this is ruled
- * out to eliminate confusion with uracil. V is the next logical choice.
- * Note that T and U may in some cases be considered to be synonyms.
- */
ambiguityCodes.put("V", new String[]
{ "G", "A", "C" });
- /**
- * 3.11. Guanine or adenine or thymine: D
- *
- * Not-C as above (section 3.8).
- */
ambiguityCodes.put("D", new String[]
{ "G", "A", "T" });
- /**
- * 3.12. Guanine or adenine or thymine or cytosine: N
- */
- ambiguityCodes.put("R", new String[]
+ ambiguityCodes.put("N", new String[]
{ "G", "A", "T", "C" });
+
// Now build codon translation table
codonHash2.put("AAA", "K");
codonHash2.put("AAG", "K");
static
{
- Lys.addElement("AAA");
- Lys.addElement("AAG");
- Asn.addElement("AAC");
- Asn.addElement("AAT");
-
- Gln.addElement("CAA");
- Gln.addElement("CAG");
- His.addElement("CAC");
- His.addElement("CAT");
-
- Glu.addElement("GAA");
- Glu.addElement("GAG");
- Asp.addElement("GAC");
- Asp.addElement("GAT");
-
- Tyr.addElement("TAC");
- Tyr.addElement("TAT");
-
- Thr.addElement("ACA");
- Thr.addElement("ACG");
- Thr.addElement("ACC");
- Thr.addElement("ACT");
-
- Pro.addElement("CCA");
- Pro.addElement("CCG");
- Pro.addElement("CCC");
- Pro.addElement("CCT");
-
- Ala.addElement("GCA");
- Ala.addElement("GCG");
- Ala.addElement("GCC");
- Ala.addElement("GCT");
-
- Ser.addElement("TCA");
- Ser.addElement("TCG");
- Ser.addElement("TCC");
- Ser.addElement("TCT");
- Ser.addElement("AGC");
- Ser.addElement("AGT");
-
- Arg.addElement("AGA");
- Arg.addElement("AGG");
- Arg.addElement("CGA");
- Arg.addElement("CGG");
- Arg.addElement("CGC");
- Arg.addElement("CGT");
-
- Gly.addElement("GGA");
- Gly.addElement("GGG");
- Gly.addElement("GGC");
- Gly.addElement("GGT");
-
- STOP.addElement("TGA");
- STOP.addElement("TAA");
- STOP.addElement("TAG");
-
- Trp.addElement("TGG");
-
- Cys.addElement("TGC");
- Cys.addElement("TGT");
-
- Ile.addElement("ATA");
- Ile.addElement("ATC");
- Ile.addElement("ATT");
-
- Met.addElement("ATG");
-
- Leu.addElement("CTA");
- Leu.addElement("CTG");
- Leu.addElement("CTC");
- Leu.addElement("CTT");
- Leu.addElement("TTA");
- Leu.addElement("TTG");
-
- Val.addElement("GTA");
- Val.addElement("GTG");
- Val.addElement("GTC");
- Val.addElement("GTT");
-
- Phe.addElement("TTC");
- Phe.addElement("TTT");
+ Lys.add("AAA");
+ Lys.add("AAG");
+ Asn.add("AAC");
+ Asn.add("AAT");
+
+ Gln.add("CAA");
+ Gln.add("CAG");
+ His.add("CAC");
+ His.add("CAT");
+
+ Glu.add("GAA");
+ Glu.add("GAG");
+ Asp.add("GAC");
+ Asp.add("GAT");
+
+ Tyr.add("TAC");
+ Tyr.add("TAT");
+
+ Thr.add("ACA");
+ Thr.add("ACG");
+ Thr.add("ACC");
+ Thr.add("ACT");
+
+ Pro.add("CCA");
+ Pro.add("CCG");
+ Pro.add("CCC");
+ Pro.add("CCT");
+
+ Ala.add("GCA");
+ Ala.add("GCG");
+ Ala.add("GCC");
+ Ala.add("GCT");
+
+ Ser.add("TCA");
+ Ser.add("TCG");
+ Ser.add("TCC");
+ Ser.add("TCT");
+ Ser.add("AGC");
+ Ser.add("AGT");
+
+ Arg.add("AGA");
+ Arg.add("AGG");
+ Arg.add("CGA");
+ Arg.add("CGG");
+ Arg.add("CGC");
+ Arg.add("CGT");
+
+ Gly.add("GGA");
+ Gly.add("GGG");
+ Gly.add("GGC");
+ Gly.add("GGT");
+
+ STOP.add("TGA");
+ STOP.add("TAA");
+ STOP.add("TAG");
+
+ Trp.add("TGG");
+
+ Cys.add("TGC");
+ Cys.add("TGT");
+
+ Ile.add("ATA");
+ Ile.add("ATC");
+ Ile.add("ATT");
+
+ Met.add("ATG");
+
+ Leu.add("CTA");
+ Leu.add("CTG");
+ Leu.add("CTC");
+ Leu.add("CTT");
+ Leu.add("TTA");
+ Leu.add("TTG");
+
+ Val.add("GTA");
+ Val.add("GTG");
+ Val.add("GTC");
+ Val.add("GTT");
+
+ Phe.add("TTC");
+ Phe.add("TTT");
}
// Stores residue codes/names and colours and other things
return hyd;
}
- public static Hashtable getAA3Hash()
+ public static Map<String, Integer> getAA3Hash()
{
return aa3Hash;
}
{
return "X";
}
- Enumeration e = codonHash.keys();
-
- while (e.hasMoreElements())
+ for (String key : codonHash.keySet())
{
- String key = (String) e.nextElement();
- Vector tmp = (Vector) codonHash.get(key);
-
- if (tmp.contains(codon))
+ if (codonHash.get(key).contains(codon))
{
return key;
}
--- /dev/null
+package jalview.structure;
+
+/**
+ * Java bean representing an atom in a PDB (or similar) structure model.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class AtomSpec
+{
+ // TODO clarify do we want pdbFile here, or pdbId?
+ // compare highlightAtom in 2.8.2 for JalviewJmolBinding and
+ // javascript.MouseOverStructureListener
+ private String pdbFile;
+
+ private String chain;
+
+ private int pdbResNum;
+
+ private int atomIndex;
+
+ /**
+ * Constructor
+ *
+ * @param pdbFile
+ * @param chain
+ * @param resNo
+ * @param atomNo
+ */
+ public AtomSpec(String pdbFile, String chain, int resNo, int atomNo)
+ {
+ this.pdbFile = pdbFile;
+ this.chain = chain;
+ this.pdbResNum = resNo;
+ this.atomIndex = atomNo;
+ }
+
+ public String getPdbFile()
+ {
+ return pdbFile;
+ }
+
+ public String getChain()
+ {
+ return chain;
+ }
+
+ public int getPdbResNum()
+ {
+ return pdbResNum;
+ }
+
+ public int getAtomIndex()
+ {
+ return atomIndex;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "pdbFile: " + pdbFile + ", chain: " + chain + ", res: "
+ + pdbResNum + ", atom: " + atomIndex;
+ }
+}
--- /dev/null
+package jalview.structure;
+
+import jalview.commands.CommandI;
+
+/**
+ * Defines a listener for commands performed on another alignment. This is to
+ * support linked editing of two alternative representations of an alignment (in
+ * particular, cDNA and protein).
+ *
+ * @author gmcarstairs
+ *
+ */
+public interface CommandListener
+{
+ /**
+ * The listener may attempt to perform the specified command; the region acted
+ * on is determined by a callback to the StructureSelectionManager (which
+ * holds mappings between alignments).
+ *
+ * @param command
+ * @param undo
+ * @param ssm
+ * @param source
+ * the originator of the command
+ */
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source);
+
+ /**
+ * Temporary workaround to make check for source == listener work.
+ *
+ * @return
+ */
+ public VamsasSource getVamsasSource();
+}
*/
package jalview.structure;
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
+
public interface SequenceListener
{
+ // TODO remove this? never called on SequenceListener type
public void mouseOverSequence(SequenceI sequence, int index, int pos);
public void highlightSequence(jalview.datamodel.SearchResults results);
+ // TODO remove this? never called
public void updateColours(SequenceI sequence, int index);
+
+ public VamsasSource getVamsasSource();
+
}
*/
package jalview.structure;
+import java.util.List;
+
public interface StructureListener
{
/**
- *
- * @return list of structure files (unique IDs/filenames) that this listener
- * handles messages for, or null if generic listener (only used by
- * removeListener method)
+ * Returns a list of structure files (unique IDs/filenames) that this listener
+ * handles messages for, or null if generic listener (only used by
+ * removeListener method)
*/
public String[] getPdbFile();
/**
- * NOT A LISTENER METHOD! called by structure viewer when the given
- * atom/structure has been moused over. Typically, implementors call
- * StructureSelectionManager.mouseOverStructure
- *
- * @param atomIndex
- * @param strInfo
- */
- public void mouseOverStructure(int atomIndex, String strInfo);
-
- /**
- * called by StructureSelectionManager to inform viewer to highlight given
- * atomspec
+ * Called by StructureSelectionManager to inform viewer to highlight given
+ * atom positions
*
- * @param atomIndex
- * @param pdbResNum
- * @param chain
- * @param pdbId
+ * @param atoms
*/
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbId);
+ public void highlightAtoms(List<AtomSpec> atoms);
/**
- * called by StructureSelectionManager when the colours of a sequence
+ * Called by StructureSelectionManager when the colours of a sequence
* associated with a structure have changed.
*
* @param source
public void updateColours(Object source);
/**
- * called by Jalview to get the colour for the given atomspec
- *
- * @param atomIndex
- * @param pdbResNum
- * @param chain
- * @param pdbId
- * @return
- */
- public java.awt.Color getColour(int atomIndex, int pdbResNum,
- String chain, String pdbId);
-
- /**
- * called by structureSelectionManager to instruct implementor to release any
+ * Called by structureSelectionManager to instruct implementor to release any
* direct references it may hold to the given object (typically, these are
* Jalview alignment panels).
*
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import java.io.PrintStream;
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.IdentityHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
import java.util.Vector;
import MCview.Atom;
{
static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
- StructureMapping[] mappings;
+ private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
- private boolean processSecondaryStructure = false,
- secStructServices = false, addTempFacAnnot = false;
+ private boolean processSecondaryStructure = false;
+
+ private boolean secStructServices = false;
+
+ private boolean addTempFacAnnot = false;
+
+ /*
+ * Set of any registered mappings between (dataset) sequences.
+ */
+ Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+
+ /*
+ * Reference counters for the above mappings. Remove mappings when ref count
+ * goes to zero.
+ */
+ Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
+
+ private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+
+ private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
/**
* @return true if will try to use external services for processing secondary
*/
public void reportMapping()
{
- if (mappings == null)
+ if (mappings.isEmpty())
{
System.err.println("reportMapping: No PDB/Sequence mappings.");
}
else
{
- System.err.println("reportMapping: There are " + mappings.length
+ System.err.println("reportMapping: There are " + mappings.size()
+ " mappings.");
- for (int m = 0; m < mappings.length; m++)
+ int i = 0;
+ for (StructureMapping sm : mappings)
{
- System.err.println("mapping " + m + " : " + mappings[m].pdbfile);
+ System.err.println("mapping " + i++ + " : " + sm.pdbfile);
}
}
}
}
}
+ /**
+ * Returns the file name for a mapped PDB id (or null if not mapped).
+ *
+ * @param pdbid
+ * @return
+ */
public String alreadyMappedToFile(String pdbid)
{
- if (mappings != null)
+ for (StructureMapping sm : mappings)
{
- for (int i = 0; i < mappings.length; i++)
+ if (sm.getPdbId().equals(pdbid))
{
- if (mappings[i].getPdbId().equals(pdbid))
- {
- return mappings[i].pdbfile;
- }
+ return sm.pdbfile;
}
}
return null;
mappingDetails.toString());
if (forStructureView)
{
-
- if (mappings == null)
- {
- mappings = new StructureMapping[1];
- }
- else
- {
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);
- mappings = tmp;
- }
-
- mappings[mappings.length - 1] = newMapping;
+ mappings.add(newMapping);
}
maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
}
}
- if (pdbs.size() > 0 && mappings != null)
+ if (pdbs.size() > 0)
{
- Vector tmp = new Vector();
- for (int i = 0; i < mappings.length; i++)
+ List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ for (StructureMapping sm : mappings)
{
- if (!pdbs.contains(mappings[i].pdbfile))
+ if (!pdbs.contains(sm.pdbfile))
{
- tmp.addElement(mappings[i]);
+ tmp.add(sm);
}
}
- mappings = new StructureMapping[tmp.size()];
- tmp.copyInto(mappings);
+ mappings = tmp;
}
}
// old or prematurely sent event
return;
}
- boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
SearchResults results = null;
SequenceI lastseq = null;
int lastipos = -1, indexpos;
{
results = new SearchResults();
}
- if (mappings != null)
+ for (StructureMapping sm : mappings)
{
- for (int j = 0; j < mappings.length; j++)
+ if (sm.pdbfile.equals(pdbfile) && sm.pdbchain.equals(chain))
{
- if (mappings[j].pdbfile.equals(pdbfile)
- && mappings[j].pdbchain.equals(chain))
+ indexpos = sm.getSeqPos(pdbResNum);
+ if (lastipos != indexpos && lastseq != sm.sequence)
{
- indexpos = mappings[j].getSeqPos(pdbResNum);
- if (lastipos != indexpos && lastseq != mappings[j].sequence)
+ results.addResult(sm.sequence, indexpos, indexpos);
+ lastipos = indexpos;
+ lastseq = sm.sequence;
+ // construct highlighted sequence list
+ for (AlignedCodonFrame acf : seqmappings)
{
- results.addResult(mappings[j].sequence, indexpos, indexpos);
- lastipos = indexpos;
- lastseq = mappings[j].sequence;
- // construct highlighted sequence list
- if (seqmappings != null)
- {
-
- Enumeration e = seqmappings.elements();
- while (e.hasMoreElements())
-
- {
- ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
- mappings[j].sequence, indexpos, results);
- }
- }
+ acf.markMappedRegion(sm.sequence, indexpos, results);
}
-
}
}
}
}
}
- Vector seqmappings = null; // should be a simpler list of mapped seuqence
-
/**
* highlight regions associated with a position (indexpos) in seq
*
* @param seq
- * the sequeence that the mouse over occured on
+ * the sequence that the mouse over occurred on
* @param indexpos
* the absolute position being mouseovered in seq (0 to seq.length())
* @param index
public void mouseOverSequence(SequenceI seq, int indexpos, int index,
VamsasSource source)
{
- boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
+ boolean hasSequenceListeners = handlingVamsasMo
+ || !seqmappings.isEmpty();
SearchResults results = null;
if (index == -1)
{
index = seq.findPosition(indexpos);
}
- StructureListener sl;
- int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
{
Object listener = listeners.elementAt(i);
if (listener == source)
{
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
continue;
}
if (listener instanceof StructureListener)
{
- sl = (StructureListener) listener;
- if (mappings == null)
- {
- continue;
- }
- for (int j = 0; j < mappings.length; j++)
- {
- if (mappings[j].sequence == seq
- || mappings[j].sequence == seq.getDatasetSequence())
- {
- atomNo = mappings[j].getAtomNum(index);
-
- if (atomNo > 0)
- {
- sl.highlightAtom(atomNo, mappings[j].getPDBResNum(index),
- mappings[j].pdbchain, mappings[j].pdbfile);
- }
- }
- }
+ highlightStructure((StructureListener) listener, seq, index);
}
else
{
- if (relaySeqMappings && hasSequenceListeners
- && listener instanceof SequenceListener)
+ if (listener instanceof SequenceListener)
{
- // DEBUG
- // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
- // index);
-
- if (results == null)
+ final SequenceListener seqListener = (SequenceListener) listener;
+ if (hasSequenceListeners
+ && seqListener.getVamsasSource() != source)
{
- results = new SearchResults();
- if (index >= seq.getStart() && index <= seq.getEnd())
+ if (relaySeqMappings)
{
- // construct highlighted sequence list
-
- if (seqmappings != null)
+ if (results == null)
{
- Enumeration e = seqmappings.elements();
- while (e.hasMoreElements())
-
- {
- ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
- seq, index, results);
- }
+ results = MappingUtils.buildSearchResults(seq, index,
+ seqmappings);
}
- // hasSequenceListeners = results.getSize() > 0;
if (handlingVamsasMo)
{
- // maybe have to resolve seq to a dataset seqeunce...
- // add in additional direct sequence and/or dataset sequence
- // highlighting
results.addResult(seq, index, index);
+
}
+ seqListener.highlightSequence(results);
}
}
- if (hasSequenceListeners)
- {
- ((SequenceListener) listener).highlightSequence(results);
- }
}
else if (listener instanceof VamsasListener && !handlingVamsasMo)
{
- // DEBUG
- // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
- // " +
- // index);
- // pass the mouse over and absolute position onto the
- // VamsasListener(s)
- ((VamsasListener) listener).mouseOver(seq, indexpos, source);
+ ((VamsasListener) listener).mouseOverSequence(seq, indexpos,
+ source);
}
else if (listener instanceof SecondaryStructureListener)
{
}
/**
+ * Send suitable messages to a StructureListener to highlight atoms
+ * corresponding to the given sequence position.
+ *
+ * @param sl
+ * @param seq
+ * @param index
+ */
+ protected void highlightStructure(StructureListener sl, SequenceI seq,
+ int index)
+ {
+ int atomNo;
+ List<AtomSpec> atoms = new ArrayList<AtomSpec>();
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
+ {
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
+ .getPDBResNum(index), atomNo));
+ }
+ }
+ }
+ sl.highlightAtoms(atoms);
+ }
+
+ /**
* true if a mouse over event from an external (ie Vamsas) source is being
* handled
*/
public StructureMapping[] getMapping(String pdbfile)
{
- Vector tmp = new Vector();
- if (mappings != null)
- {
- for (int i = 0; i < mappings.length; i++)
+ List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ for (StructureMapping sm : mappings)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ if (sm.pdbfile.equals(pdbfile))
{
- tmp.addElement(mappings[i]);
+ tmp.add(sm);
}
- }
}
- StructureMapping[] ret = new StructureMapping[tmp.size()];
- for (int i = 0; i < tmp.size(); i++)
- {
- ret[i] = (StructureMapping) tmp.elementAt(i);
- }
-
- return ret;
+ return tmp.toArray(new StructureMapping[tmp.size()]);
}
public String printMapping(String pdbfile)
{
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < mappings.length; i++)
+ StringBuilder sb = new StringBuilder(64);
+ for (StructureMapping sm : mappings)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ if (sm.pdbfile.equals(pdbfile))
{
- sb.append(mappings[i].mappingDetails);
+ sb.append(sm.mappingDetails);
}
}
return sb.toString();
}
- private int[] seqmappingrefs = null; // refcount for seqmappings elements
-
- private synchronized void modifySeqMappingList(boolean add,
- AlignedCodonFrame[] codonFrames)
+ /**
+ * Decrement the reference counter for each of the given mappings, and remove
+ * it entirely if its reference counter reduces to zero.
+ *
+ * @param set
+ */
+ public void removeMappings(Set<AlignedCodonFrame> set)
{
- if (!add && (seqmappings == null || seqmappings.size() == 0))
- {
- return;
- }
- if (seqmappings == null)
+ if (set != null)
{
- seqmappings = new Vector();
+ for (AlignedCodonFrame acf : set)
+ {
+ removeMapping(acf);
+ }
}
- if (codonFrames != null && codonFrames.length > 0)
+ }
+
+ /**
+ * Decrement the reference counter for the given mapping, and remove it
+ * entirely if its reference counter reduces to zero.
+ *
+ * @param acf
+ */
+ public void removeMapping(AlignedCodonFrame acf)
+ {
+ if (acf != null && seqmappings.contains(acf))
{
- for (int cf = 0; cf < codonFrames.length; cf++)
+ int count = seqMappingRefCounts.get(acf);
+ count--;
+ if (count > 0)
{
- if (seqmappings.contains(codonFrames[cf]))
- {
- if (add)
- {
- seqmappingrefs[seqmappings.indexOf(codonFrames[cf])]++;
- }
- else
- {
- if (--seqmappingrefs[seqmappings.indexOf(codonFrames[cf])] <= 0)
- {
- int pos = seqmappings.indexOf(codonFrames[cf]);
- int[] nr = new int[seqmappingrefs.length - 1];
- if (pos > 0)
- {
- System.arraycopy(seqmappingrefs, 0, nr, 0, pos);
- }
- if (pos < seqmappingrefs.length - 1)
- {
- System.arraycopy(seqmappingrefs, pos + 1, nr, 0,
- seqmappingrefs.length - pos - 2);
- }
- }
- }
- }
- else
- {
- if (add)
- {
- seqmappings.addElement(codonFrames[cf]);
-
- int[] nsr = new int[(seqmappingrefs == null) ? 1
- : seqmappingrefs.length + 1];
- if (seqmappingrefs != null && seqmappingrefs.length > 0)
- {
- System.arraycopy(seqmappingrefs, 0, nsr, 0,
- seqmappingrefs.length);
- }
- nsr[(seqmappingrefs == null) ? 0 : seqmappingrefs.length] = 1;
- seqmappingrefs = nsr;
- }
- }
+ seqMappingRefCounts.put(acf, count);
+ }
+ else
+ {
+ seqmappings.remove(acf);
+ seqMappingRefCounts.remove(acf);
}
}
}
- public void removeMappings(AlignedCodonFrame[] codonFrames)
+ /**
+ * Add each of the given codonFrames to the stored set. If not aready present,
+ * increments its reference count instead.
+ *
+ * @param set
+ */
+ public void addMappings(Set<AlignedCodonFrame> set)
{
- modifySeqMappingList(false, codonFrames);
+ if (set != null)
+ {
+ for (AlignedCodonFrame acf : set)
+ {
+ addMapping(acf);
+ }
+ }
}
- public void addMappings(AlignedCodonFrame[] codonFrames)
+ /**
+ * Add the given mapping to the stored set, or if already stored, increment
+ * its reference counter.
+ */
+ public void addMapping(AlignedCodonFrame acf)
{
- modifySeqMappingList(true, codonFrames);
+ if (acf != null)
+ {
+ if (seqmappings.contains(acf))
+ {
+ seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1);
+ }
+ else
+ {
+ seqmappings.add(acf);
+ seqMappingRefCounts.put(acf, 1);
+ }
+ }
}
- Vector<SelectionListener> sel_listeners = new Vector<SelectionListener>();
-
public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
{
- sel_listeners.addElement(selecter);
+ sel_listeners.add(selecter);
}
}
{
if (sel_listeners.contains(toremove))
{
- sel_listeners.removeElement(toremove);
+ sel_listeners.remove(toremove);
}
}
jalview.datamodel.SequenceGroup selection,
jalview.datamodel.ColumnSelection colsel, SelectionSource source)
{
- if (sel_listeners != null && sel_listeners.size() > 0)
+ for (SelectionListener slis : sel_listeners)
{
- Enumeration listeners = sel_listeners.elements();
- while (listeners.hasMoreElements())
+ if (slis != source)
{
- SelectionListener slis = ((SelectionListener) listeners
- .nextElement());
- if (slis != source)
- {
- slis.selection(selection, colsel, source);
- }
- ;
+ slis.selection(selection, colsel, source);
}
}
}
}
}
- public void finalize() throws Throwable
- {
- if (listeners != null)
- {
- listeners.clear();
- listeners = null;
- }
- if (pdbIdFileName != null)
- {
- pdbIdFileName.clear();
- pdbIdFileName = null;
- }
- if (sel_listeners != null)
- {
- sel_listeners.clear();
- sel_listeners = null;
- }
- if (view_listeners != null)
- {
- view_listeners.clear();
- view_listeners = null;
- }
- mappings = null;
- seqmappingrefs = null;
- }
-
/**
* release all references associated with this manager provider
*
} catch (Throwable x)
{
}
- ;
}
}
}
}
}
+ public void addCommandListener(CommandListener cl)
+ {
+ if (!commandListeners.contains(cl))
+ {
+ commandListeners.add(cl);
+ }
+ }
+
+ public boolean hasCommandListener(CommandListener cl)
+ {
+ return this.commandListeners.contains(cl);
+ }
+
+ public boolean removeCommandListener(CommandListener l)
+ {
+ return commandListeners.remove(l);
+ }
+
+ /**
+ * Forward a command to any command listeners (except for the command's
+ * source).
+ *
+ * @param command
+ * the command to be broadcast (in its form after being performed)
+ * @param undo
+ * if true, the command was being 'undone'
+ * @param source
+ */
+ public void commandPerformed(CommandI command, boolean undo,
+ VamsasSource source)
+ {
+ for (CommandListener listener : commandListeners)
+ {
+ listener.mirrorCommand(command, undo, this, source);
+ }
+ }
+
+ /**
+ * Returns a new CommandI representing the given command as mapped to the
+ * given sequences. If no mapping could be made, or the command is not of a
+ * mappable kind, returns null.
+ *
+ * @param command
+ * @param undo
+ * @param mapTo
+ * @param gapChar
+ * @return
+ */
+ public CommandI mapCommand(CommandI command, boolean undo,
+ final AlignmentI mapTo, char gapChar)
+ {
+ if (command instanceof EditCommand)
+ {
+ return MappingUtils.mapEditCommand((EditCommand) command, undo,
+ mapTo, gapChar, seqmappings);
+ }
+ else if (command instanceof OrderCommand)
+ {
+ return MappingUtils.mapOrderCommand((OrderCommand) command, undo,
+ mapTo, seqmappings);
+ }
+ return null;
+ }
}
*/
public interface VamsasListener
{
- public void mouseOver(SequenceI seq, int index, VamsasSource source);
+ public void mouseOverSequence(SequenceI seq, int index,
+ VamsasSource source);
}
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import java.awt.event.ComponentEvent;
import java.util.ArrayList;
import java.util.List;
/**
+ *
* A base class to hold common function for protein structure model binding.
* Initial version created by refactoring JMol and Chimera binding models, but
* other structure viewers could in principle be accommodated in future.
}
}
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ if (atoms != null)
+ {
+ for (AtomSpec atom : atoms)
+ {
+ highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ }
+ }
+ }
+
+ // TODO Jmol and Chimera seem to expect pdbFile, javascript listener pdbId
+ protected abstract void highlightAtom(int atomIndex, int pdbResNum,
+ String chain, String pdbFile);
+
}
\ No newline at end of file
*/
package jalview.util;
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Assorted methods for analysing or comparing sequences.
*/
public class Comparison
{
- /** DOCUMENT ME!! */
- public static final String GapChars = " .-";
+ private static final int EIGHTY_FIVE = 85;
+
+ private static final int TO_UPPER_CASE = 'a' - 'A';
+
+ private static final char GAP_SPACE = ' ';
+
+ private static final char GAP_DOT = '.';
+
+ private static final char GAP_DASH = '-';
+
+ public static final String GapChars = new String(new char[]
+ { GAP_SPACE, GAP_DOT, GAP_DASH });
/**
* DOCUMENT ME!
int ilen = si.length() - 1;
int jlen = sj.length() - 1;
- while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+ while (Comparison.isGap(si.charAt(start + ilen)))
{
ilen--;
}
- while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+ while (Comparison.isGap(sj.charAt(start + jlen)))
{
jlen--;
}
}
/**
- * DOCUMENT ME!
+ * Answers true if the supplied character is a recognised gap character, else
+ * false. Currently hard-coded to recognise '-', '-' or ' ' (hyphen / dot /
+ * space).
*
* @param c
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
public static final boolean isGap(char c)
{
- return (c == '-' || c == '.' || c == ' ') ? true : false;
+ return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false;
}
+ /**
+ * Answers true if more than 85% of the sequence residues (ignoring gaps) are
+ * A, G, C, T or U, else false. This is just a heuristic guess and may give a
+ * wrong answer (as AGCT are also animo acid codes).
+ *
+ * @param seqs
+ * @return
+ */
public static final boolean isNucleotide(SequenceI[] seqs)
{
- int i = 0, iSize = seqs.length, j, jSize;
- float nt = 0, aa = 0;
- char c;
- while (i < iSize)
+ if (seqs == null)
+ {
+ return false;
+ }
+ int ntCount = 0;
+ int aaCount = 0;
+ for (SequenceI seq : seqs)
{
- jSize = seqs[i].getLength();
- for (j = 0; j < jSize; j++)
+ for (char c : seq.getSequence())
{
- c = seqs[i].getCharAt(j);
if ('a' <= c && c <= 'z')
{
- c -= ('a' - 'A');
+ c -= TO_UPPER_CASE;
}
if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
{
- nt++;
+ ntCount++;
}
- else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
+ else if (!Comparison.isGap(c))
{
- aa++;
+ aaCount++;
}
}
- i++;
}
- if ((nt / (nt + aa)) > 0.85f)
+ /*
+ * Check for nucleotide count > 85% of total count (in a form that evades
+ * int / float conversion or divide by zero).
+ */
+ if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
{
return true;
}
*/
package jalview.util;
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
public class DBRefUtils
{
{
return dbrefs;
}
- Hashtable srcs = new Hashtable();
- Vector res = new Vector();
+ Map<String, Integer> srcs = new HashMap<String, Integer>();
+ ArrayList<DBRefEntry> res = new ArrayList<DBRefEntry>();
for (int i = 0; i < sources.length; i++)
{
{
if (srcs.containsKey(dbrefs[i].getSource()))
{
- res.addElement(dbrefs[i]);
+ res.add(dbrefs[i]);
}
}
if (res.size() > 0)
{
DBRefEntry[] reply = new DBRefEntry[res.size()];
- for (int i = 0; i < res.size(); i++)
- {
- reply[i] = (DBRefEntry) res.elementAt(i);
- }
- return reply;
+ return res.toArray(reply);
}
res = null;
// there are probable memory leaks in the hashtable!
DbRefComp comparator)
{
if (ref == null || entry == null)
+ {
return null;
+ }
Vector rfs = new Vector();
for (int i = 0; i < ref.length; i++)
{
{
if ((refa.getMap() == null && refb.getMap() == null)
|| (refa.getMap() != null && refb.getMap() != null))
+ {
if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
|| (refb.getMap().getMap() != null
&& refa.getMap().getMap() != null && refb
{
return true;
}
+ }
}
}
return false;
private char fmt; // one of cdeEfgGiosxXos
+ private final String formatString;
+
/**
* Creates a new Format object.
*
*/
public Format(String s)
{
+ formatString = s;
width = 0;
precision = -1;
pre = "";
/**
* Formats a character into a string (like sprintf in C)
*
- * @param x
+ * @param debounceTrap
* the value to format
* @return the formatted string
*/
/**
* Formats a string into a larger string (like sprintf in C)
*
- * @param x
+ * @param debounceTrap
* the value to format
* @return the formatted string
*/
return f + p.substring(p.length() - 3, p.length());
}
+
+ @Override
+ public String toString()
+ {
+ return formatString;
+ }
}
*/
package jalview.util;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
/**
- * MapList Simple way of bijectively mapping a non-contiguous linear range to
- * another non-contiguous linear range Use at your own risk! TODO: efficient
- * implementation of private posMap method TODO: test/ensure that sense of from
- * and to ratio start position is conserved (codon start position recovery)
- * TODO: optimize to use int[][] arrays rather than vectors.
+ * A simple way of bijectively mapping a non-contiguous linear range to another
+ * non-contiguous linear range.
+ *
+ * Use at your own risk!
+ *
+ * TODO: efficient implementation of private posMap method
+ *
+ * TODO: test/ensure that sense of from and to ratio start position is conserved
+ * (codon start position recovery)
*/
public class MapList
{
+
/*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
+ * Subregions (base 1) described as { [start1, end1], [start2, end2], ...}
+ */
+ private List<int[]> fromShifts = new ArrayList<int[]>();
+
+ /*
+ * Same format as fromShifts, for the 'mapped to' sequence
+ */
+ private List<int[]> toShifts = new ArrayList<int[]>();
+
+ /*
+ * number of steps in fromShifts to one toRatio unit
+ */
+ private int fromRatio;
+
+ /*
+ * number of steps in toShifts to one fromRatio
+ */
+ private int toRatio;
+
+ /*
+ * lowest and highest value in the from Map
+ */
+ private int fromLowest;
+
+ private int fromHighest;
+
+ /*
+ * lowest and highest value in the to Map
+ */
+ private int toLowest;
+
+ private int toHighest;
+
+ /**
+ * Two MapList objects are equal if they are the same object, or they both
+ * have populated shift ranges and all values are the same.
*/
- public boolean equals(MapList obj)
+ @Override
+ public boolean equals(Object o)
{
+ // TODO should also override hashCode to ensure equal objects have equal
+ // hashcodes
+ if (o == null || !(o instanceof MapList))
+ {
+ return false;
+ }
+
+ MapList obj = (MapList) o;
if (obj == this)
- return true;
- if (obj != null && obj.fromRatio == fromRatio && obj.toRatio == toRatio
- && obj.fromShifts != null && obj.toShifts != null)
{
- int i, iSize = fromShifts.size(), j, jSize = obj.fromShifts.size();
- if (iSize != jSize)
- return false;
- for (i = 0, iSize = fromShifts.size(), j = 0, jSize = obj.fromShifts
- .size(); i < iSize;)
- {
- int[] mi = (int[]) fromShifts.elementAt(i++);
- int[] mj = (int[]) obj.fromShifts.elementAt(j++);
- if (mi[0] != mj[0] || mi[1] != mj[1])
- return false;
- }
- iSize = toShifts.size();
- jSize = obj.toShifts.size();
- if (iSize != jSize)
- return false;
- for (i = 0, j = 0; i < iSize;)
- {
- int[] mi = (int[]) toShifts.elementAt(i++);
- int[] mj = (int[]) obj.toShifts.elementAt(j++);
- if (mi[0] != mj[0] || mi[1] != mj[1])
- return false;
- }
return true;
}
- return false;
+ if (obj.fromRatio != fromRatio || obj.toRatio != toRatio
+ || obj.fromShifts == null || obj.toShifts == null)
+ {
+ return false;
+ }
+ return Arrays
+ .deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
+ && Arrays
+ .deepEquals(toShifts.toArray(), obj.toShifts.toArray());
}
- public Vector fromShifts;
-
- public Vector toShifts;
-
- int fromRatio; // number of steps in fromShifts to one toRatio unit
-
- int toRatio; // number of steps in toShifts to one fromRatio
-
/**
+ * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
*
- * @return series of intervals mapped in from
+ * @return
*/
- public int[] getFromRanges()
+ public List<int[]> getFromRanges()
{
- return getRanges(fromShifts);
+ return fromShifts;
}
- public int[] getToRanges()
+ /**
+ * Returns the 'to' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
+ */
+ public List<int[]> getToRanges()
{
- return getRanges(toShifts);
+ return toShifts;
}
- private int[] getRanges(Vector shifts)
+ /**
+ * Flattens a list of [start, end] into a single [start1, end1, start2,
+ * end2,...] array.
+ *
+ * @param shifts
+ * @return
+ */
+ protected static int[] getRanges(List<int[]> shifts)
{
int[] rnges = new int[2 * shifts.size()];
- Enumeration e = shifts.elements();
int i = 0;
- while (e.hasMoreElements())
+ for (int[] r : shifts)
{
- int r[] = (int[]) e.nextElement();
rnges[i++] = r[0];
rnges[i++] = r[1];
}
}
/**
- * lowest and highest value in the from Map
- */
- int[] fromRange = null;
-
- /**
- * lowest and highest value in the to Map
- */
- int[] toRange = null;
-
- /**
*
* @return length of mapped phrase in from
*/
public int getFromLowest()
{
- return fromRange[0];
+ return fromLowest;
}
public int getFromHighest()
{
- return fromRange[1];
+ return fromHighest;
}
public int getToLowest()
{
- return toRange[0];
+ return toLowest;
}
public int getToHighest()
{
- return toRange[1];
- }
-
- private void ensureRange(int[] limits, int pos)
- {
- if (limits[0] > pos)
- limits[0] = pos;
- if (limits[1] < pos)
- limits[1] = pos;
+ return toHighest;
}
+ /**
+ * Constructor.
+ *
+ * @param from
+ * contiguous regions as [start1, end1, start2, end2, ...]
+ * @param to
+ * same format as 'from'
+ * @param fromRatio
+ * phrase length in 'from' (e.g. 3 for dna)
+ * @param toRatio
+ * phrase length in 'to' (e.g. 1 for protein)
+ */
public MapList(int from[], int to[], int fromRatio, int toRatio)
{
- fromRange = new int[]
- { from[0], from[1] };
- toRange = new int[]
- { to[0], to[1] };
-
- fromShifts = new Vector();
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
+ fromLowest = from[0];
+ fromHighest = from[1];
for (int i = 0; i < from.length; i += 2)
{
- ensureRange(fromRange, from[i]);
- ensureRange(fromRange, from[i + 1]);
+ fromLowest = Math.min(fromLowest, from[i]);
+ fromHighest = Math.max(fromHighest, from[i + 1]);
- fromShifts.addElement(new int[]
+ fromShifts.add(new int[]
{ from[i], from[i + 1] });
}
- toShifts = new Vector();
+
+ toLowest = to[0];
+ toHighest = to[1];
for (int i = 0; i < to.length; i += 2)
{
- ensureRange(toRange, to[i]);
- ensureRange(toRange, to[i + 1]);
- toShifts.addElement(new int[]
+ toLowest = Math.min(toLowest, to[i]);
+ toHighest = Math.max(toHighest, to[i + 1]);
+ toShifts.add(new int[]
{ to[i], to[i + 1] });
}
- this.fromRatio = fromRatio;
- this.toRatio = toRatio;
}
+ /**
+ * Copy constructor. Creates an identical mapping.
+ *
+ * @param map
+ */
public MapList(MapList map)
{
- this.fromRange = new int[]
- { map.fromRange[0], map.fromRange[1] };
- this.toRange = new int[]
- { map.toRange[0], map.toRange[1] };
+ // TODO not used - remove?
+ this.fromLowest = map.fromLowest;
+ this.fromHighest = map.fromHighest;
+ this.toLowest = map.toLowest;
+ this.toHighest = map.toHighest;
+
this.fromRatio = map.fromRatio;
this.toRatio = map.toRatio;
if (map.fromShifts != null)
{
- this.fromShifts = new Vector();
- Enumeration e = map.fromShifts.elements();
- while (e.hasMoreElements())
+ for (int[] r : map.fromShifts)
{
- int[] el = (int[]) e.nextElement();
- fromShifts.addElement(new int[]
- { el[0], el[1] });
+ fromShifts.add(new int[]
+ { r[0], r[1] });
}
}
if (map.toShifts != null)
{
- this.toShifts = new Vector();
- Enumeration e = map.toShifts.elements();
- while (e.hasMoreElements())
+ for (int[] r : map.toShifts)
{
- int[] el = (int[]) e.nextElement();
- toShifts.addElement(new int[]
- { el[0], el[1] });
+ toShifts.add(new int[]
+ { r[0], r[1] });
}
}
}
/**
+ * Constructor given ranges as lists of [start, end] positions
+ *
+ * @param fromRange
+ * @param toRange
+ * @param fromRatio
+ * @param toRatio
+ */
+ public MapList(List<int[]> fromRange, List<int[]> toRange,
+ int fromRatio, int toRatio)
+ {
+ this.fromShifts = fromRange;
+ this.toShifts = toRange;
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
+
+ fromLowest = Integer.MAX_VALUE;
+ fromHighest = 0;
+ for (int[] range : fromRange) {
+ fromLowest = Math.min(fromLowest, range[0]);
+ fromHighest = Math.max(fromHighest, range[1]);
+ }
+
+ toLowest = Integer.MAX_VALUE;
+ toHighest = 0;
+ for (int[] range : toRange)
+ {
+ toLowest = Math.min(toLowest, range[0]);
+ toHighest = Math.max(toHighest, range[1]);
+ }
+ }
+
+ /**
* get all mapped positions from 'from' to 'to'
*
* @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int
* [fromFinish-fromStart+2] { toStart..toFinish mappings}}
*/
- public int[][] makeFromMap()
+ protected int[][] makeFromMap()
{
+ // TODO not used - remove??
return posMap(fromShifts, fromRatio, toShifts, toRatio);
}
*
* @return int[to position]=position mapped in from
*/
- public int[][] makeToMap()
+ protected int[][] makeToMap()
{
+ // TODO not used - remove??
return posMap(toShifts, toRatio, fromShifts, fromRatio);
}
/**
* construct an int map for intervals in intVals
*
- * @param intVals
+ * @param shiftTo
* @return int[] { from, to pos in range }, int[range.to-range.from+1]
* returning mapped position
*/
- private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
+ private int[][] posMap(List<int[]> shiftTo, int ratio,
+ List<int[]> shiftFrom,
int toRatio)
{
- int iv = 0, ivSize = intVals.size();
+ // TODO not used - remove??
+ int iv = 0, ivSize = shiftTo.size();
if (iv >= ivSize)
{
return null;
}
- int[] intv = (int[]) intVals.elementAt(iv++);
+ int[] intv = shiftTo.get(iv++);
int from = intv[0], to = intv[1];
if (from > to)
{
}
while (iv < ivSize)
{
- intv = (int[]) intVals.elementAt(iv++);
+ intv = shiftTo.get(iv++);
if (intv[0] < from)
{
from = intv[0];
int mp[][] = new int[to - from + 2][];
for (int i = 0; i < mp.length; i++)
{
- int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);
+ int[] m = shift(i + from, shiftTo, ratio, shiftFrom, toRatio);
if (m != null)
{
if (i == 0)
* shifts.insertElementAt(new int[] { pos, shift}, sidx); else
* rshift[1]+=shift; }
*/
+
/**
* shift from pos to To(pos)
*
/**
*
- * @param fromShifts
+ * @param shiftTo
* @param fromRatio
- * @param toShifts
+ * @param shiftFrom
* @param toRatio
* @return
*/
- private int[] shift(int pos, Vector fromShifts, int fromRatio,
- Vector toShifts, int toRatio)
+ protected static int[] shift(int pos, List<int[]> shiftTo, int fromRatio,
+ List<int[]> shiftFrom, int toRatio)
{
- int[] fromCount = countPos(fromShifts, pos);
+ // TODO: javadoc; tests
+ int[] fromCount = countPos(shiftTo, pos);
if (fromCount == null)
{
return null;
}
int fromRemainder = (fromCount[0] - 1) % fromRatio;
int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
- int[] toPos = countToPos(toShifts, toCount);
+ int[] toPos = countToPos(shiftFrom, toCount);
if (toPos == null)
{
return null; // throw new Error("Bad Mapping!");
/**
* count how many positions pos is along the series of intervals.
*
- * @param intVals
+ * @param shiftTo
* @param pos
* @return number of positions or null if pos is not within intervals
*/
- private int[] countPos(Vector intVals, int pos)
+ protected static int[] countPos(List<int[]> shiftTo, int pos)
{
- int count = 0, intv[], iv = 0, ivSize = intVals.size();
+ int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
while (iv < ivSize)
{
- intv = (int[]) intVals.elementAt(iv++);
+ intv = shiftTo.get(iv++);
if (intv[0] <= intv[1])
{
if (pos >= intv[0] && pos <= intv[1])
/**
* count out pos positions into a series of intervals and return the position
*
- * @param intVals
+ * @param shiftFrom
* @param pos
* @return position pos in interval set
*/
- private int[] countToPos(Vector intVals, int pos)
+ protected static int[] countToPos(List<int[]> shiftFrom, int pos)
{
- int count = 0, diff = 0, iv = 0, ivSize = intVals.size(), intv[] =
+ int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
+ int[] intv =
{ 0, 0 };
while (iv < ivSize)
{
- intv = (int[]) intVals.elementAt(iv++);
+ intv = shiftFrom.get(iv++);
diff = intv[1] - intv[0];
if (diff >= 0)
{
* find series of intervals mapping from start-end in the From map.
*
* @param start
- * position in to map
+ * position mapped 'to'
* @param end
- * position in to map
- * @return series of ranges in from map
+ * position mapped 'to'
+ * @return series of [start, end] ranges in sequence mapped 'from'
*/
public int[] locateInFrom(int start, int end)
{
// inefficient implementation
int fromStart[] = shiftTo(start);
- int fromEnd[] = shiftTo(end); // needs to be inclusive of end of symbol
- // position
- if (fromStart == null || fromEnd == null)
- return null;
- int iv[] = getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
- return iv;
+ // needs to be inclusive of end of symbol position
+ int fromEnd[] = shiftTo(end);
+
+ return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
}
/**
* find series of intervals mapping from start-end in the to map.
*
* @param start
- * position in from map
+ * position mapped 'from'
* @param end
- * position in from map
- * @return series of ranges in to map
+ * position mapped 'from'
+ * @return series of [start, end] ranges in sequence mapped 'to'
*/
public int[] locateInTo(int start, int end)
{
- // inefficient implementation
int toStart[] = shiftFrom(start);
int toEnd[] = shiftFrom(end);
- if (toStart == null || toEnd == null)
- return null;
- int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
- return iv;
+ return getIntervals(toShifts, toStart, toEnd, toRatio);
}
/**
* like shift - except returns the intervals in the given vector of shifts
* which were spanned in traversing fromStart to fromEnd
*
- * @param fromShifts2
+ * @param shiftFrom
* @param fromStart
* @param fromEnd
* @param fromRatio2
* @return series of from,to intervals from from first position of starting
* region to final position of ending region inclusive
*/
- private int[] getIntervals(Vector fromShifts2, int[] fromStart,
+ protected static int[] getIntervals(List<int[]> shiftFrom,
+ int[] fromStart,
int[] fromEnd, int fromRatio2)
{
+ if (fromStart == null || fromEnd == null)
+ {
+ return null;
+ }
int startpos, endpos;
startpos = fromStart[0]; // first position in fromStart
endpos = fromEnd[0]; // last position in fromEnd
int endindx = (fromRatio2 - 1); // additional positions to get to last
// position from endpos
- int intv = 0, intvSize = fromShifts2.size();
+ int intv = 0, intvSize = shiftFrom.size();
int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
// search intervals to locate ones containing startpos and count endindx
// positions on from endpos
while (intv < intvSize && (fs == -1 || fe == -1))
{
- iv = (int[]) fromShifts2.elementAt(intv++);
+ iv = shiftFrom.get(intv++);
if (fe_s > -1)
{
endpos = iv[0]; // start counting from beginning of interval
i++;
}
if (fs == fe && fe == -1)
+ {
return null;
- Vector ranges = new Vector();
+ }
+ List<int[]> ranges = new ArrayList<int[]>();
if (fs <= fe)
{
intv = fs;
i = fs;
// truncate initial interval
- iv = (int[]) fromShifts2.elementAt(intv++);
+ iv = shiftFrom.get(intv++);
iv = new int[]
{ iv[0], iv[1] };// clone
if (i == fs)
+ {
iv[0] = startpos;
+ }
while (i != fe)
{
- ranges.addElement(iv); // add initial range
- iv = (int[]) fromShifts2.elementAt(intv++); // get next interval
+ ranges.add(iv); // add initial range
+ iv = shiftFrom.get(intv++); // get next interval
iv = new int[]
{ iv[0], iv[1] };// clone
i++;
}
if (i == fe)
+ {
iv[1] = endpos;
- ranges.addElement(iv); // add only - or final range
+ }
+ ranges.add(iv); // add only - or final range
}
else
{
// walk from end of interval.
- i = fromShifts2.size() - 1;
+ i = shiftFrom.size() - 1;
while (i > fs)
{
i--;
}
- iv = (int[]) fromShifts2.elementAt(i);
+ iv = shiftFrom.get(i);
iv = new int[]
{ iv[1], iv[0] };// reverse and clone
// truncate initial interval
}
while (--i != fe)
{ // fix apparent logic bug when fe==-1
- ranges.addElement(iv); // add (truncated) reversed interval
- iv = (int[]) fromShifts2.elementAt(i);
+ ranges.add(iv); // add (truncated) reversed interval
+ iv = shiftFrom.get(i);
iv = new int[]
{ iv[1], iv[0] }; // reverse and clone
}
// interval is already reversed
iv[1] = endpos;
}
- ranges.addElement(iv); // add only - or final range
+ ranges.add(iv); // add only - or final range
}
// create array of start end intervals.
int[] range = null;
i = 0;
while (intv < intvSize)
{
- iv = (int[]) ranges.elementAt(intv);
+ iv = ranges.get(intv);
range[i++] = iv[0];
range[i++] = iv[1];
- ranges.setElementAt(null, intv++); // remove
+ ranges.set(intv++, null); // remove
}
}
return range;
*/
public int getToPosition(int mpos)
{
+ // TODO not used - remove??
int[] mp = shiftTo(mpos);
if (mp != null)
{
*/
public int getMappedPosition(int pos)
{
+ // TODO not used - remove??
int[] mp = shiftFrom(pos);
if (mp != null)
{
public int[] getMappedWord(int pos)
{
+ // TODO not used - remove??
int[] mp = shiftFrom(pos);
if (mp != null)
{
}
/**
- * test routine. not incremental.
- *
- * @param ml
- * @param fromS
- * @param fromE
- */
- public static void testMap(MapList ml, int fromS, int fromE)
- {
- for (int from = 1; from <= 25; from++)
- {
- int[] too = ml.shiftFrom(from);
- System.out.print("ShiftFrom(" + from + ")==");
- if (too == null)
- {
- System.out.print("NaN\n");
- }
- else
- {
- System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
- System.out.print("\t+--+\t");
- int[] toofrom = ml.shiftTo(too[0]);
- if (toofrom != null)
- {
- if (toofrom[0] != from)
- {
- System.err.println("Mapping not reflexive:" + from + " "
- + too[0] + "->" + toofrom[0]);
- }
- System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
- + " % " + toofrom[1] + " (" + toofrom[2] + ")");
- }
- else
- {
- System.out.println("ShiftTo(" + too[0] + ")=="
- + "NaN! - not Bijective Mapping!");
- }
- }
- }
- int mmap[][] = ml.makeFromMap();
- System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
- + mmap[0][2] + " " + mmap[0][3] + " ");
- for (int i = 1; i <= mmap[1].length; i++)
- {
- if (mmap[1][i - 1] == -1)
- {
- System.out.print(i + "=XXX");
-
- }
- else
- {
- System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
- }
- if (i % 20 == 0)
- {
- System.out.print("\n");
- }
- else
- {
- System.out.print(",");
- }
- }
- // test range function
- System.out.print("\nTest locateInFrom\n");
- {
- int f = mmap[0][2], t = mmap[0][3];
- while (f <= t)
- {
- System.out.println("Range " + f + " to " + t);
- int rng[] = ml.locateInFrom(f, t);
- if (rng != null)
- {
- for (int i = 0; i < rng.length; i++)
- {
- System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
- }
- }
- else
- {
- System.out.println("No range!");
- }
- System.out.print("\nReversed\n");
- rng = ml.locateInFrom(t, f);
- if (rng != null)
- {
- for (int i = 0; i < rng.length; i++)
- {
- System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
- }
- }
- else
- {
- System.out.println("No range!");
- }
- System.out.print("\n");
- f++;
- t--;
- }
- }
- System.out.print("\n");
- mmap = ml.makeToMap();
- System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
- + mmap[0][2] + " " + mmap[0][3] + " ");
- for (int i = 1; i <= mmap[1].length; i++)
- {
- if (mmap[1][i - 1] == -1)
- {
- System.out.print(i + "=XXX");
-
- }
- else
- {
- System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
- }
- if (i % 20 == 0)
- {
- System.out.print("\n");
- }
- else
- {
- System.out.print(",");
- }
- }
- System.out.print("\n");
- // test range function
- System.out.print("\nTest locateInTo\n");
- {
- int f = mmap[0][2], t = mmap[0][3];
- while (f <= t)
- {
- System.out.println("Range " + f + " to " + t);
- int rng[] = ml.locateInTo(f, t);
- if (rng != null)
- {
- for (int i = 0; i < rng.length; i++)
- {
- System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
- }
- }
- else
- {
- System.out.println("No range!");
- }
- System.out.print("\nReversed\n");
- rng = ml.locateInTo(t, f);
- if (rng != null)
- {
- for (int i = 0; i < rng.length; i++)
- {
- System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
- }
- }
- else
- {
- System.out.println("No range!");
- }
- f++;
- t--;
- System.out.print("\n");
- }
- }
-
- }
-
- public static void main(String argv[])
- {
- MapList ml = new MapList(new int[]
- { 1, 5, 10, 15, 25, 20 }, new int[]
- { 51, 1 }, 1, 3);
- MapList ml1 = new MapList(new int[]
- { 1, 3, 17, 4 }, new int[]
- { 51, 1 }, 1, 3);
- MapList ml2 = new MapList(new int[]
- { 1, 60 }, new int[]
- { 1, 20 }, 3, 1);
- // test internal consistency
- int to[] = new int[51];
- MapList.testMap(ml, 1, 60);
- MapList mldna = new MapList(new int[]
- { 2, 2, 6, 8, 12, 16 }, new int[]
- { 1, 3 }, 3, 1);
- int[] frm = mldna.locateInFrom(1, 1);
- testLocateFrom(mldna, 1, 1, new int[]
- { 2, 2, 6, 7 });
- MapList.testMap(mldna, 1, 3);
- /*
- * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
- * toofrom=ml.shiftFrom(too[0]);
- * System.out.println("ShiftFrom("+from+")=="+too[0]+" %
- * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
- */
- System.out.print("Success?\n"); // if we get here - something must be
- // working!
- }
-
- private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
- {
- int[] frm = mldna.locateInFrom(i, j);
- if (frm == ks || java.util.Arrays.equals(frm, ks))
- {
- System.out.println("Success test locate from " + i + " to " + j);
- }
- else
- {
- System.err.println("Failed test locate from " + i + " to " + j);
- for (int c = 0; c < frm.length; c++)
- {
- System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));
- }
- System.err.println("Expected");
- for (int c = 0; c < ks.length; c++)
- {
- System.err.print(ks[c] + ((c % 2 == 0) ? "," : ";"));
- }
- }
- }
-
- /**
*
* @return a MapList whose From range is this maplist's To Range, and vice
* versa
*/
public boolean containsEither(boolean local, MapList map)
{
+ // TODO not used - remove?
if (local)
{
return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= map
--- /dev/null
+package jalview.util;
+
+import jalview.analysis.AlignmentSorter;
+import jalview.api.AlignViewportI;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * Helper methods for manipulations involving sequence mappings.
+ *
+ * @author gmcarstairs
+ *
+ */
+public final class MappingUtils
+{
+
+ /**
+ * Helper method to map a CUT or PASTE command.
+ *
+ * @param edit
+ * the original command
+ * @param undo
+ * if true, the command is to be undone
+ * @param targetSeqs
+ * the mapped sequences to apply the mapped command to
+ * @param result
+ * the mapped EditCommand to add to
+ * @param mappings
+ */
+ protected static void mapCutOrPaste(Edit edit, boolean undo,
+ List<SequenceI> targetSeqs, EditCommand result,
+ Set<AlignedCodonFrame> mappings)
+ {
+ Action action = edit.getAction();
+ if (undo)
+ {
+ action = action.getUndoAction();
+ }
+ // TODO write this
+ System.err.println("MappingUtils.mapCutOrPaste not yet implemented");
+ }
+
+ /**
+ * Returns a new EditCommand representing the given command as mapped to the
+ * given sequences. If there is no mapping, returns null.
+ *
+ * @param command
+ * @param undo
+ * @param mapTo
+ * @param gapChar
+ * @param mappings
+ * @return
+ */
+ public static EditCommand mapEditCommand(EditCommand command,
+ boolean undo, final AlignmentI mapTo, char gapChar,
+ Set<AlignedCodonFrame> mappings)
+ {
+ /*
+ * For now, only support mapping from protein edits to cDna
+ */
+ if (!mapTo.isNucleotide())
+ {
+ return null;
+ }
+
+ /*
+ * Cache a copy of the target sequences so we can mimic successive edits on
+ * them. This lets us compute mappings for all edits in the set.
+ */
+ Map<SequenceI, SequenceI> targetCopies = new HashMap<SequenceI, SequenceI>();
+ for (SequenceI seq : mapTo.getSequences())
+ {
+ SequenceI ds = seq.getDatasetSequence();
+ if (ds != null)
+ {
+ final SequenceI copy = new Sequence(seq);
+ copy.setDatasetSequence(ds);
+ targetCopies.put(ds, copy);
+ }
+ }
+
+ /*
+ * Compute 'source' sequences as they were before applying edits:
+ */
+ Map<SequenceI, SequenceI> originalSequences = command.priorState(undo);
+
+ EditCommand result = new EditCommand();
+ Iterator<Edit> edits = command.getEditIterator(!undo);
+ while (edits.hasNext())
+ {
+ Edit edit = edits.next();
+ if (edit.getAction() == Action.CUT
+ || edit.getAction() == Action.PASTE)
+ {
+ mapCutOrPaste(edit, undo, mapTo.getSequences(), result, mappings);
+ }
+ else if (edit.getAction() == Action.INSERT_GAP
+ || edit.getAction() == Action.DELETE_GAP)
+ {
+ mapInsertOrDelete(edit, undo, originalSequences,
+ mapTo.getSequences(), targetCopies, gapChar, result,
+ mappings);
+ }
+ }
+ return result.getSize() > 0 ? result : null;
+ }
+
+ /**
+ * Helper method to map an edit command to insert or delete gaps.
+ *
+ * @param edit
+ * the original command
+ * @param undo
+ * if true, the action is to undo the command
+ * @param originalSequences
+ * the sequences the command acted on
+ * @param targetSeqs
+ * @param targetCopies
+ * @param gapChar
+ * @param result
+ * the new EditCommand to add mapped commands to
+ * @param mappings
+ */
+ protected static void mapInsertOrDelete(Edit edit, boolean undo,
+ Map<SequenceI, SequenceI> originalSequences,
+ final List<SequenceI> targetSeqs,
+ Map<SequenceI, SequenceI> targetCopies, char gapChar,
+ EditCommand result, Set<AlignedCodonFrame> mappings)
+ {
+ Action action = edit.getAction();
+
+ /*
+ * Invert sense of action if an Undo.
+ */
+ if (undo)
+ {
+ action = action.getUndoAction();
+ }
+ final int count = edit.getNumber();
+ final int editPos = edit.getPosition();
+ for (SequenceI seq : edit.getSequences())
+ {
+ /*
+ * Get residue position at (or to right of) edit location. Note we use our
+ * 'copy' of the sequence before editing for this.
+ */
+ SequenceI ds = seq.getDatasetSequence();
+ if (ds == null)
+ {
+ continue;
+ }
+ final SequenceI actedOn = originalSequences.get(ds);
+ final int seqpos = actedOn.findPosition(editPos);
+
+ /*
+ * Determine all mappings from this position to mapped sequences.
+ */
+ SearchResults sr = buildSearchResults(seq, seqpos, mappings);
+
+ if (!sr.isEmpty())
+ {
+ for (SequenceI targetSeq : targetSeqs)
+ {
+ ds = targetSeq.getDatasetSequence();
+ if (ds == null)
+ {
+ continue;
+ }
+ SequenceI copyTarget = targetCopies.get(ds);
+ final int[] match = sr.getResults(copyTarget, 0,
+ copyTarget.getLength());
+ if (match != null)
+ {
+ final int ratio = 3; // TODO: compute this - how?
+ final int mappedCount = count * ratio;
+
+ /*
+ * Shift Delete start position left, as it acts on positions to its
+ * right.
+ */
+ int mappedEditPos = action == Action.DELETE_GAP ? match[0]
+ - mappedCount : match[0];
+ Edit e = result.new Edit(action, new SequenceI[]
+ { targetSeq }, mappedEditPos, mappedCount, gapChar);
+ result.addEdit(e);
+
+ /*
+ * and 'apply' the edit to our copy of its target sequence
+ */
+ if (action == Action.INSERT_GAP)
+ {
+ copyTarget.setSequence(new String(StringUtils.insertCharAt(
+ copyTarget.getSequence(), mappedEditPos, mappedCount,
+ gapChar)));
+ }
+ else if (action == Action.DELETE_GAP)
+ {
+ copyTarget.setSequence(new String(StringUtils.deleteChars(
+ copyTarget.getSequence(), mappedEditPos,
+ mappedEditPos + mappedCount)));
+ }
+ }
+ }
+ }
+ /*
+ * and 'apply' the edit to our copy of its source sequence
+ */
+ if (action == Action.INSERT_GAP)
+ {
+ actedOn.setSequence(new String(StringUtils.insertCharAt(
+ actedOn.getSequence(), editPos, count, gapChar)));
+ }
+ else if (action == Action.DELETE_GAP)
+ {
+ actedOn.setSequence(new String(StringUtils.deleteChars(
+ actedOn.getSequence(), editPos, editPos + count)));
+ }
+ }
+ }
+
+ /**
+ * Returns a SearchResults object describing the mapped region corresponding
+ * to the specified sequence position.
+ *
+ * @param seq
+ * @param index
+ * @param seqmappings
+ * @return
+ */
+ public static SearchResults buildSearchResults(SequenceI seq, int index,
+ Set<AlignedCodonFrame> seqmappings)
+ {
+ SearchResults results;
+ results = new SearchResults();
+ if (index >= seq.getStart() && index <= seq.getEnd())
+ {
+ for (AlignedCodonFrame acf : seqmappings)
+ {
+ acf.markMappedRegion(seq, index, results);
+ }
+ }
+ return results;
+ }
+
+ /**
+ * Returns a (possibly empty) SequenceGroup containing any sequences in the
+ * mapped viewport corresponding to the given group in the source viewport.
+ *
+ * @param sg
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ public static SequenceGroup mapSequenceGroup(SequenceGroup sg,
+ AlignViewportI mapFrom, AlignViewportI mapTo)
+ {
+ /*
+ * Note the SequenceGroup holds aligned sequences, the mappings hold dataset
+ * sequences.
+ */
+ boolean targetIsNucleotide = mapTo.isNucleotide();
+ AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
+ Set<AlignedCodonFrame> codonFrames = protein.getAlignment()
+ .getCodonFrames();
+
+ /*
+ * Copy group name, name colours, but not sequences or sequence colour
+ * scheme
+ */
+ SequenceGroup mappedGroup = new SequenceGroup(sg);
+ mappedGroup.cs = mapTo.getGlobalColourScheme();
+ mappedGroup.clear();
+ // TODO set width of mapped group
+
+ for (SequenceI selected : sg.getSequences())
+ {
+ for (AlignedCodonFrame acf : codonFrames)
+ {
+ SequenceI mappedSequence = targetIsNucleotide ? acf
+ .getDnaForAaSeq(selected) : acf.getAaForDnaSeq(selected);
+ if (mappedSequence != null)
+ {
+ for (SequenceI seq : mapTo.getAlignment().getSequences())
+ {
+ if (seq.getDatasetSequence() == mappedSequence)
+ {
+ mappedGroup.addSequence(seq, false);
+ break;
+ }
+ }
+ }
+ }
+ }
+ return mappedGroup;
+ }
+
+ /**
+ * Returns an OrderCommand equivalent to the given one, but acting on mapped
+ * sequences as described by the mappings, or null if no mapping can be made.
+ *
+ * @param command
+ * the original order command
+ * @param undo
+ * if true, the action is to undo the sort
+ * @param mapTo
+ * the alignment we are mapping to
+ * @param mappings
+ * the mappings available
+ * @return
+ */
+ public static CommandI mapOrderCommand(OrderCommand command,
+ boolean undo, AlignmentI mapTo, Set<AlignedCodonFrame> mappings)
+ {
+ SequenceI[] sortOrder = command.getSequenceOrder(undo);
+ List<SequenceI> mappedOrder = new ArrayList<SequenceI>();
+ int j = 0;
+ for (SequenceI seq : sortOrder)
+ {
+ for (AlignedCodonFrame acf : mappings)
+ {
+ /*
+ * Try protein-to-Dna, failing that try dna-to-protein
+ */
+ SequenceI mappedSeq = acf.getDnaForAaSeq(seq);
+ if (mappedSeq == null)
+ {
+ mappedSeq = acf.getAaForDnaSeq(seq);
+ }
+ if (mappedSeq != null)
+ {
+ for (SequenceI seq2 : mapTo.getSequences())
+ {
+ if (seq2.getDatasetSequence() == mappedSeq)
+ {
+ mappedOrder.add(seq2);
+ j++;
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ /*
+ * Return null if no mappings made.
+ */
+ if (j == 0)
+ {
+ return null;
+ }
+
+ /*
+ * Add any unmapped sequences on the end of the sort in their original
+ * ordering.
+ */
+ if (j < mapTo.getHeight())
+ {
+ for (SequenceI seq : mapTo.getSequences())
+ {
+ if (!mappedOrder.contains(seq))
+ {
+ mappedOrder.add(seq);
+ }
+ }
+ }
+
+ /*
+ * Have to sort the sequences before constructing the OrderCommand - which
+ * then resorts them?!?
+ */
+ final SequenceI[] mappedOrderArray = mappedOrder
+ .toArray(new SequenceI[mappedOrder.size()]);
+ SequenceI[] oldOrder = mapTo.getSequencesArray();
+ AlignmentSorter.sortBy(mapTo, new AlignmentOrder(mappedOrderArray));
+ final OrderCommand result = new OrderCommand(command.getDescription(),
+ oldOrder, mapTo);
+ return result;
+ }
+
+ /**
+ * Returns a ColumnSelection in the 'mapTo' view which corresponds to the
+ * given selection in the 'mapFrom' view. We assume one is nucleotide, the
+ * other is protein (and holds the mappings from codons to protein residues).
+ *
+ * @param colsel
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ public static ColumnSelection mapColumnSelection(ColumnSelection colsel,
+ AlignViewportI mapFrom, AlignViewportI mapTo)
+ {
+ boolean targetIsNucleotide = mapTo.isNucleotide();
+ AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
+ Set<AlignedCodonFrame> codonFrames = protein.getAlignment()
+ .getCodonFrames();
+ ColumnSelection mappedColumns = new ColumnSelection();
+ char fromGapChar = mapFrom.getAlignment().getGapCharacter();
+
+ // FIXME allow for hidden columns
+
+ /*
+ * For each mapped column, find the range of columns that residues in that
+ * column map to.
+ */
+ for (Object obj : colsel.getSelected())
+ {
+ int col = ((Integer) obj).intValue();
+ int mappedToMin = Integer.MAX_VALUE;
+ int mappedToMax = Integer.MIN_VALUE;
+
+ /*
+ * For each sequence in the 'from' alignment
+ */
+ for (SequenceI fromSeq : mapFrom.getAlignment().getSequences())
+ {
+ /*
+ * Ignore gaps (unmapped anyway)
+ */
+ if (fromSeq.getCharAt(col) == fromGapChar)
+ {
+ continue;
+ }
+
+ /*
+ * Get the residue position and find the mapped position.
+ */
+ int residuePos = fromSeq.findPosition(col);
+ SearchResults sr = buildSearchResults(fromSeq, residuePos,
+ codonFrames);
+ for (Match m : sr.getResults())
+ {
+ int mappedStartResidue = m.getStart();
+ int mappedEndResidue = m.getEnd();
+ SequenceI mappedSeq = m.getSequence();
+
+ /*
+ * Locate the aligned sequence whose dataset is mappedSeq. TODO a
+ * datamodel that can do this efficiently.
+ */
+ for (SequenceI toSeq : mapTo.getAlignment().getSequences())
+ {
+ if (toSeq.getDatasetSequence() == mappedSeq)
+ {
+ int mappedStartCol = toSeq.findIndex(mappedStartResidue);
+ int mappedEndCol = toSeq.findIndex(mappedEndResidue);
+ mappedToMin = Math.min(mappedToMin, mappedStartCol);
+ mappedToMax = Math.max(mappedToMax, mappedEndCol);
+ // System.out.println(fromSeq.getName() + " mapped to cols "
+ // + mappedStartCol + ":" + mappedEndCol);
+ break;
+ // note: remove break if we ever want to map one to many sequences
+ }
+ }
+ }
+ }
+ /*
+ * Add the range of mapped columns to the mapped selection (converting
+ * base 1 to base 0). Note that this may include intron-only regions which
+ * lie between the start and end ranges of the selection.
+ */
+ for (int i = mappedToMin; i <= mappedToMax; i++)
+ {
+ mappedColumns.addElement(i - 1);
+ }
+ }
+ return mappedColumns;
+ }
+
+ /**
+ * Returns the mapped codon for a given aligned sequence column position (base
+ * 0).
+ *
+ * @param seq
+ * an aligned peptide sequence
+ * @param col
+ * an aligned column position (base 0)
+ * @param mappings
+ * a set of codon mappings
+ * @return the bases of the mapped codon in the cDNA dataset sequence, or null
+ * if not found
+ */
+ public static char[] findCodonFor(SequenceI seq, int col,
+ Set<AlignedCodonFrame> mappings)
+ {
+ int dsPos = seq.findPosition(col);
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ if (mapping.involvesSequence(seq))
+ {
+ return mapping.getMappedCodon(seq.getDatasetSequence(), dsPos);
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Converts a series of [start, end] ranges into an array of individual
+ * positions.
+ *
+ * @param ranges
+ * @return
+ */
+ public static int[] flattenRanges(int[] ranges)
+ {
+ /*
+ * Count how many positions altogether
+ */
+ int count = 0;
+ for (int i = 0; i < ranges.length - 1; i += 2)
+ {
+ count += ranges[i + 1] - ranges[i] + 1;
+ }
+
+ int[] result = new int[count];
+ int k = 0;
+ for (int i = 0; i < ranges.length - 1; i += 2)
+ {
+ for (int j = ranges[i]; j <= ranges[i + 1]; j++)
+ {
+ result[k++] = j;
+ }
+ }
+ return result;
+ }
+}
public static String formatMessage(String key, Object... params)
{
+ return MessageFormat.format(rb.getString(key), params);
+ }
+
+ public static String formatMessage(String key, String[] params)
+ {
return MessageFormat.format(rb.getString(key), (Object[]) params);
}
*/
public class ParseHtmlBodyAndLinks
{
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+
String orig = null;
public String getOrig()
{
// instead of parsing the html into plaintext
// clean the description ready for embedding in html
- sb = new StringBuffer(Pattern.compile("<").matcher(description)
+ sb = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(description)
.replaceAll("<"));
}
*/
package jalview.util;
+import java.util.Arrays;
+import java.util.Comparator;
+
+/**
+ * A class to perform efficient sorting of arrays of objects based on arrays of
+ * scores or other attributes. For example, residues by percentage frequency.
+ *
+ * @author gmcarstairs
+ *
+ */
public class QuickSort
{
+ static class FloatComparator implements Comparator<Integer>
+ {
+
+ private final float[] values;
+
+ FloatComparator(float[] v)
+ {
+ values = v;
+ }
+
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ return Float.compare(values[o1], values[o2]);
+ }
+
+ }
+
+ static class IntComparator implements Comparator<Integer>
+ {
+
+ private final int[] values;
+
+ IntComparator(int[] v)
+ {
+ values = v;
+ }
+
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ return Integer.compare(values[o1], values[o2]);
+ }
+
+ }
+
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
public static void sort(int[] arr, Object[] s)
{
sort(arr, 0, arr.length - 1, s);
}
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
public static void sort(float[] arr, Object[] s)
{
sort(arr, 0, arr.length - 1, s);
}
+ /**
+ * Sorts both arrays with respect to ascending order of the items in the first
+ * array.
+ *
+ * @param arr
+ * @param s
+ */
public static void sort(double[] arr, Object[] s)
{
sort(arr, 0, arr.length - 1, s);
}
+ /**
+ * Sorts both arrays with respect to descending order of the items in the
+ * first array.
+ *
+ * @param arr
+ * @param s
+ */
public static void sort(String[] arr, Object[] s)
{
stringSort(arr, 0, arr.length - 1, s);
}
- public static void stringSort(String[] arr, int p, int r, Object[] s)
+ static void stringSort(String[] arr, int p, int r, Object[] s)
{
int q;
}
}
- public static void sort(float[] arr, int p, int r, Object[] s)
+ static void sort(float[] arr, int p, int r, Object[] s)
{
int q;
}
}
- public static void sort(double[] arr, int p, int r, Object[] s)
+ static void sort(double[] arr, int p, int r, Object[] s)
{
int q;
}
}
- public static void sort(int[] arr, int p, int r, Object[] s)
+ static void sort(int[] arr, int p, int r, Object[] s)
{
int q;
}
}
- private static int partition(float[] arr, int p, int r, Object[] s)
+ static int partition(float[] arr, int p, int r, Object[] s)
{
float x = arr[p];
int i = p - 1;
}
}
- private static int partition(int[] arr, int p, int r, Object[] s)
+ static int partition(float[] arr, int p, int r, char[] s)
+ {
+ float x = arr[p];
+ int i = p - 1;
+ int j = r + 1;
+
+ while (true)
+ {
+ do
+ {
+ j = j - 1;
+ } while (arr[j] > x);
+
+ do
+ {
+ i = i + 1;
+ } while (arr[i] < x);
+
+ if (i < j)
+ {
+ float tmp = arr[i];
+ arr[i] = arr[j];
+ arr[j] = tmp;
+
+ char tmp2 = s[i];
+ s[i] = s[j];
+ s[j] = tmp2;
+ }
+ else
+ {
+ return j;
+ }
+ }
+ }
+
+ static int partition(int[] arr, int p, int r, Object[] s)
{
int x = arr[p];
int i = p - 1;
}
}
- private static int partition(double[] arr, int p, int r, Object[] s)
+ static int partition(double[] arr, int p, int r, Object[] s)
{
double x = arr[p];
int i = p - 1;
}
}
- private static int stringPartition(String[] arr, int p, int r, Object[] s)
+ static int stringPartition(String[] arr, int p, int r, Object[] s)
{
String x = arr[p];
int i = p - 1;
}
}
}
+
+ /**
+ * Sorts both arrays to give ascending order in the first array, by first
+ * partitioning into zero and non-zero values before sorting the latter.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(float[] arr, char[] s)
+ {
+ /*
+ * Sort all zero values to the front
+ */
+ float[] f1 = new float[arr.length];
+ char[] s1 = new char[s.length];
+ int nextZeroValue = 0;
+ int nextNonZeroValue = arr.length - 1;
+ for (int i = 0; i < arr.length; i++)
+ {
+ float val = arr[i];
+ if (val > 0f)
+ {
+ f1[nextNonZeroValue] = val;
+ s1[nextNonZeroValue] = s[i];
+ nextNonZeroValue--;
+ }
+ else
+ {
+ f1[nextZeroValue] = val;
+ s1[nextZeroValue] = s[i];
+ nextZeroValue++;
+ }
+ }
+
+ /*
+ * Copy zero values back to original arrays
+ */
+ System.arraycopy(f1, 0, arr, 0, nextZeroValue);
+ System.arraycopy(s1, 0, s, 0, nextZeroValue);
+
+ if (nextZeroValue == arr.length)
+ {
+ return; // all zero
+ }
+ /*
+ * Sort the non-zero values
+ */
+ float[] nonZeroFloats = Arrays
+ .copyOfRange(f1, nextZeroValue, f1.length);
+ char[] nonZeroChars = Arrays.copyOfRange(s1, nextZeroValue, s1.length);
+ externalSort(nonZeroFloats, nonZeroChars);
+ // sort(nonZeroFloats, 0, nonZeroFloats.length - 1, nonZeroChars);
+
+ /*
+ * Assemble sorted non-zero results
+ */
+ System.arraycopy(nonZeroFloats, 0, arr, nextZeroValue,
+ nonZeroFloats.length);
+ System.arraycopy(nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length);
+ }
+
+ /**
+ * Sort by making an array of indices, and sorting it using a comparator that
+ * refers to the float values.
+ *
+ * @see http
+ * ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
+ * after-sorting
+ * @param arr
+ * @param s
+ */
+ protected static void externalSort(float[] arr, char[] s)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new FloatComparator(arr));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ float[] sortedFloats = new float[length];
+ char[] sortedChars = new char[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedFloats[i] = arr[indices[i]];
+ sortedChars[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedFloats, 0, arr, 0, length);
+ System.arraycopy(sortedChars, 0, s, 0, s.length);
+ }
+
+ /**
+ * Make an array whose values are 0...length.
+ *
+ * @param length
+ * @return
+ */
+ protected static Integer[] makeIndexArray(final int length)
+ {
+ Integer[] indices = new Integer[length];
+ for (int i = 0; i < length; i++)
+ {
+ indices[i] = i;
+ }
+ return indices;
+ }
+
+ static void sort(float[] arr, int p, int r, char[] s)
+ {
+ int q;
+ if (p < r)
+ {
+ q = partition(arr, p, r, s);
+ sort(arr, p, q, s);
+ sort(arr, q + 1, r, s);
+ }
+ }
+
+ /**
+ * Sorts both arrays to give ascending order in the first array, by first
+ * partitioning into zero and non-zero values before sorting the latter.
+ *
+ * @param arr
+ * @param s
+ */
+ public static void sort(int[] arr, char[] s)
+ {
+ /*
+ * Sort all zero values to the front
+ */
+ int[] f1 = new int[arr.length];
+ char[] s1 = new char[s.length];
+ int nextZeroValue = 0;
+ int nextNonZeroValue = arr.length - 1;
+ for (int i = 0; i < arr.length; i++)
+ {
+ int val = arr[i];
+ if (val > 0f)
+ {
+ f1[nextNonZeroValue] = val;
+ s1[nextNonZeroValue] = s[i];
+ nextNonZeroValue--;
+ }
+ else
+ {
+ f1[nextZeroValue] = val;
+ s1[nextZeroValue] = s[i];
+ nextZeroValue++;
+ }
+ }
+
+ /*
+ * Copy zero values back to original arrays
+ */
+ System.arraycopy(f1, 0, arr, 0, nextZeroValue);
+ System.arraycopy(s1, 0, s, 0, nextZeroValue);
+
+ if (nextZeroValue == arr.length)
+ {
+ return; // all zero
+ }
+ /*
+ * Sort the non-zero values
+ */
+ int[] nonZeroInts = Arrays
+ .copyOfRange(f1, nextZeroValue, f1.length);
+ char[] nonZeroChars = Arrays.copyOfRange(s1, nextZeroValue, s1.length);
+ externalSort(nonZeroInts, nonZeroChars);
+ // sort(nonZeroFloats, 0, nonZeroFloats.length - 1, nonZeroChars);
+
+ /*
+ * Assemble sorted non-zero results
+ */
+ System.arraycopy(nonZeroInts, 0, arr, nextZeroValue, nonZeroInts.length);
+ System.arraycopy(nonZeroChars, 0, s, nextZeroValue, nonZeroChars.length);
+ }
+
+ /**
+ * Sort by making an array of indices, and sorting it using a comparator that
+ * refers to the float values.
+ *
+ * @see http
+ * ://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-
+ * after-sorting
+ * @param arr
+ * @param s
+ */
+ protected static void externalSort(int[] arr, char[] s)
+ {
+ final int length = arr.length;
+ Integer[] indices = makeIndexArray(length);
+ Arrays.sort(indices, new IntComparator(arr));
+
+ /*
+ * Copy the array values as per the sorted indices
+ */
+ int[] sortedInts = new int[length];
+ char[] sortedChars = new char[s.length];
+ for (int i = 0; i < length; i++)
+ {
+ sortedInts[i] = arr[indices[i]];
+ sortedChars[i] = s[indices[i]];
+ }
+
+ /*
+ * And copy the sorted values back into the arrays
+ */
+ System.arraycopy(sortedInts, 0, arr, 0, length);
+ System.arraycopy(sortedChars, 0, s, 0, s.length);
+ }
}
--- /dev/null
+package jalview.util;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+
+/**
+ * An iterator that traverses a list backwards.
+ *
+ * @author gmcarstairs (and checked against
+ * org.codehaus.groovey.runtime.ReverseListIterator)
+ *
+ * @param <E>
+ */
+public class ReverseListIterator<E> implements Iterator<E>
+{
+
+ private ListIterator<E> iterator;
+
+ public ReverseListIterator(List<E> stuff)
+ {
+ this.iterator = stuff.listIterator(stuff.size());
+ }
+ @Override
+ public boolean hasNext()
+ {
+ return iterator.hasPrevious();
+ }
+
+ @Override
+ public E next()
+ {
+ return iterator.previous();
+ }
+
+ @Override
+ public void remove()
+ {
+ iterator.remove();
+ }
+
+}
*/
package jalview.util;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
/**
* ShiftList Simple way of mapping a linear series to a new linear range with
*/
public class ShiftList
{
- public Vector shifts;
+ private List<int[]> shifts;
public ShiftList()
{
- shifts = new Vector();
+ shifts = new ArrayList<int[]>();
}
/**
*/
public void addShift(int pos, int shift)
{
- int sidx = 0;
- int[] rshift = null;
- while (sidx < shifts.size()
- && (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)
- {
- sidx++;
- }
- if (sidx == shifts.size())
+ synchronized (shifts)
{
- shifts.insertElementAt(new int[]
- { pos, shift }, sidx);
- }
- else
- {
- rshift[1] += shift;
+ int sidx = 0;
+ int[] rshift = null;
+ while (sidx < shifts.size() && (rshift = shifts.get(sidx))[0] < pos)
+ {
+ sidx++;
+ }
+ if (sidx == shifts.size())
+ {
+ shifts.add(sidx, new int[]
+ { pos, shift });
+ }
+ else
+ {
+ rshift[1] += shift;
+ }
}
}
int sidx = 0;
int rshift[];
while (sidx < shifts.size()
- && (rshift = ((int[]) shifts.elementAt(sidx++)))[0] <= pos)
+ && (rshift = (shifts.get(sidx++)))[0] <= pos)
{
shifted += rshift[1];
}
/**
* clear all shifts
*/
- public void clear()
+ public synchronized void clear()
{
- shifts.removeAllElements();
+ shifts.clear();
}
/**
public ShiftList getInverse()
{
ShiftList inverse = new ShiftList();
- if (shifts != null)
+ synchronized (shifts)
{
- for (int i = 0, j = shifts.size(); i < j; i++)
+ if (shifts != null)
{
- int[] sh = (int[]) shifts.elementAt(i);
- if (sh != null)
+ for (int[] sh : shifts)
{
- inverse.shifts.addElement(new int[]
- { sh[0], -sh[1] });
+ if (sh != null)
+ {
+ inverse.shifts.add(new int[]
+ { sh[0], -sh[1] });
+ }
}
}
}
}
/**
- * parse a 1d map of position 1<i<n to L<pos[i]<N such as that returned from
- * SequenceI.gapMap()
+ * parse a 1d map of position 1<i<n to L<pos[i]<N such as that
+ * returned from SequenceI.gapMap()
*
* @param gapMap
* @return shifts from map index to mapped position
}
return shiftList;
}
+
+ public List<int[]> getShifts()
+ {
+ return shifts;
+ }
}
--- /dev/null
+package jalview.util;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
+
+public class StringUtils
+{
+ private static final Pattern DELIMITERS_PATTERN = Pattern.compile(".*='[^']*(?!')");
+
+ private static final boolean DEBUG = false;
+
+ /**
+ * Returns a new character array, after inserting characters into the given
+ * character array.
+ *
+ * @param in
+ * the character array to insert into
+ * @param position
+ * the 0-based position for insertion
+ * @param count
+ * the number of characters to insert
+ * @param ch
+ * the character to insert
+ */
+ public static final char[] insertCharAt(char[] in, int position,
+ int count,
+ char ch)
+ {
+ char[] tmp = new char[in.length + count];
+
+ if (position >= in.length)
+ {
+ System.arraycopy(in, 0, tmp, 0, in.length);
+ position = in.length;
+ }
+ else
+ {
+ System.arraycopy(in, 0, tmp, 0, position);
+ }
+
+ int index = position;
+ while (count > 0)
+ {
+ tmp[index++] = ch;
+ count--;
+ }
+
+ if (position < in.length)
+ {
+ System.arraycopy(in, position, tmp, index,
+ in.length - position);
+ }
+
+ return tmp;
+ }
+
+ /**
+ * Delete
+ *
+ * @param in
+ * @param from
+ * @param to
+ * @return
+ */
+ public static final char[] deleteChars(char[] in, int from, int to)
+ {
+ if (from >= in.length)
+ {
+ return in;
+ }
+
+ char[] tmp;
+
+ if (to >= in.length)
+ {
+ tmp = new char[from];
+ System.arraycopy(in, 0, tmp, 0, from);
+ to = in.length;
+ }
+ else
+ {
+ tmp = new char[in.length - to + from];
+ System.arraycopy(in, 0, tmp, 0, from);
+ System.arraycopy(in, to, tmp, from, in.length - to);
+ }
+ return tmp;
+ }
+
+ /**
+ * Returns the last part of 'input' after the last occurrence of 'token'. For
+ * example to extract only the filename from a full path or URL.
+ *
+ * @param input
+ * @param token
+ * a delimiter which must be in regular expression format
+ * @return
+ */
+ public static String getLastToken(String input, String token)
+ {
+ if (input == null)
+ {
+ return null;
+ }
+ if (token == null)
+ {
+ return input;
+ }
+ String[] st = input.split(token);
+ return st[st.length - 1];
+ }
+
+ /**
+ * Parses the input string into components separated by the delimiter. Unlike
+ * String.split(), this method will ignore occurrences of the delimiter which
+ * are nested within single quotes in name-value pair values, e.g. a='b,c'.
+ *
+ * @param input
+ * @param delimiter
+ * @return elements separated by separator
+ */
+ public static String[] separatorListToArray(String input, String delimiter)
+ {
+ int seplen = delimiter.length();
+ if (input == null || input.equals("") || input.equals(delimiter))
+ {
+ return null;
+ }
+ List<String> jv = new ArrayList<String>();
+ int cp = 0, pos, escape;
+ boolean wasescaped = false, wasquoted = false;
+ String lstitem = null;
+ while ((pos = input.indexOf(delimiter, cp)) >= cp)
+ {
+ escape = (pos > 0 && input.charAt(pos - 1) == '\\') ? -1 : 0;
+ if (wasescaped || wasquoted)
+ {
+ // append to previous pos
+ jv.set(jv.size() - 1,
+ lstitem = lstitem + delimiter
+ + input.substring(cp, pos + escape));
+ }
+ else
+ {
+ jv.add(lstitem = input.substring(cp, pos + escape));
+ }
+ cp = pos + seplen;
+ wasescaped = escape == -1;
+ // last separator may be in an unmatched quote
+ wasquoted = DELIMITERS_PATTERN.matcher(lstitem).matches();
+ }
+ if (cp < input.length())
+ {
+ String c = input.substring(cp);
+ if (wasescaped || wasquoted)
+ {
+ // append final separator
+ jv.set(jv.size() - 1, lstitem + delimiter + c);
+ }
+ else
+ {
+ if (!c.equals(delimiter))
+ {
+ jv.add(c);
+ }
+ }
+ }
+ if (jv.size() > 0)
+ {
+ String[] v = jv.toArray(new String[jv.size()]);
+ jv.clear();
+ if (DEBUG)
+ {
+ System.err.println("Array from '" + delimiter
+ + "' separated List:\n" + v.length);
+ for (int i = 0; i < v.length; i++)
+ {
+ System.err.println("item " + i + " '" + v[i] + "'");
+ }
+ }
+ return v;
+ }
+ if (DEBUG)
+ {
+ System.err.println("Empty Array from '" + delimiter
+ + "' separated List");
+ }
+ return null;
+ }
+
+ /**
+ * Returns a string which contains the list elements delimited by the
+ * separator. Null items are ignored. If the input is null or has length zero,
+ * a single delimiter is returned.
+ *
+ * @param list
+ * @param separator
+ * @return concatenated string
+ */
+ public static String arrayToSeparatorList(String[] list, String separator)
+ {
+ StringBuffer v = new StringBuffer();
+ if (list != null && list.length > 0)
+ {
+ for (int i = 0, iSize = list.length; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ if (v.length() > 0)
+ {
+ v.append(separator);
+ }
+ // TODO - escape any separator values in list[i]
+ v.append(list[i]);
+ }
+ }
+ if (DEBUG)
+ {
+ System.err.println("Returning '" + separator
+ + "' separated List:\n");
+ System.err.println(v);
+ }
+ return v.toString();
+ }
+ if (DEBUG)
+ {
+ System.err.println("Returning empty '" + separator
+ + "' separated List\n");
+ }
+ return "" + separator;
+ }
+}
*/
package jalview.viewmodel;
+import java.awt.Color;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeaturesDisplayedI;
+import jalview.api.ViewStyleI;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
+import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
+import jalview.structure.CommandListener;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
+import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
* @author jimp
*
*/
-public abstract class AlignmentViewport implements AlignViewportI
+public abstract class AlignmentViewport implements AlignViewportI,
+ ViewStyleI, CommandListener, VamsasSource
{
+ protected ViewStyleI viewStyle = new ViewStyle();
+
/**
- * alignment displayed in the viewport. Please use get/setter
+ * A viewport that hosts the cDna view of this (protein), or vice versa (if
+ * set).
*/
- protected AlignmentI alignment;
+ AlignViewportI codingComplement = null;
- protected String sequenceSetID;
+ FeaturesDisplayedI featuresDisplayed = null;
+
+ protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+
+ protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
/**
- * probably unused indicator that view is of a dataset rather than an
- * alignment
+ * @param name
+ * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
*/
- protected boolean isDataset = false;
+ public void setFontName(String name)
+ {
+ viewStyle.setFontName(name);
+ }
- private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+ /**
+ * @param style
+ * @see jalview.api.ViewStyleI#setFontStyle(int)
+ */
+ public void setFontStyle(int style)
+ {
+ viewStyle.setFontStyle(style);
+ }
- protected ColumnSelection colSel = new ColumnSelection();
+ /**
+ * @param size
+ * @see jalview.api.ViewStyleI#setFontSize(int)
+ */
+ public void setFontSize(int size)
+ {
+ viewStyle.setFontSize(size);
+ }
- public boolean autoCalculateConsensus = true;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontStyle()
+ */
+ public int getFontStyle()
+ {
+ return viewStyle.getFontStyle();
+ }
- protected boolean autoCalculateStrucConsensus = true;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontName()
+ */
+ public String getFontName()
+ {
+ return viewStyle.getFontName();
+ }
- protected boolean ignoreGapsInConsensusCalculation = false;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontSize()
+ */
+ public int getFontSize()
+ {
+ return viewStyle.getFontSize();
+ }
- protected ColourSchemeI globalColourScheme = null;
+ /**
+ * @param upperCasebold
+ * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
+ */
+ public void setUpperCasebold(boolean upperCasebold)
+ {
+ viewStyle.setUpperCasebold(upperCasebold);
+ }
/**
- * gui state - changes to colour scheme propagated to all groups
+ * @return
+ * @see jalview.api.ViewStyleI#isUpperCasebold()
*/
- private boolean colourAppliesToAllGroups;
+ public boolean isUpperCasebold()
+ {
+ return viewStyle.isUpperCasebold();
+ }
/**
- * @param value
- * indicating if subsequent colourscheme changes will be propagated
- * to all groups
+ * @return
+ * @see jalview.api.ViewStyleI#isSeqNameItalics()
+ */
+ public boolean isSeqNameItalics()
+ {
+ return viewStyle.isSeqNameItalics();
+ }
+
+ /**
+ * @param colourByReferenceSeq
+ * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
+ */
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+ {
+ viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
+ }
+
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
*/
public void setColourAppliesToAllGroups(boolean b)
{
- colourAppliesToAllGroups = b;
+ viewStyle.setColourAppliesToAllGroups(b);
}
/**
- *
- *
- * @return flag indicating if colourchanges propagated to all groups
+ * @return
+ * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
*/
public boolean getColourAppliesToAllGroups()
{
- return colourAppliesToAllGroups;
+ return viewStyle.getColourAppliesToAllGroups();
}
- boolean abovePIDThreshold = false;
-
/**
- * GUI state
- *
- * @return true if percent identity threshold is applied to shading
+ * @return
+ * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
*/
public boolean getAbovePIDThreshold()
{
- return abovePIDThreshold;
+ return viewStyle.getAbovePIDThreshold();
+ }
+
+ /**
+ * @param inc
+ * @see jalview.api.ViewStyleI#setIncrement(int)
+ */
+ public void setIncrement(int inc)
+ {
+ viewStyle.setIncrement(inc);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getIncrement()
+ */
+ public int getIncrement()
+ {
+ return viewStyle.getIncrement();
}
/**
- * GUI state
- *
- *
* @param b
- * indicate if percent identity threshold is applied to shading
+ * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
*/
- public void setAbovePIDThreshold(boolean b)
+ public void setConservationSelected(boolean b)
{
- abovePIDThreshold = b;
+ viewStyle.setConservationSelected(b);
}
- int threshold;
+ /**
+ * @param show
+ * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
+ */
+ public void setShowHiddenMarkers(boolean show)
+ {
+ viewStyle.setShowHiddenMarkers(show);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
+ */
+ public boolean getShowHiddenMarkers()
+ {
+ return viewStyle.getShowHiddenMarkers();
+ }
+
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
+ */
+ public void setScaleRightWrapped(boolean b)
+ {
+ viewStyle.setScaleRightWrapped(b);
+ }
+
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
+ */
+ public void setScaleLeftWrapped(boolean b)
+ {
+ viewStyle.setScaleLeftWrapped(b);
+ }
+
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
+ */
+ public void setScaleAboveWrapped(boolean b)
+ {
+ viewStyle.setScaleAboveWrapped(b);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
+ */
+ public boolean getScaleLeftWrapped()
+ {
+ return viewStyle.getScaleLeftWrapped();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
+ */
+ public boolean getScaleAboveWrapped()
+ {
+ return viewStyle.getScaleAboveWrapped();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleRightWrapped()
+ */
+ public boolean getScaleRightWrapped()
+ {
+ return viewStyle.getScaleRightWrapped();
+ }
+
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
+ */
+ public void setAbovePIDThreshold(boolean b)
+ {
+ viewStyle.setAbovePIDThreshold(b);
+ }
/**
- * DOCUMENT ME!
- *
* @param thresh
- * DOCUMENT ME!
+ * @see jalview.api.ViewStyleI#setThreshold(int)
*/
public void setThreshold(int thresh)
{
- threshold = thresh;
+ viewStyle.setThreshold(thresh);
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return
+ * @see jalview.api.ViewStyleI#getThreshold()
*/
public int getThreshold()
{
- return threshold;
+ return viewStyle.getThreshold();
}
- int increment;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowJVSuffix()
+ */
+ public boolean getShowJVSuffix()
+ {
+ return viewStyle.getShowJVSuffix();
+ }
/**
- *
- * @param inc
- * set the scalar for bleaching colourschemes according to degree of
- * conservation
+ * @param b
+ * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
*/
- public void setIncrement(int inc)
+ public void setShowJVSuffix(boolean b)
{
- increment = inc;
+ viewStyle.setShowJVSuffix(b);
}
/**
- * GUI State
- *
- * @return get scalar for bleaching colourschemes by conservation
+ * @param state
+ * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
*/
- public int getIncrement()
+ public void setWrapAlignment(boolean state)
{
- return increment;
+ viewStyle.setWrapAlignment(state);
}
- boolean conservationColourSelected = false;
+ /**
+ * @param state
+ * @see jalview.api.ViewStyleI#setShowText(boolean)
+ */
+ public void setShowText(boolean state)
+ {
+ viewStyle.setShowText(state);
+ }
/**
- * GUI state
- *
- * @return true if conservation based shading is enabled
+ * @param state
+ * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
*/
- public boolean getConservationSelected()
+ public void setRenderGaps(boolean state)
{
- return conservationColourSelected;
+ viewStyle.setRenderGaps(state);
}
/**
- * GUI state
- *
- * @param b
- * enable conservation based shading
+ * @return
+ * @see jalview.api.ViewStyleI#getColourText()
*/
- public void setConservationSelected(boolean b)
+ public boolean getColourText()
+ {
+ return viewStyle.getColourText();
+ }
+
+ /**
+ * @param state
+ * @see jalview.api.ViewStyleI#setColourText(boolean)
+ */
+ public void setColourText(boolean state)
+ {
+ viewStyle.setColourText(state);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getWrapAlignment()
+ */
+ public boolean getWrapAlignment()
+ {
+ return viewStyle.getWrapAlignment();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowText()
+ */
+ public boolean getShowText()
+ {
+ return viewStyle.getShowText();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getWrappedWidth()
+ */
+ public int getWrappedWidth()
+ {
+ return viewStyle.getWrappedWidth();
+ }
+
+ /**
+ * @param w
+ * @see jalview.api.ViewStyleI#setWrappedWidth(int)
+ */
+ public void setWrappedWidth(int w)
+ {
+ viewStyle.setWrappedWidth(w);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getCharHeight()
+ */
+ public int getCharHeight()
+ {
+ return viewStyle.getCharHeight();
+ }
+
+ /**
+ * @param h
+ * @see jalview.api.ViewStyleI#setCharHeight(int)
+ */
+ public void setCharHeight(int h)
+ {
+ viewStyle.setCharHeight(h);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getCharWidth()
+ */
+ public int getCharWidth()
+ {
+ return viewStyle.getCharWidth();
+ }
+
+ /**
+ * @param w
+ * @see jalview.api.ViewStyleI#setCharWidth(int)
+ */
+ public void setCharWidth(int w)
+ {
+ viewStyle.setCharWidth(w);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowBoxes()
+ */
+ public boolean getShowBoxes()
+ {
+ return viewStyle.getShowBoxes();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowUnconserved()
+ */
+ public boolean getShowUnconserved()
+ {
+ return viewStyle.getShowUnconserved();
+ }
+
+ /**
+ * @param showunconserved
+ * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
+ */
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ viewStyle.setShowUnconserved(showunconserved);
+ }
+
+ /**
+ * @param default1
+ * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
+ */
+ public void setSeqNameItalics(boolean default1)
+ {
+ viewStyle.setSeqNameItalics(default1);
+ }
+
+ /**
+ * @param selected
+ * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean)
+ */
+ public void setShowSeqFeaturesHeight(boolean selected)
+ {
+ viewStyle.setShowSeqFeaturesHeight(selected);
+ }
+
+ /**
+ * alignment displayed in the viewport. Please use get/setter
+ */
+ protected AlignmentI alignment;
+
+ @Override
+ public AlignmentI getAlignment()
{
- conservationColourSelected = b;
+ return alignment;
}
@Override
+ public char getGapCharacter()
+ {
+ return alignment.getGapCharacter();
+ }
+
+ protected String sequenceSetID;
+
+ /**
+ * probably unused indicator that view is of a dataset rather than an
+ * alignment
+ */
+ protected boolean isDataset = false;
+
+ public void setDataset(boolean b)
+ {
+ isDataset = b;
+ }
+
+ public boolean isDataset()
+ {
+ return isDataset;
+ }
+
+
+ private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+
+ protected ColumnSelection colSel = new ColumnSelection();
+
+ public boolean autoCalculateConsensus = true;
+
+ protected boolean autoCalculateStrucConsensus = true;
+
+ protected boolean ignoreGapsInConsensusCalculation = false;
+
+ protected ColourSchemeI globalColourScheme = null;
+
+
+ @Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
// TODO: logic refactored from AlignFrame changeColour -
|| cs instanceof Blosum62ColourScheme)
{
recalc = true;
- cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
+ cs.setThreshold(viewStyle.getThreshold(),
+ ignoreGapsInConsensusCalculation);
}
else
{
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
- sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
+ sg.cs.setThreshold(viewStyle.getThreshold(),
+ isIgnoreGapsConsensus());
recalc = true;
}
else
{
- sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, isIgnoreGapsConsensus());
}
if (getConservationSelected())
protected AlignmentAnnotation consensus;
+ protected AlignmentAnnotation complementConsensus;
+
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
protected Hashtable[] hconsensus = null;
/**
+ * results of cDNA complement consensus visible portion of view
+ */
+ protected Hashtable[] hcomplementConsensus = null;
+
+ /**
* results of secondary structure base pair consensus for visible portion of
* view
*/
public void setSequenceConsensusHash(Hashtable[] hconsensus)
{
this.hconsensus = hconsensus;
+ }
+ @Override
+ public void setComplementConsensusHash(Hashtable[] hconsensus)
+ {
+ this.hcomplementConsensus = hconsensus;
}
@Override
}
@Override
+ public Hashtable[] getComplementConsensusHash()
+ {
+ return hcomplementConsensus;
+ }
+
+ @Override
public Hashtable[] getRnaStructureConsensusHash()
{
return hStrucConsensus;
}
@Override
+ public AlignmentAnnotation getComplementConsensusAnnotation()
+ {
+ return complementConsensus;
+ }
+
+ @Override
public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
{
return strucConsensus;
{
calculator.registerWorker(new ConsensusThread(this, ap));
}
+
+ /*
+ * A separate thread to compute cDNA consensus for a protein alignment
+ */
+ final AlignmentI al = this.getAlignment();
+ if (!al.isNucleotide() && al.getCodonFrames() != null
+ && !al.getCodonFrames().isEmpty())
+ {
+ if (calculator
+ .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ {
+ calculator.registerWorker(new ComplementConsensusThread(this, ap));
+ }
+ }
}
// --------START Structure Conservation
// annotation update method from alignframe to viewport
this.showSequenceLogo = showSequenceLogo;
calculator.updateAnnotationFor(ConsensusThread.class);
+ calculator.updateAnnotationFor(ComplementConsensusThread.class);
calculator.updateAnnotationFor(StrucConsensusThread.class);
}
this.showSequenceLogo = showSequenceLogo;
return this.showConsensusHistogram;
}
- /**
- * show non-conserved residues only
- */
- protected boolean showUnconserved = false;
-
- /**
- * when set, updateAlignment will always ensure sequences are of equal length
- */
- private boolean padGaps = false;
-
- /**
- * when set, alignment should be reordered according to a newly opened tree
- */
- public boolean sortByTree = false;
-
- public boolean getShowUnconserved()
- {
- return showUnconserved;
- }
-
- public void setShowUnconserved(boolean showunconserved)
- {
- showUnconserved = showunconserved;
- }
+ /**
+ * when set, updateAlignment will always ensure sequences are of equal length
+ */
+ private boolean padGaps = false;
/**
- * @param showNonconserved
- * the showUnconserved to set
+ * when set, alignment should be reordered according to a newly opened tree
*/
- public void setShowunconserved(boolean displayNonconserved)
- {
- this.showUnconserved = displayNonconserved;
- }
+ public boolean sortByTree = false;
+
/**
*
*/
protected String viewId = null;
+ @Override
public String getViewId()
{
if (viewId == null)
}
@Override
- public boolean getIgnoreGapsConsensus()
+ public boolean isIgnoreGapsConsensus()
{
return ignoreGapsInConsensusCalculation;
}
protected boolean showConsensus = true;
- Hashtable sequenceColours;
+ private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+
+ protected SequenceAnnotationOrder sortAnnotationsBy = null;
+
+ protected boolean showAutocalculatedAbove;
/**
* Property change listener for changes in alignment
}
@Override
- public abstract void sendSelection();
-
- @Override
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth());
AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
for (int i = 0; i < sequences.length; i++)
{
- sequences[i] = new Sequence(sequences[i], annots); // construct new
- // sequence with
- // subset of visible
- // annotation
+ // construct new sequence with subset of visible annotation
+ sequences[i] = new Sequence(sequences[i], annots);
}
}
else
@Override
- public jalview.datamodel.CigarArray getViewAsCigars(
+ public CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
- return new jalview.datamodel.CigarArray(alignment, colSel,
+ return new CigarArray(alignment, colSel,
(selectedRegionOnly ? selectionGroup : null));
}
@Override
- public int[][] getVisibleRegionBoundaries(int min, int max)
+ public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
- Vector regions = new Vector();
+ ArrayList<int[]> regions = new ArrayList<int[]>();
int start = min;
int end = max;
}
}
- regions.addElement(new int[]
+ regions.add(new int[]
{ start, end });
if (colSel != null && colSel.hasHiddenColumns())
int[][] startEnd = new int[regions.size()][2];
- regions.copyInto(startEnd);
-
- return startEnd;
-
+ return regions;
}
@Override
{
initRNAStructure();
}
- initConsensus();
+ consensus = new AlignmentAnnotation("Consensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ initConsensus(consensus);
+
+ initComplementConsensus();
}
}
- private void initConsensus()
+ /**
+ * If this is a protein alignment and there are mappings to cDNA, add the cDNA
+ * consensus annotation.
+ */
+ protected void initComplementConsensus()
{
+ if (!alignment.isNucleotide())
+ {
+ final Set<AlignedCodonFrame> codonMappings = alignment
+ .getCodonFrames();
+ if (codonMappings != null && !codonMappings.isEmpty())
+ {
+ complementConsensus = new AlignmentAnnotation("cDNA Consensus",
+ "PID for cDNA", new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
+ initConsensus(complementConsensus);
+ }
+ }
+ }
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
+ private void initConsensus(AlignmentAnnotation aa)
+ {
+ aa.hasText = true;
+ aa.autoCalculated = true;
if (showConsensus)
{
- alignment.addAnnotation(consensus);
+ alignment.addAnnotation(aa);
}
}
public int calcPanelHeight()
{
// setHeight of panels
- AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
+ AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
int height = 0;
int charHeight = getCharHeight();
- if (aa != null)
+ if (anns != null)
{
BitSet graphgrp = new BitSet();
- for (int i = 0; i < aa.length; i++)
+ for (AlignmentAnnotation aa : anns)
{
- if (aa[i] == null)
+ if (aa == null)
{
System.err.println("Null annotation row: ignoring.");
continue;
}
- if (!aa[i].visible)
+ if (!aa.visible)
{
continue;
}
- if (aa[i].graphGroup > -1)
+ if (aa.graphGroup > -1)
{
- if (graphgrp.get(aa[i].graphGroup))
+ if (graphgrp.get(aa.graphGroup))
{
continue;
}
else
{
- graphgrp.set(aa[i].graphGroup);
+ graphgrp.set(aa.graphGroup);
}
}
- aa[i].height = 0;
+ aa.height = 0;
- if (aa[i].hasText)
+ if (aa.hasText)
{
- aa[i].height += charHeight;
+ aa.height += charHeight;
}
- if (aa[i].hasIcons)
+ if (aa.hasIcons)
{
- aa[i].height += 16;
+ aa.height += 16;
}
- if (aa[i].graph > 0)
+ if (aa.graph > 0)
{
- aa[i].height += aa[i].graphHeight;
+ aa.height += aa.graphHeight;
}
- if (aa[i].height == 0)
+ if (aa.height == 0)
{
- aa[i].height = 20;
+ aa.height = 20;
}
- height += aa[i].height;
+ height += aa.height;
}
}
if (height == 0)
}
oldrfs.clear();
}
- /**
- * show the reference sequence in the alignment view
- */
- private boolean displayReferenceSeq=false;
- /**
- * colour according to the reference sequence defined on the alignment
- */
- private boolean colourByReferenceSeq=false;
-
@Override
public boolean isDisplayReferenceSeq()
{
- return alignment.hasSeqrep() && displayReferenceSeq;
+ return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
}
@Override
public void setDisplayReferenceSeq(boolean displayReferenceSeq)
{
- this.displayReferenceSeq = displayReferenceSeq;
+ viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
}
+ @Override
public boolean isColourByReferenceSeq()
{
- return alignment.hasSeqrep() && colourByReferenceSeq;
- }
-
- public void setColourByReferenceSeq(boolean colourByReferenceSeq)
- {
- this.colourByReferenceSeq = colourByReferenceSeq;
+ return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
}
@Override
public Color getSequenceColour(SequenceI seq)
{
- Color sqc = Color.white;
- if (sequenceColours != null)
- {
- sqc = (Color) sequenceColours.get(seq);
- if (sqc == null)
- {
- sqc = Color.white;
- }
- }
- return sqc;
+ Color sqc = sequenceColours.get(seq);
+ return (sqc == null ? Color.white : sqc);
}
@Override
public void setSequenceColour(SequenceI seq, Color col)
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
if (col == null)
{
sequenceColours.remove(seq);
@Override
public void updateSequenceIdColours()
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
for (SequenceGroup sg : alignment.getGroups())
{
if (sg.idColour != null)
@Override
public void clearSequenceColours()
{
- sequenceColours = null;
+ sequenceColours.clear();
};
- FeaturesDisplayedI featuresDisplayed = null;
+ @Override
+ public AlignViewportI getCodingComplement()
+ {
+ return this.codingComplement;
+ }
+
+ /**
+ * Set this as the (cDna/protein) complement of the given viewport. Also
+ * ensures the reverse relationship is set on the given viewport.
+ */
+ @Override
+ public void setCodingComplement(AlignViewportI av)
+ {
+ if (this == av)
+ {
+ System.err.println("Ignoring recursive setCodingComplement request");
+ }
+ else
+ {
+ this.codingComplement = av;
+ // avoid infinite recursion!
+ if (av.getCodingComplement() != this)
+ {
+ av.setCodingComplement(this);
+ }
+ }
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ return getAlignment() == null ? false : getAlignment().isNucleotide();
+ }
@Override
public FeaturesDisplayedI getFeaturesDisplayed()
}
/**
- * display setting for showing/hiding sequence features on alignment view
- */
- boolean showSequenceFeatures = false;
-
- /**
* set the flag
*
* @param b
@Override
public void setShowSequenceFeatures(boolean b)
{
- showSequenceFeatures = b;
+ viewStyle.setShowSequenceFeatures(b);
}
@Override
public boolean isShowSequenceFeatures()
{
- return showSequenceFeatures;
+ return viewStyle.isShowSequenceFeatures();
}
- boolean showSeqFeaturesHeight;
-
@Override
public void setShowSequenceFeaturesHeight(boolean selected)
{
- showSeqFeaturesHeight = selected;
+ viewStyle.setShowSeqFeaturesHeight(selected);
}
@Override
public boolean isShowSequenceFeaturesHeight()
{
- return showSeqFeaturesHeight;
+ return viewStyle.isShowSequenceFeaturesHeight();
}
- private boolean showAnnotation = true;
-
- private boolean rightAlignIds = false;
@Override
public void setShowAnnotation(boolean b)
{
- showAnnotation = b;
+ viewStyle.setShowAnnotation(b);
}
@Override
public boolean isShowAnnotation()
{
- return showAnnotation;
+ return viewStyle.isShowAnnotation();
}
@Override
public boolean isRightAlignIds()
{
- return rightAlignIds;
+ return viewStyle.isRightAlignIds();
}
@Override
public void setRightAlignIds(boolean rightAlignIds)
{
- this.rightAlignIds = rightAlignIds;
+ viewStyle.setRightAlignIds(rightAlignIds);
+ }
+
+ @Override
+ public boolean getConservationSelected()
+ {
+ return viewStyle.getConservationSelected();
+ }
+
+ @Override
+ public void setShowBoxes(boolean state)
+ {
+ viewStyle.setShowBoxes(state);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getTextColour()
+ */
+ public Color getTextColour()
+ {
+ return viewStyle.getTextColour();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getTextColour2()
+ */
+ public Color getTextColour2()
+ {
+ return viewStyle.getTextColour2();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getThresholdTextColour()
+ */
+ public int getThresholdTextColour()
+ {
+ return viewStyle.getThresholdTextColour();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isConservationColourSelected()
+ */
+ public boolean isConservationColourSelected()
+ {
+ return viewStyle.isConservationColourSelected();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isRenderGaps()
+ */
+ public boolean isRenderGaps()
+ {
+ return viewStyle.isRenderGaps();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowColourText()
+ */
+ public boolean isShowColourText()
+ {
+ return viewStyle.isShowColourText();
+ }
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()
+ */
+ public boolean isShowSeqFeaturesHeight()
+ {
+ return viewStyle.isShowSeqFeaturesHeight();
+ }
+
+ /**
+ * @param conservationColourSelected
+ * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
+ */
+ public void setConservationColourSelected(
+ boolean conservationColourSelected)
+ {
+ viewStyle.setConservationColourSelected(conservationColourSelected);
+ }
+
+ /**
+ * @param showColourText
+ * @see jalview.api.ViewStyleI#setShowColourText(boolean)
+ */
+ public void setShowColourText(boolean showColourText)
+ {
+ viewStyle.setShowColourText(showColourText);
+ }
+
+ /**
+ * @param textColour
+ * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
+ */
+ public void setTextColour(Color textColour)
+ {
+ viewStyle.setTextColour(textColour);
+ }
+
+ /**
+ * @param thresholdTextColour
+ * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
+ */
+ public void setThresholdTextColour(int thresholdTextColour)
+ {
+ viewStyle.setThresholdTextColour(thresholdTextColour);
+ }
+
+ /**
+ * @param textColour2
+ * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
+ */
+ public void setTextColour2(Color textColour2)
+ {
+ viewStyle.setTextColour2(textColour2);
+ }
+
+ @Override
+ public ViewStyleI getViewStyle()
+ {
+ return new ViewStyle(viewStyle);
+ }
+
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
+ {
+ viewStyle = new ViewStyle(settingsForView);
+ }
+
+ @Override
+ public boolean sameStyle(ViewStyleI them)
+ {
+ return viewStyle.sameStyle(them);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getIdWidth()
+ */
+ public int getIdWidth()
+ {
+ return viewStyle.getIdWidth();
+ }
+
+ /**
+ * @param i
+ * @see jalview.api.ViewStyleI#setIdWidth(int)
+ */
+ public void setIdWidth(int i)
+ {
+ viewStyle.setIdWidth(i);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isCentreColumnLabels()
+ */
+ public boolean isCentreColumnLabels()
+ {
+ return viewStyle.isCentreColumnLabels();
+ }
+
+ /**
+ * @param centreColumnLabels
+ * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
+ */
+ public void setCentreColumnLabels(boolean centreColumnLabels)
+ {
+ viewStyle.setCentreColumnLabels(centreColumnLabels);
+ }
+
+ /**
+ * @param showdbrefs
+ * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
+ */
+ public void setShowDBRefs(boolean showdbrefs)
+ {
+ viewStyle.setShowDBRefs(showdbrefs);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowDBRefs()
+ */
+ public boolean isShowDBRefs()
+ {
+ return viewStyle.isShowDBRefs();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowNPFeats()
+ */
+ public boolean isShowNPFeats()
+ {
+ return viewStyle.isShowNPFeats();
+ }
+
+ /**
+ * @param shownpfeats
+ * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
+ */
+ public void setShowNPFeats(boolean shownpfeats)
+ {
+ viewStyle.setShowNPFeats(shownpfeats);
+ }
+
+ public abstract StructureSelectionManager getStructureSelectionManager();
+
+ /**
+ * Add one command to the command history list.
+ *
+ * @param command
+ */
+ public void addToHistoryList(CommandI command)
+ {
+ if (this.historyList != null)
+ {
+ this.historyList.push(command);
+ broadcastCommand(command, false);
+ }
+ }
+
+ protected void broadcastCommand(CommandI command, boolean undo)
+ {
+ getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
+ }
+
+ /**
+ * Add one command to the command redo list.
+ *
+ * @param command
+ */
+ public void addToRedoList(CommandI command)
+ {
+ if (this.redoList != null)
+ {
+ this.redoList.push(command);
+ }
+ broadcastCommand(command, true);
+ }
+
+ /**
+ * Clear the command redo list.
+ */
+ public void clearRedoList()
+ {
+ if (this.redoList != null)
+ {
+ this.redoList.clear();
+ }
+ }
+
+ public void setHistoryList(Deque<CommandI> list)
+ {
+ this.historyList = list;
+ }
+
+ public Deque<CommandI> getHistoryList()
+ {
+ return this.historyList;
+ }
+
+ public void setRedoList(Deque<CommandI> list)
+ {
+ this.redoList = list;
+ }
+
+ public Deque<CommandI> getRedoList()
+ {
+ return this.redoList;
+ }
+
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ return this;
+ }
+
+ public SequenceAnnotationOrder getSortAnnotationsBy()
+ {
+ return sortAnnotationsBy;
}
+ public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ {
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
+
+ public boolean isShowAutocalculatedAbove()
+ {
+ return showAutocalculatedAbove;
+ }
+
+ public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
+ }
}
ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
SequenceFeature[] features = sequence.getSequenceFeatures();
- while (features == null && sequence.getDatasetSequence() != null)
- {
- sequence = sequence.getDatasetSequence();
- features = sequence.getSequenceFeatures();
- }
-
if (features != null)
{
for (int i = 0; i < features.length; i++)
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceI asq = alignment.getSequenceAt(i);
- SequenceI dasq = asq.getDatasetSequence();
- SequenceFeature[] features = dasq != null ? dasq
- .getSequenceFeatures() : asq.getSequenceFeatures();
+ SequenceFeature[] features = asq.getSequenceFeatures();
if (features == null)
{
--- /dev/null
+package jalview.viewmodel.styles;
+
+import jalview.api.ViewStyleI;
+
+import java.awt.Color;
+import java.lang.reflect.Method;
+import java.util.HashMap;
+
+/**
+ * A container for holding alignment view properties. View properties are
+ * data-independent, which means they can be safely copied between views
+ * involving different alignment data without causing exceptions in the
+ * rendering system.
+ *
+ * @author jprocter
+ *
+ */
+public class ViewStyle implements ViewStyleI
+{
+
+ private boolean abovePIDThreshold = false;
+
+ int charHeight;
+
+ int charWidth;
+
+ int idWidth = -1;
+
+ /**
+ * gui state - changes to colour scheme propagated to all groups
+ */
+ private boolean colourAppliesToAllGroups;
+
+ /**
+ * centre columnar annotation labels in displayed alignment annotation
+ */
+ boolean centreColumnLabels = false;
+
+ private boolean showdbrefs;
+
+ private boolean shownpfeats;
+
+ // --------END Structure Conservation
+
+ /**
+ * colour according to the reference sequence defined on the alignment
+ */
+ private boolean colourByReferenceSeq = false;
+
+ boolean conservationColourSelected = false;
+
+ /**
+ * show the reference sequence in the alignment view
+ */
+ private boolean displayReferenceSeq = false;
+
+ private int increment;
+
+ /**
+ * display gap characters
+ */
+ boolean renderGaps = true;
+
+ private boolean rightAlignIds = false;
+
+ boolean scaleAboveWrapped = false;
+
+ boolean scaleLeftWrapped = true;
+
+ boolean scaleRightWrapped = true;
+
+ boolean seqNameItalics;
+
+ /**
+ * show annotation tracks on the alignment
+ */
+ private boolean showAnnotation = true;
+
+ /**
+ * render each residue in a coloured box
+ */
+ boolean showBoxes = true;
+
+ /**
+ * Colour sequence text
+ */
+ boolean showColourText = false;
+
+ /**
+ * show blue triangles
+ */
+ boolean showHiddenMarkers = true;
+
+ /**
+ * show /start-end in ID panel
+ */
+ boolean showJVSuffix = true;
+
+ /**
+ * scale features height according to score
+ */
+ boolean showSeqFeaturesHeight;
+
+ /**
+ * display setting for showing/hiding sequence features on alignment view
+ */
+ boolean showSequenceFeatures = false;
+
+ /**
+ * display sequence symbols
+ */
+ boolean showText = true;
+
+ /**
+ * show non-conserved residues only
+ */
+ protected boolean showUnconserved = false;
+
+ Color textColour = Color.black;
+
+ Color textColour2 = Color.white;
+
+ /**
+ * PID or consensus threshold
+ */
+ int threshold;
+
+ /**
+ * threshold for switching between textColour & textColour2
+ */
+ int thresholdTextColour = 0;
+
+ /**
+ * upper case characters in sequence are shown in bold
+ */
+ boolean upperCasebold = false;
+
+ /**
+ * name of base font for view
+ */
+ private String fontName;
+ /**
+ * size for base font
+ */
+ private int fontSize;
+
+ public ViewStyle(ViewStyleI viewStyle)
+ {
+ ViewStyle.configureFrom(this, viewStyle);
+ }
+
+ public ViewStyle()
+ {
+ }
+
+ private static HashMap<String, Method> getters, isErs, setters;
+ static
+ {
+ getters = new HashMap<String, Method>();
+ isErs = new HashMap<String, Method>();
+ setters = new HashMap<String, Method>();
+ // Match Getters and Setters
+ for (Method m : ViewStyleI.class.getMethods())
+ {
+ if (m.getDeclaringClass() == ViewStyleI.class)
+ {
+ if (m.getName().startsWith("get"))
+ {
+ getters.put(m.getName().substring(3), m);
+ }
+ if (m.getName().startsWith("is"))
+ {
+ isErs.put(m.getName().substring(2), m);
+ }
+ if (m.getName().startsWith("set"))
+ {
+ setters.put(m.getName().substring(3), m);
+ }
+ }
+ }
+ }
+
+ private static void configureFrom(ViewStyle us, ViewStyleI viewStyle)
+ {
+ // try and do the set thing
+ for (String prop : setters.keySet())
+ {
+ Method getter = getters.get(prop);
+ Method setter = setters.get(prop);
+ if (getter == null)
+ {
+ getter = isErs.get(prop);
+ }
+ if (getter != null && setter != null)
+ {
+ try
+ {
+ setter.invoke(us, getter.invoke(viewStyle));
+ } catch (Exception q)
+ {
+ System.err.println("Unexpected exception setting view property "
+ + prop + " by reflection");
+ q.printStackTrace();
+ }
+
+ }
+ }
+ }
+
+ private static boolean equivalent(ViewStyle us, ViewStyleI them)
+ {
+ // look for properties we can set
+ for (String prop : setters.keySet())
+ {
+ Method getter = getters.get(prop);
+ if (getter == null)
+ {
+ getter = isErs.get(prop);
+ }
+ if (getter != null)
+ {
+ try
+ {
+ if (!getter.invoke(them).equals(getter.invoke(us)))
+ {
+ return false;
+ }
+ } catch (Exception q)
+ {
+ System.err.println("Unexpected exception testing equivalence of property "
+ + prop + " by reflection");
+ q.printStackTrace();
+ }
+ }
+ }
+
+ return true;
+ }
+
+ public boolean equals(ViewStyleI other)
+ {
+ return other == null ? false : equivalent(this, other);
+ }
+
+ /**
+ * @return the upperCasebold
+ */
+ @Override
+ public boolean isUpperCasebold()
+ {
+ return upperCasebold;
+ }
+
+ /**
+ * @param upperCasebold
+ * the upperCasebold to set
+ */
+ @Override
+ public void setUpperCasebold(boolean upperCasebold)
+ {
+ this.upperCasebold = upperCasebold;
+ }
+
+ /**
+ * flag for wrapping
+ */
+ boolean wrapAlignment = false;
+
+ /**
+ * number columns in wrapped alignment
+ */
+ int wrappedWidth;
+
+ private int fontStyle;
+
+ /**
+ * GUI state
+ *
+ * @return true if percent identity threshold is applied to shading
+ */
+ @Override
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getCharHeight()
+ {
+ return charHeight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getCharWidth()
+ {
+ return charWidth;
+ }
+
+ /**
+ *
+ *
+ * @return flag indicating if colourchanges propagated to all groups
+ */
+ @Override
+ public boolean getColourAppliesToAllGroups()
+ {
+ return colourAppliesToAllGroups;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * GUI state
+ *
+ * @return true if conservation based shading is enabled
+ */
+ @Override
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ /**
+ * GUI State
+ *
+ * @return get scalar for bleaching colourschemes by conservation
+ */
+ @Override
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getScaleAboveWrapped()
+ {
+ return scaleAboveWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getScaleLeftWrapped()
+ {
+ return scaleLeftWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getScaleRightWrapped()
+ {
+ return scaleRightWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getShowBoxes()
+ {
+ return showBoxes;
+ }
+
+ @Override
+ public boolean getShowHiddenMarkers()
+ {
+ return showHiddenMarkers;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getShowJVSuffix()
+ {
+ return showJVSuffix;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getShowText()
+ {
+ return showText;
+ }
+
+ @Override
+ public boolean getShowUnconserved()
+ {
+ return showUnconserved;
+ }
+
+ /**
+ * @return the textColour
+ */
+ @Override
+ public Color getTextColour()
+ {
+ return textColour;
+ }
+
+ /**
+ * @return the textColour2
+ */
+ @Override
+ public Color getTextColour2()
+ {
+ return textColour2;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * @return the thresholdTextColour
+ */
+ @Override
+ public int getThresholdTextColour()
+ {
+ return thresholdTextColour;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public boolean getWrapAlignment()
+ {
+ return wrapAlignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getWrappedWidth()
+ {
+ return wrappedWidth;
+ }
+
+ @Override
+ public boolean isColourByReferenceSeq()
+ {
+ return colourByReferenceSeq;
+ }
+
+ /**
+ * @return the conservationColourSelected
+ */
+ @Override
+ public boolean isConservationColourSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ @Override
+ public boolean isDisplayReferenceSeq()
+ {
+ return displayReferenceSeq;
+ }
+
+ /**
+ * @return the renderGaps
+ */
+ @Override
+ public boolean isRenderGaps()
+ {
+ return renderGaps;
+ }
+
+ @Override
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ /**
+ * @return the seqNameItalics
+ */
+ @Override
+ public boolean isSeqNameItalics()
+ {
+ return seqNameItalics;
+ }
+
+ @Override
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ /**
+ * @return the showColourText
+ */
+ @Override
+ public boolean isShowColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * @return the showSeqFeaturesHeight
+ */
+ @Override
+ public boolean isShowSeqFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
+ }
+
+ @Override
+ public boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ @Override
+ public boolean isShowSequenceFeaturesHeight()
+ {
+
+ return showSeqFeaturesHeight;
+ }
+
+ /**
+ * GUI state
+ *
+ *
+ * @param b
+ * indicate if percent identity threshold is applied to shading
+ */
+ @Override
+ public void setAbovePIDThreshold(boolean b)
+ {
+ abovePIDThreshold = b;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param h
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setCharHeight(int h)
+ {
+ this.charHeight = h;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setCharWidth(int w)
+ {
+ this.charWidth = w;
+ }
+
+
+ /**
+ * @param value
+ * indicating if subsequent colourscheme changes will be propagated
+ * to all groups
+ */
+ @Override
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ colourAppliesToAllGroups = b;
+ }
+
+ @Override
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+ {
+ this.colourByReferenceSeq = colourByReferenceSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setColourText(boolean state)
+ {
+ showColourText = state;
+ }
+
+ /**
+ * @param conservationColourSelected
+ * the conservationColourSelected to set
+ */
+ @Override
+ public void setConservationColourSelected(
+ boolean conservationColourSelected)
+ {
+ this.conservationColourSelected = conservationColourSelected;
+ }
+
+ /**
+ * GUI state
+ *
+ * @param b
+ * enable conservation based shading
+ */
+ @Override
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+
+ @Override
+ public void setDisplayReferenceSeq(boolean displayReferenceSeq)
+ {
+ this.displayReferenceSeq = displayReferenceSeq;
+ }
+
+ /**
+ *
+ * @param inc
+ * set the scalar for bleaching colourschemes according to degree of
+ * conservation
+ */
+ @Override
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setRenderGaps(boolean state)
+ {
+ renderGaps = state;
+ }
+
+ @Override
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setScaleAboveWrapped(boolean b)
+ {
+ scaleAboveWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setScaleLeftWrapped(boolean b)
+ {
+ scaleLeftWrapped = b;
+ }
+
+ /**
+ *
+ *
+ * @param scaleRightWrapped
+ * - true or false
+ */
+
+ @Override
+ public void setScaleRightWrapped(boolean b)
+ {
+ scaleRightWrapped = b;
+ }
+
+ @Override
+ public void setSeqNameItalics(boolean italics)
+ {
+ seqNameItalics = italics;
+ }
+
+ @Override
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setShowBoxes(boolean state)
+ {
+ showBoxes = state;
+ }
+
+ /**
+ * @param showColourText
+ * the showColourText to set
+ */
+ @Override
+ public void setShowColourText(boolean showColourText)
+ {
+ this.showColourText = showColourText;
+ }
+
+ @Override
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setShowJVSuffix(boolean b)
+ {
+ showJVSuffix = b;
+ }
+
+ @Override
+ public void setShowSeqFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+
+ }
+
+ /**
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
+ */
+ @Override
+ public void setShowSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setShowText(boolean state)
+ {
+ showText = state;
+ }
+
+ @Override
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ showUnconserved = showunconserved;
+ }
+
+ /**
+ * @param textColour
+ * the textColour to set
+ */
+ @Override
+ public void setTextColour(Color textColour)
+ {
+ this.textColour = textColour;
+ }
+
+ /**
+ * @param textColour2
+ * the textColour2 to set
+ */
+ @Override
+ public void setTextColour2(Color textColour2)
+ {
+ this.textColour2 = textColour2;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thresh
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ /**
+ * @param thresholdTextColour
+ * the thresholdTextColour to set
+ */
+ @Override
+ public void setThresholdTextColour(int thresholdTextColour)
+ {
+ this.thresholdTextColour = thresholdTextColour;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setWrapAlignment(boolean state)
+ {
+ wrapAlignment = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setWrappedWidth(int w)
+ {
+ this.wrappedWidth = w;
+ }
+
+ @Override
+ public boolean sameStyle(ViewStyleI them)
+ {
+ return equivalent(this, them);
+ }
+
+ @Override
+ public String getFontName()
+ {
+ return fontName;
+ }
+
+ @Override
+ public int getFontSize()
+ {
+ return fontSize;
+ }
+
+ @Override
+ public int getFontStyle()
+ {
+ return fontStyle;
+ }
+
+ @Override
+ public void setFontName(String name)
+ {
+ fontName = name;
+ }
+
+ @Override
+ public void setFontSize(int size)
+ {
+ fontSize = size;
+
+ }
+
+ @Override
+ public void setFontStyle(int style)
+ {
+ fontStyle = style;
+ }
+
+ @Override
+ public int getIdWidth()
+ {
+ return idWidth;
+ }
+
+ /**
+ * @param idWidth
+ * the idWidth to set
+ */
+ @Override
+ public void setIdWidth(int idWidth)
+ {
+ this.idWidth = idWidth;
+ }
+
+ /**
+ * @return the centreColumnLabels
+ */
+ @Override
+ public boolean isCentreColumnLabels()
+ {
+ return centreColumnLabels;
+ }
+
+ /**
+ * @param centreColumnLabels
+ * the centreColumnLabels to set
+ */
+ @Override
+ public void setCentreColumnLabels(boolean centreColumnLabels)
+ {
+ this.centreColumnLabels = centreColumnLabels;
+ }
+
+ /**
+ * @return the showdbrefs
+ */
+ @Override
+ public boolean isShowDBRefs()
+ {
+ return showdbrefs;
+ }
+
+ /**
+ * @param showdbrefs
+ * the showdbrefs to set
+ */
+ @Override
+ public void setShowDBRefs(boolean showdbrefs)
+ {
+ this.showdbrefs = showdbrefs;
+ }
+
+ /**
+ * @return the shownpfeats
+ */
+ @Override
+ public boolean isShowNPFeats()
+ {
+ return shownpfeats;
+ }
+
+ /**
+ * @param shownpfeats
+ * the shownpfeats to set
+ */
+ @Override
+ public void setShowNPFeats(boolean shownpfeats)
+ {
+ this.shownpfeats = shownpfeats;
+ }
+}
*/
package jalview.workers;
+import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignCalcWorkerI;
+import jalview.datamodel.AlignmentAnnotation;
+
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
-import jalview.api.AlignCalcManagerI;
-import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentAnnotation;
-
public class AlignCalcManager implements AlignCalcManagerI
{
private volatile List<AlignCalcWorkerI> restartable = Collections
for (List<AlignCalcWorkerI> workers : updating.values())
{
for (AlignCalcWorkerI worker : workers)
+ {
if (worker.involves(alignmentAnnotation))
{
return true;
}
+ }
}
}
return false;
AlignCalcWorkerI[] workers;
synchronized (canUpdate)
{
- workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
+ workers = canUpdate.toArray(new AlignCalcWorkerI[canUpdate.size()]);
}
for (AlignCalcWorkerI worker : workers)
{
--- /dev/null
+package jalview.workers;
+
+import java.util.Hashtable;
+
+import jalview.analysis.AAFrequency;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+/**
+ * A thread to recompute the consensus of the cDNA complement for a linked
+ * protein alignment.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class ComplementConsensusThread extends ConsensusThread
+{
+
+ public ComplementConsensusThread(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ @Override
+ protected AlignmentAnnotation getConsensusAnnotation()
+ {
+ return alignViewport.getComplementConsensusAnnotation();
+ }
+
+ @Override
+ protected Hashtable[] getViewportConsensus()
+ {
+ return alignViewport.getComplementConsensusHash();
+ }
+
+ @Override
+ protected void computeConsensus(AlignmentI alignment)
+ {
+ Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+
+ SequenceI[] aseqs = getSequences();
+ AAFrequency.calculateCdna(alignment, hconsensus);
+
+ alignViewport.setComplementConsensusHash(hconsensus);
+ }
+
+ /**
+ * Convert the computed consensus data into the desired annotation for
+ * display.
+ *
+ * @param consensusAnnotation
+ * the annotation to be populated
+ * @param consensusData
+ * the computed consensus data
+ */
+ @Override
+ protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
+ Hashtable[] consensusData)
+ {
+ AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
+ alignViewport.isShowSequenceLogo(), getSequences().length);
+ }
+
+}
*/
package jalview.workers;
+import java.util.Hashtable;
+
import jalview.analysis.AAFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
-import java.util.Hashtable;
-
public class ConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
- private long nseq = -1;
-
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
long started = System.currentTimeMillis();
try
{
- AlignmentAnnotation consensus = alignViewport
- .getAlignmentConsensusAnnotation();
+ AlignmentAnnotation consensus = getConsensusAnnotation();
if (consensus == null || calcMan.isPending(this))
{
calcMan.workerComplete(this);
if (alignment == null || (aWidth = alignment.getWidth()) < 0)
{
calcMan.workerComplete(this);
- // .updatingConservation = false;
- // AlignViewport.UPDATING_CONSERVATION = false;
-
return;
}
- consensus = alignViewport.getAlignmentConsensusAnnotation();
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
- Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
- hconsensus = new Hashtable[aWidth];
- try
- {
- SequenceI aseqs[] = alignment.getSequencesArray();
- nseq = aseqs.length;
- AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
- true);
- } catch (ArrayIndexOutOfBoundsException x)
- {
- // this happens due to a race condition -
- // alignment was edited at same time as calculation was running
- //
- // calcMan.workerCannotRun(this);
- calcMan.workerComplete(this);
- return;
- }
- alignViewport.setSequenceConsensusHash(hconsensus);
+ eraseConsensus(aWidth);
+ computeConsensus(alignment);
updateResultAnnotation(true);
- ColourSchemeI globalColourScheme = alignViewport
- .getGlobalColourScheme();
- if (globalColourScheme != null)
+
+ if (ap != null)
{
- globalColourScheme.setConsensus(hconsensus);
+ ap.paintAlignment(true);
}
-
} catch (OutOfMemoryError error)
{
calcMan.workerCannotRun(this);
-
- // consensus = null;
- // hconsensus = null;
ap.raiseOOMWarning("calculating consensus", error);
+ } finally
+ {
+ /*
+ * e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
+ * - alignment was edited at same time as calculation was running
+ */
+ calcMan.workerComplete(this);
}
+ }
+
+ /**
+ * Clear out any existing consensus annotations
+ *
+ * @param aWidth
+ * the width (number of columns) of the annotated alignment
+ */
+ protected void eraseConsensus(int aWidth)
+ {
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ consensus.annotations = new Annotation[aWidth];
+ }
+
+ /**
+ * @param alignment
+ */
+ protected void computeConsensus(AlignmentI alignment)
+ {
+ Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+
+ SequenceI[] aseqs = getSequences();
+ AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
+ true);
- calcMan.workerComplete(this);
- if (ap != null)
+ alignViewport.setSequenceConsensusHash(hconsensus);
+ setColourSchemeConsensus(hconsensus);
+ }
+
+ /**
+ * @return
+ */
+ protected SequenceI[] getSequences()
+ {
+ return alignViewport.getAlignment().getSequencesArray();
+ }
+
+ /**
+ * @param hconsensus
+ */
+ protected void setColourSchemeConsensus(Hashtable[] hconsensus)
+ {
+ ColourSchemeI globalColourScheme = alignViewport
+ .getGlobalColourScheme();
+ if (globalColourScheme != null)
{
- ap.paintAlignment(true);
+ globalColourScheme.setConsensus(hconsensus);
}
}
/**
+ * Get the Consensus annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getConsensusAnnotation()
+ {
+ return alignViewport.getAlignmentConsensusAnnotation();
+ }
+
+ /**
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
public void updateResultAnnotation(boolean immediate)
{
- AlignmentAnnotation consensus = alignViewport
- .getAlignmentConsensusAnnotation();
- Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ Hashtable[] hconsensus = getViewportConsensus();
if (immediate || !calcMan.isWorking(this) && consensus != null
&& hconsensus != null)
{
- AAFrequency.completeConsensus(consensus, hconsensus, 0,
- hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo(), nseq);
+ deriveConsensus(consensus, hconsensus);
}
}
+
+ /**
+ * Convert the computed consensus data into the desired annotation for
+ * display.
+ *
+ * @param consensusAnnotation
+ * the annotation to be populated
+ * @param consensusData
+ * the computed consensus data
+ */
+ protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
+ Hashtable[] consensusData)
+ {
+ long nseq = getSequences().length;
+ AAFrequency.completeConsensus(consensusAnnotation, consensusData, 0,
+ consensusData.length, alignViewport.isIgnoreGapsConsensus(),
+ alignViewport.isShowSequenceLogo(), nseq);
+ }
+
+ /**
+ * Get the consensus data stored on the viewport.
+ *
+ * @return
+ */
+ protected Hashtable[] getViewportConsensus()
+ {
+ return alignViewport.getSequenceConsensusHash();
+ }
}
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
- alignViewport.getIgnoreGapsConsensus(),
+ alignViewport.isIgnoreGapsConsensus(),
alignViewport.isShowSequenceLogo(), nseq);
}
}
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
-import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+
+import java.util.LinkedHashSet;
+import java.util.Set;
public abstract class AWSThread extends Thread
{
/**
* dataset sequence relationships to be propagated onto new results
*/
- protected AlignedCodonFrame[] codonframe = null;
+ protected Set<AlignedCodonFrame> codonframe = null;
/**
* are there jobs still running in this thread.
*/
protected String WsUrl = null;
+ /*
+ * The AlignFrame from which the service was requested.
+ */
+ private AlignFrame alignFrame;
+
/**
* generic web service job/subjob poll loop
*/
} catch (Exception ex)
{
// Deal with Transaction exceptions
- wsInfo.appendProgressText(jobs[j].jobnum,
- MessageManager.formatMessage("info.server_exception", new String[]{WebServiceName,ex.getMessage()}));
+ wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
+ .formatMessage("info.server_exception", new Object[]
+ { WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
{
Cache.log
.debug("WebServiceJob poll loop finished with no jobs created.");
- wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
}
SequenceI[] alignment = al.getSequencesArray();
for (int sq = 0; sq < alignment.length; sq++)
{
- for (int i = 0; i < codonframe.length; i++)
+ for (AlignedCodonFrame acf : codonframe)
{
- if (codonframe[i] != null
- && codonframe[i].involvesSequence(alignment[sq]))
+ final SequenceI seq = alignment[sq];
+ if (acf != null && acf.involvesSequence(seq))
{
- al.addCodonFrame(codonframe[i]);
- codonframe[i] = null;
+ al.addCodonFrame(acf);
break;
}
}
AlignmentView alview, String wsurl2)
{
super();
- // this.alignFrame = alframe;
+ this.alignFrame = alframe;
currentView = alframe.getCurrentView().getAlignment();
featureSettings = alframe.getFeatureRenderer().getSettings();
defGapChar = alframe.getViewport().getGapCharacter();
WsUrl = wsurl2;
if (alframe != null)
{
- AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+ Set<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
.getCodonFrames();
if (cf != null)
{
- codonframe = new AlignedCodonFrame[cf.length];
- System.arraycopy(cf, 0, codonframe, 0, cf.length);
+ codonframe = new LinkedHashSet<AlignedCodonFrame>();
+ codonframe.addAll(cf);
}
}
}
+
+ protected AlignFrame getRequestingAlignFrame()
+ {
+ return this.alignFrame;
+ }
}
import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.http.params.BasicHttpParams;
import org.apache.http.params.CoreProtocolPNames;
+import org.apache.http.params.HttpConnectionParams;
import org.apache.http.params.HttpParams;
/**
* @throws Exception
*/
public static BufferedReader doHttpUrlPost(String postUrl,
- List<NameValuePair> vals) throws ClientProtocolException,
+ List<NameValuePair> vals, int connectionTimeoutMs,
+ int readTimeoutMs) throws ClientProtocolException,
IOException
{
+ // todo use HttpClient 4.3 or later and class RequestConfig
HttpParams params = new BasicHttpParams();
params.setParameter(CoreProtocolPNames.PROTOCOL_VERSION,
HttpVersion.HTTP_1_1);
+ if (connectionTimeoutMs > 0)
+ {
+ HttpConnectionParams
+ .setConnectionTimeout(params, connectionTimeoutMs);
+ }
+ if (readTimeoutMs > 0)
+ {
+ HttpConnectionParams.setSoTimeout(params, readTimeoutMs);
+ }
HttpClient httpclient = new DefaultHttpClient(params);
HttpPost httppost = new HttpPost(postUrl);
UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
*/
package jalview.ws;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
-
/**
* This is the the concrete implementation of the sequence retrieval interface
* and abstract class in jalview.ws.seqfetcher. This implements the run-time
addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
- addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
- // alignment is
- // 'default' for
- // PFAM
+ addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class);
+ // ensures Seed alignment is 'default' for PFAM
addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
if (addDas)
String db = dbSources[dbsource];
// skip me
if (db.equals(DBRefSource.PDB))
+ {
continue;
+ }
for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
{
System.out.println("Source: " + sp.getDbName() + " (" + db
System.out.println("ERROR:No alignment retrieved.");
StringBuffer raw = sp.getRawRecords();
if (raw != null)
+ {
System.out.println(raw.toString());
+ }
else
+ {
System.out.println("ERROR:No Raw results.");
+ }
}
else
{
--- /dev/null
+package jalview.ws.dbsources;
+
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.ws.rs.core.MediaType;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+import com.sun.jersey.api.client.Client;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.api.client.config.ClientConfig;
+import com.sun.jersey.api.client.config.DefaultClientConfig;
+import com.sun.jersey.api.json.JSONConfiguration;
+
+/**
+ * A rest client for querying the Search endpoing of the PDB REST API
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBRestClient
+{
+ private static String PDB_SEARCH_ENDPOINT = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
+
+ private static int DEFAULT_RESPONSE_SIZE = 200;
+
+ /**
+ * Takes a PDBRestRequest object and returns a response upon execution
+ *
+ * @param pdbRestRequest
+ * the PDBRestRequest instance to be processed
+ * @return the pdbResponse object for the given request
+ */
+ public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
+ {
+ ClientConfig clientConfig = new DefaultClientConfig();
+ clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
+ Boolean.TRUE);
+ Client client = Client.create(clientConfig);
+
+ String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
+ .getWantedFields());
+ int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+ : pdbRestRequest.getResponseSize();
+ String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
+ .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
+ .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
+ : " desc"));
+
+ // Build request parameters for the REST Request
+ WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
+ .queryParam("wt", "json").queryParam("fl", wantedFields)
+ .queryParam("rows", String.valueOf(responseSize))
+ .queryParam("q", pdbRestRequest.getQuery())
+ .queryParam("sort", sortParam);
+
+ // Execute the REST request
+ ClientResponse clientResponse = webResource.accept(
+ MediaType.APPLICATION_JSON).get(ClientResponse.class);
+
+ // Get the JSON string from the response object
+ String responseString = clientResponse.getEntity(String.class);
+
+ // Check the response status and report exception if one occurs
+ if (clientResponse.getStatus() != 200)
+ {
+ String errorMessage = "";
+ if (clientResponse.getStatus() == 400)
+ {
+ errorMessage = parseJsonExceptionString(responseString);
+ throw new RuntimeException(errorMessage);
+ }
+ else
+ {
+ errorMessage = "Failed : HTTP error code : "
+ + clientResponse.getStatus();
+ throw new RuntimeException(errorMessage);
+ }
+ }
+
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ clientResponse = null;
+ client = null;
+
+ // Process the response and return the result to the caller.
+ return parsePDBJsonResponse(responseString, pdbRestRequest);
+ }
+
+ /**
+ * Process error response from PDB server if/when one occurs.
+ *
+ * @param jsonResponse
+ * the JSON string containing error message from the server
+ * @return the processed error message from the JSON string
+ */
+ public static String parseJsonExceptionString(String jsonErrorResponse)
+ {
+ String errorMessage = "RunTime error";
+ try
+ {
+ JSONParser jsonParser = new JSONParser();
+ JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
+ JSONObject errorResponse = (JSONObject) jsonObj.get("error");
+ errorMessage = errorResponse.get("msg").toString();
+
+ JSONObject responseHeader = (JSONObject) jsonObj
+ .get("responseHeader");
+ errorMessage += responseHeader.get("params").toString();
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ }
+ return errorMessage;
+ }
+
+ /**
+ * Parses the JSON response string from PDB REST API. The response is dynamic
+ * hence, only fields specifically requested for in the 'wantedFields'
+ * parameter is fetched/processed
+ *
+ * @param pdbJsonResponseString
+ * the JSON string to be parsed
+ * @param pdbRestRequest
+ * the request object which contains parameters used to process the
+ * JSON string
+ * @return
+ */
+ @SuppressWarnings("unchecked")
+ public static PDBRestResponse parsePDBJsonResponse(
+ String pdbJsonResponseString, PDBRestRequest pdbRestRequest)
+ {
+ PDBRestResponse searchResult = new PDBRestResponse();
+ List<PDBResponseSummary> result = null;
+ try
+ {
+ JSONParser jsonParser = new JSONParser();
+ JSONObject jsonObj = (JSONObject) jsonParser
+ .parse(pdbJsonResponseString);
+
+ JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
+ String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
+ "QTime").toString();
+ int numFound = Integer
+ .valueOf(pdbResponse.get("numFound").toString());
+ if (numFound > 0)
+ {
+ result = new ArrayList<PDBResponseSummary>();
+ JSONArray docs = (JSONArray) pdbResponse.get("docs");
+ for (Iterator<JSONObject> docIter = docs.iterator(); docIter
+ .hasNext();)
+ {
+ JSONObject doc = docIter.next();
+ result.add(searchResult.new PDBResponseSummary(doc,
+ pdbRestRequest));
+ }
+ searchResult.setNumberOfItemsFound(numFound);
+ searchResult.setResponseTime(queryTime);
+ searchResult.setSearchSummary(result);
+ }
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ }
+ return searchResult;
+ }
+
+ /**
+ * Takes a collection of PDBDocField and converts its 'code' Field values into
+ * a comma delimited string.
+ *
+ * @param pdbDocfields
+ * the collection of PDBDocField to process
+ * @return the comma delimited string from the pdbDocFields collection
+ */
+ public static String getPDBDocFieldsAsCommaDelimitedString(
+ Collection<PDBDocField> pdbDocfields)
+ {
+ String result = "";
+ if (pdbDocfields != null && !pdbDocfields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (PDBDocField field : pdbDocfields)
+ {
+ returnedFields.append(",").append(field.getCode());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
+ /**
+ * Determines the column index for 'PDB Id' Fields in the dynamic summary
+ * table. The PDB Id serves as a unique identifier for a given row in the
+ * summary table
+ *
+ * @param wantedFeilds
+ * the available table columns in no particular order
+ * @return the pdb id field column index
+ */
+ public static int getPDBIdColumIndex(
+ Collection<PDBDocField> wantedFeilds, boolean hasRefSeq)
+ {
+
+ // If a reference sequence is attached then start counting from 1 else
+ // start from zero
+ int pdbFeildIndexCounter = hasRefSeq ? 1 : 0;
+
+ for (PDBDocField feild : wantedFeilds)
+ {
+ if (feild.equals(PDBDocField.PDB_ID))
+ {
+ break; // Once PDB Id index is determined exit iteration
+ }
+ ++pdbFeildIndexCounter;
+ }
+ return pdbFeildIndexCounter;
+ }
+
+ /**
+ * This enum represents the fields available in the PDB JSON response
+ *
+ */
+ public enum PDBDocField
+ {
+ PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
+ "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type",
+ "molecule_type"), MOLECULE_SEQUENCE("Sequence",
+ "molecule_sequence"), PFAM_ACCESSION("PFAM Accession",
+ "pfam_accession"), PFAM_NAME("PFAM Name", "pfam_name"), INTERPRO_NAME(
+ "InterPro Name", "interpro_name"), INTERPRO_ACCESSION(
+ "InterPro Accession", "interpro_accession"), UNIPROT_ID(
+ "UniProt Id", "uniprot_id"), UNIPROT_ACCESSION(
+ "UniProt Accession", "uniprot_accession"), UNIPROT_COVERAGE(
+ "UniProt Coverage", "uniprot_coverage"), UNIPROT_FEATURES(
+ "Uniprot Features", "uniprot_features"), R_FACTOR("R Factor",
+ "r_factor"), RESOLUTION("Resolution", "resolution"), DATA_QUALITY(
+ "Data Quality", "data_quality"), OVERALL_QUALITY(
+ "Overall Quality", "overall_quality"), POLYMER_COUNT(
+ "Number of Polymers", "number_of_polymers"), PROTEIN_CHAIN_COUNT(
+ "Number of Protein Chains", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
+ "Number of Bound Molecule", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
+ "Number of Polymer Residue", "number_of_polymer_residues"), GENUS(
+ "GENUS", "genus"), GENE_NAME("Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
+ "Experimental Method", "experimental_method"), GO_ID("GO Id",
+ "go_id"), ASSEMBLY_ID("Assembly Id", "assembly_form"), ASSEMBLY_FORM(
+ "Assembly Form", "assembly_id"), ASSEMBLY_TYPE("Assembly Type",
+ "assembly_type"), SPACE_GROUP("Space Group", "spacegroup"), CATH_CODE(
+ "Cath Code", "cath_code"), TAX_ID("Tax Id", "tax_id"), TAX_QUERY(
+ "Tax Query", "tax_query"), INTERACTING_ENTRY_ID(
+ "Interacting Entry Id", "interacting_entry_id"), INTERACTING_ENTITY_ID(
+ "Interacting Entity Id", "interacting_entity_id"), INTERACTING_MOLECULES(
+ "Interacting Molecules", "interacting_molecules"), PUBMED_ID(
+ "Pubmed Id", "pubmed_id"), STATUS("Status", "status"), MODEL_QUALITY(
+ "Model Quality", "model_quality"), PIVOT_RESOLUTION(
+ "Pivot Resolution", "pivot_resolution"), DATA_REDUCTION_SOFTWARE(
+ "Data reduction software", "data_reduction_software"), MAX_OBSERVED_RES(
+ "Max observed residues", "max_observed_residues"), ORG_SCI_NAME(
+ "Organism scientific name", "organism_scientific_name"), SUPER_KINGDOM(
+ "Super kingdom", "superkingdom"), RANK("Rank", "rank"), CRYSTALLISATION_PH(
+ "Crystallisation Ph", "crystallisation_ph"), BIOLOGICAL_FUNCTION(
+ "Biological Function", "biological_function"), BIOLOGICAL_PROCESS(
+ "Biological Process", "biological_process"), BIOLOGICAL_CELL_COMPONENT(
+ "Biological Cell Component", "biological_cell_component"), COMPOUND_NAME(
+ "Compound Name", "compound_name"), COMPOUND_ID("Compound Id",
+ "compound_id"), COMPOUND_WEIGHT("Compound Weight",
+ "compound_weight"), COMPOUND_SYSTEMATIC_NAME(
+ "Compound Systematic Name", "compound_systematic_name"), INTERACTING_LIG(
+ "Interacting Ligands", "interacting_ligands"), JOURNAL(
+ "Journal", "journal"), ALL_AUTHORS("All Authors", "all_authors"), EXPERIMENTAL_DATA_AVAILABLE(
+ "Experiment Data Available", "experiment_data_available"), DIFFRACTION_PROTOCOL(
+ "Diffraction Protocol", "diffraction_protocol"), REFINEMENT_SOFTWARE(
+ "Refinement Software", "refinement_software"), STRUCTURE_DETERMINATION_METHOD(
+ "Structure Determination Method",
+ "structure_determination_method"), SYNCHROTON_SITE(
+ "Synchrotron Site", "synchrotron_site"), SAMPLE_PREP_METHOD(
+ "Sample Preparation Method", "sample_preparation_method"), ENTRY_AUTHORS(
+ "Entry Authors", "entry_authors"), CITATION_TITLE(
+ "Citation Title", "citation_title"), STRUCTURE_SOLUTION_SOFTWARE(
+ "Structure Solution Software", "structure_solution_software"), ENTRY_ENTITY(
+ "Entry Entity", "entry_entity"), R_FREE("R Free", "r_free"), NO_OF_POLYMER_ENTITIES(
+ "Number of Polymer Entities", "number_of_polymer_entities"), NO_OF_BOUND_ENTITIES(
+ "Number of Bound Entities", "number_of_bound_entities"), CRYSTALLISATION_RESERVOIR(
+ "Crystallisation Reservoir", "crystallisation_reservoir"), DATA_SCALING_SW(
+ "Data Scalling Software", "data_scaling_software"), DETECTOR(
+ "Detector", "detector"), DETECTOR_TYPE("Detector Type",
+ "detector_type"), MODIFIED_RESIDUE_FLAG(
+ "Modified Residue Flag", "modified_residue_flag"), NUMBER_OF_COPIES(
+ "Number of Copies", "number_of_copies"), STRUCT_ASYM_ID(
+ "Struc Asym Id", "struct_asym_id"), HOMOLOGUS_PDB_ENTITY_ID(
+ "Homologus PDB Entity Id", "homologus_pdb_entity_id"), MOLECULE_SYNONYM(
+ "Molecule Synonym", "molecule_synonym"), DEPOSITION_SITE(
+ "Deposition Site", "deposition_site"), SYNCHROTRON_BEAMLINE(
+ "Synchrotron Beamline", "synchrotron_beamline"), ENTITY_ID(
+ "Entity Id", "entity_id"), BEAM_SOURCE_NAME("Beam Source Name",
+ "beam_source_name"), PROCESSING_SITE("Processing Site",
+ "processing_site"), ENTITY_WEIGHT("Entity Weight",
+ "entity_weight"), VERSION("Version", "_version_"), ALL("ALL",
+ "text");
+
+ private String name;
+
+ private String code;
+
+ PDBDocField(String name, String code)
+ {
+ this.name = name;
+ this.code = code;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public String toString()
+ {
+ return name;
+ }
+ }
+}
\ No newline at end of file
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.JpredAlignment;
return "calculating consensus secondary structure prediction using JPred service";
}
- private static HashMap<String, String[]> jpredRowLabels = new HashMap<String, String[]>();
+ private static Map<String, String[]> jpredRowLabels = new HashMap<String, String[]>();
- private static HashSet<String> jpredRes_graph, jpredRes_ssonly;
+ private static final Set<String> jpredRes_graph;
+
+ private static final Set<String> jpredRes_ssonly;
+ static
{
- jpredRes_ssonly = new HashSet();
+ jpredRes_ssonly = new HashSet<String>();
jpredRes_ssonly.add("jnetpred".toLowerCase());
jpredRes_ssonly.add("jnetpssm".toLowerCase());
jpredRes_ssonly.add("jnethmm".toLowerCase());
- jpredRes_graph = new HashSet();
+ jpredRes_graph = new HashSet<String>();
jpredRes_graph.add("jnetconf".toLowerCase());
jpredRes_graph.add("jnet burial".toLowerCase());
}
import jalview.analysis.AlignSeq;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.SplitFrame;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import java.util.Map;
import java.util.Vector;
+import javax.swing.JInternalFrame;
+
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
* @param presorder
* boolean
*/
- MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
+ private MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, AlignmentView alview,
String wsname, boolean subgaps, boolean presorder)
{
wsInfo.setProgressBar(null, progbar);
}
+ /**
+ * Display alignment results in a new frame (or - not currently supported -
+ * added to an existing alignment).
+ *
+ * @param newFrame
+ */
void displayResults(boolean newFrame)
{
// view input or result data for each block
- Vector alorders = new Vector();
+ List<AlignmentOrder> alorders = new ArrayList<AlignmentOrder>();
SequenceI[][] results = new SequenceI[jobs.length][];
AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
String lastProgram = null;
msjob = (MsaWSJob) jobs[j];
Object[] res = msjob.getAlignment();
lastProgram = msjob.getAlignmentProgram();
- alorders.add(res[1]);
+ alorders.add((AlignmentOrder) res[1]);
results[j] = (SequenceI[]) res[0];
orders[j] = (AlignmentOrder) res[1];
if (newFrame)
{
- AlignFrame af = new AlignFrame(al, columnselection,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ displayInNewFrame(al, alorders, columnselection);
- // initialise with same renderer settings as in parent alignframe.
- af.getFeatureRenderer().transferSettings(this.featureSettings);
- // update orders
- if (alorders.size() > 0)
- {
- if (alorders.size() == 1)
- {
- af.addSortByOrderMenuItem(WebServiceName + " Ordering",
- (AlignmentOrder) alorders.get(0));
- }
- else
- {
- // construct a non-redundant ordering set
- Vector names = new Vector();
- for (int i = 0, l = alorders.size(); i < l; i++)
- {
- String orderName = new String(" Region " + i);
- int j = i + 1;
+ }
+ else
+ {
+ System.out.println("MERGE WITH OLD FRAME");
+ // TODO: modify alignment in original frame, replacing old for new
+ // alignment using the commands.EditCommand model to ensure the update can
+ // be undone
+ }
+ }
- while (j < l)
- {
- if (((AlignmentOrder) alorders.get(i))
- .equals(((AlignmentOrder) alorders.get(j))))
- {
- alorders.remove(j);
- l--;
- orderName += "," + j;
- }
- else
- {
- j++;
- }
- }
+ /**
+ * Display the alignment result in a new frame.
+ *
+ * @param al
+ * @param alorders
+ * @param columnselection
+ */
+ protected void displayInNewFrame(AlignmentI al,
+ List<AlignmentOrder> alorders, ColumnSelection columnselection)
+ {
+ AlignFrame af = new AlignFrame(al, columnselection,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- if (i == 0 && j == 1)
- {
- names.add(new String(""));
- }
- else
- {
- names.add(orderName);
- }
- }
- for (int i = 0, l = alorders.size(); i < l; i++)
- {
- af.addSortByOrderMenuItem(
- WebServiceName + ((String) names.get(i)) + " Ordering",
- (AlignmentOrder) alorders.get(i));
- }
- }
+ // initialise with same renderer settings as in parent alignframe.
+ af.getFeatureRenderer().transferSettings(this.featureSettings);
+
+ if (alorders.size() > 0)
+ {
+ addSortByMenuItems(af, alorders);
+ }
+
+ /*
+ * If alignment was requested from one half of a SplitFrame, show in a
+ * SplitFrame with the other pane similarly aligned.
+ */
+ AlignFrame requestedBy = getRequestingAlignFrame();
+ if (requestedBy != null && requestedBy.getSplitViewContainer() != null)
+ {
+ AlignmentI complement = requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy);
+ String complementTitle = requestedBy.getSplitViewContainer()
+ .getComplementTitle(requestedBy);
+ AlignmentI copyComplement = new Alignment(complement);
+ copyComplement.alignAs(al);
+ if (copyComplement.getHeight() > 0)
+ {
+ af.setTitle(alTitle);
+ AlignFrame af2 = new AlignFrame(copyComplement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ af2.setTitle(complementTitle);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ JInternalFrame splitFrame = new SplitFrame(al.isNucleotide() ? af
+ : af2, al.isNucleotide() ? af2 : af);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+ return;
}
+ }
- Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ /*
+ * Not from SplitFrame, or failed to created a complementary alignment
+ */
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ /**
+ * Add sort order options to the AlignFrame menus.
+ *
+ * @param af
+ * @param alorders
+ */
+ protected void addSortByMenuItems(AlignFrame af,
+ List<AlignmentOrder> alorders)
+ {
+ // update orders
+ if (alorders.size() == 1)
+ {
+ af.addSortByOrderMenuItem(WebServiceName + " Ordering",
+ alorders.get(0));
}
else
{
- System.out.println("MERGE WITH OLD FRAME");
- // TODO: modify alignment in original frame, replacing old for new
- // alignment using the commands.EditCommand model to ensure the update can
- // be undone
+ // construct a non-redundant ordering set
+ List<String> names = new ArrayList<String>();
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ String orderName = " Region " + i;
+ int j = i + 1;
+
+ while (j < l)
+ {
+ if (alorders.get(i).equals(alorders.get(j)))
+ {
+ alorders.remove(j);
+ l--;
+ orderName += "," + j;
+ }
+ else
+ {
+ j++;
+ }
+ }
+
+ if (i == 0 && j == 1)
+ {
+ names.add("");
+ }
+ else
+ {
+ names.add(orderName);
+ }
+ }
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ af.addSortByOrderMenuItem(WebServiceName + (names.get(i))
+ + " Ordering", alorders.get(i));
+ }
}
}
*/
public abstract class InputType
{
+ private static final Pattern URL_PATTERN = Pattern.compile("^([^=]+)=?'?([^']*)?'?");
+
/**
* not used yet
*/
boolean valid = true;
for (String tok : tokenstring)
{
- Matcher mtch = Pattern.compile("^([^=]+)=?'?([^']*)?'?").matcher(tok);
+ Matcher mtch = URL_PATTERN.matcher(tok);
if (mtch.find())
{
try
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.ws.uimodel;
+
+
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+import java.util.Collection;
+
+/**
+ * Represents the PDB request to be consumed by the PDBRestClient
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBRestRequest
+{
+ private String fieldToSearchBy;
+
+ private String searchTerm;
+
+ private String fieldToSortBy;
+
+ private String associatedSequence;
+
+ private boolean allowEmptySequence;
+
+ private int responseSize;
+
+ private boolean isSortAscending;
+
+ private Collection<PDBDocField> wantedFields;// = new
+ // Collection<PDBDocField>();
+
+ public String getFieldToSearchBy()
+ {
+ return fieldToSearchBy;
+ }
+
+ public void setFieldToSearchBy(String fieldToSearchBy)
+ {
+ this.fieldToSearchBy = fieldToSearchBy;
+ }
+
+ public String getSearchTerm()
+ {
+ return searchTerm;
+ }
+
+ public void setSearchTerm(String searchTerm)
+ {
+ this.searchTerm = searchTerm;
+ }
+
+ public boolean isAllowEmptySeq()
+ {
+ return allowEmptySequence;
+ }
+
+ public void setAllowEmptySeq(boolean allowEmptySeq)
+ {
+ this.allowEmptySequence = allowEmptySeq;
+ }
+
+ public int getResponseSize()
+ {
+ return responseSize;
+ }
+
+ public void setResponseSize(int responseSize)
+ {
+ this.responseSize = responseSize;
+ }
+
+ public Collection<PDBDocField> getWantedFields()
+ {
+ return wantedFields;
+ }
+
+ public void setWantedFields(Collection<PDBDocField> wantedFields)
+ {
+ this.wantedFields = wantedFields;
+ }
+
+ public String getFieldToSortBy()
+ {
+ return fieldToSortBy;
+ }
+
+ public void setFieldToSortBy(String fieldToSortBy, boolean isSortAscending)
+ {
+ this.fieldToSortBy = fieldToSortBy;
+ this.isSortAscending = isSortAscending;
+ }
+
+ public boolean isAscending()
+ {
+ return isSortAscending;
+ }
+
+ public String getAssociatedSequence()
+ {
+ return associatedSequence;
+ }
+
+ public void setAssociatedSequence(String associatedSequence)
+ {
+ this.associatedSequence = associatedSequence;
+ }
+
+ public String getQuery()
+ {
+ return fieldToSearchBy + searchTerm
+ + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]");
+ }
+
+ public String toString()
+ {
+ return "Query : " + getQuery() + " sort field: " + fieldToSortBy
+ + " isAsc: " + isAscending() + " Associated Seq : "
+ + associatedSequence;
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.ws.uimodel;
+
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+import java.util.Collection;
+import java.util.Objects;
+
+import javax.swing.table.DefaultTableModel;
+
+import org.json.simple.JSONObject;
+
+/**
+ * Represents the response model produced by the PDBRestClient upon successful
+ * execution of a given request
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBRestResponse
+{
+ private int numberOfItemsFound;
+
+ private String responseTime;
+
+ private Collection<PDBResponseSummary> searchSummary;
+
+ public int getNumberOfItemsFound()
+ {
+ return numberOfItemsFound;
+ }
+
+ public void setNumberOfItemsFound(int itemFound)
+ {
+ this.numberOfItemsFound = itemFound;
+ }
+
+ public String getResponseTime()
+ {
+ return responseTime;
+ }
+
+ public void setResponseTime(String responseTime)
+ {
+ this.responseTime = responseTime;
+ }
+
+ public Collection<PDBResponseSummary> getSearchSummary()
+ {
+ return searchSummary;
+ }
+
+ public void setSearchSummary(Collection<PDBResponseSummary> searchSummary)
+ {
+ this.searchSummary = searchSummary;
+ }
+
+
+ /**
+ * Convenience method to obtain a Table model for a given summary List based
+ * on the request parameters
+ *
+ * @param request
+ * the PDBRestRequest object which holds useful information for
+ * creating a table model
+ * @param summariesList
+ * the summary list which contains the data for populating the
+ * table's rows
+ * @return the table model which was dynamically generated
+ */
+ public static DefaultTableModel getTableModel(PDBRestRequest request,
+ Collection<PDBResponseSummary> summariesList)
+ {
+ DefaultTableModel tableModel = new DefaultTableModel();
+
+ if (request.getAssociatedSequence() != null)
+ {
+ tableModel.addColumn("Sequence"); // Create sequence column header if
+ // exists in the request
+ }
+ for (PDBDocField field : request.getWantedFields())
+ {
+ tableModel.addColumn(field.getName()); // Create sequence column header if
+ // exists in the request
+ }
+
+ for (PDBResponseSummary res : summariesList)
+ {
+ tableModel.addRow(res.getSummaryData()); // Populate table rows with
+ // summary list
+ }
+
+ return tableModel;
+ }
+
+ /**
+ * Model for a unique response summary
+ *
+ */
+ public class PDBResponseSummary
+ {
+ private String pdbId;
+
+ private String[] summaryRowData;
+
+ private String associatedSequence;
+
+ public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request)
+ {
+ Collection<PDBDocField> diplayFields = request.getWantedFields();
+ String associatedSeq = request.getAssociatedSequence();
+ int colCounter = 0;
+ summaryRowData = new String[(associatedSeq != null) ? diplayFields
+ .size() + 1 : diplayFields.size()];
+ if (associatedSeq != null)
+ {
+ this.associatedSequence = (associatedSeq.length() > 18) ? associatedSeq
+ .substring(0, 18) : associatedSeq;
+ summaryRowData[0] = associatedSequence;
+ colCounter = 1;
+ }
+
+ for (PDBDocField field : diplayFields)
+ {
+ String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
+ : pdbJsonDoc
+ .get(field.getCode()).toString();
+ if (field.equals(PDBDocField.PDB_ID))
+ {
+ this.pdbId = fieldData;
+ summaryRowData[colCounter++] = this.pdbId;
+ }
+ else
+ {
+ summaryRowData[colCounter++] = fieldData;
+ }
+ }
+ }
+
+ public String getPdbId()
+ {
+ return pdbId;
+ }
+
+ public void setPdbId(String pdbId)
+ {
+ this.pdbId = pdbId;
+ }
+
+ public String[] getSummaryData()
+ {
+ return summaryRowData;
+ }
+
+ public void setSummaryData(String[] summaryData)
+ {
+ this.summaryRowData = summaryData;
+ }
+
+ /**
+ * Returns a string representation of this object;
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder summaryFieldValues = new StringBuilder();
+ for (String summaryField : summaryRowData)
+ {
+ summaryFieldValues.append(summaryField).append("\t");
+ }
+ return summaryFieldValues.toString();
+ }
+
+ /**
+ * Returns hash code value for this object
+ */
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(this.pdbId, this.toString());
+ }
+
+ /**
+ * Indicates whether some object is equal to this one
+ */
+ @Override
+ public boolean equals(Object that)
+ {
+ if (!(that instanceof PDBResponseSummary))
+ {
+ return false;
+ }
+ PDBResponseSummary another = (PDBResponseSummary) that;
+ return this.toString().equals(another.toString());
+ }
+
+ }
+
+}
+
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
+ if (obj == null)
+ {
+ return false;
+ }
if (!(obj instanceof CrossReference))
+ {
return false;
+ }
CrossReference other = (CrossReference) obj;
- if (obj == null)
- return false;
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ /**
+ * hashCode designed to ensure that if two instances satisfy o1.equals(o2)
+ * then they have the same hashcode.
+ */
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
+ if (obj == null)
+ {
+ return false;
+ }
if (!(obj instanceof UPEntry))
+ {
return false;
+ }
UPEntry other = (UPEntry) obj;
- if (obj == null)
- return false;
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof Data))
+ if (obj == null)
{
return false;
}
- Data other = (Data) obj;
- if (obj == null)
+ if (!(obj instanceof Data))
{
return false;
}
+ Data other = (Data) obj;
if (this == obj)
{
return true;
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof InputParams))
+ if (obj == null)
{
return false;
}
- InputParams other = (InputParams) obj;
- if (obj == null)
+ if (!(obj instanceof InputParams))
{
return false;
}
+ InputParams other = (InputParams) obj;
if (this == obj)
{
return true;
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof WSFile))
+ if (obj == null)
{
return false;
}
- WSFile other = (WSFile) obj;
- if (obj == null)
+ if (!(obj instanceof WSFile))
{
return false;
}
+ WSFile other = (WSFile) obj;
if (this == obj)
{
return true;
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
+ if (obj == null)
+ {
+ return false;
+ }
if (!(obj instanceof Alignment))
+ {
return false;
+ }
Alignment other = (Alignment) obj;
- if (obj == null)
- return false;
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof JpredResult))
+ if (obj == null)
{
return false;
}
- JpredResult other = (JpredResult) obj;
- if (obj == null)
+ if (!(obj instanceof JpredResult))
{
return false;
}
+ JpredResult other = (JpredResult) obj;
if (this == obj)
{
return true;
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
this.msa = msa;
}
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof MsaResult))
+ if (obj == null)
{
return false;
}
-
- MsaResult other = (MsaResult) obj;
-
- if (obj == null)
+ if (!(obj instanceof MsaResult))
{
return false;
}
+ MsaResult other = (MsaResult) obj;
+
if (this == obj)
{
return true;
return _equals;
}
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof Msfalignment))
+ if (obj == null)
{
return false;
}
- Msfalignment other = (Msfalignment) obj;
- if (obj == null)
+ if (!(obj instanceof Msfalignment))
{
return false;
}
+ Msfalignment other = (Msfalignment) obj;
if (this == obj)
{
return true;
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof Object))
- return false;
- Object other = (Object) obj;
if (obj == null)
+ {
+ return false;
+ }
+ if (!(obj instanceof Object))
+ {
return false;
+ }
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
+ if (obj == null)
+ {
+ return false;
+ }
if (!(obj instanceof Result))
+ {
return false;
+ }
Result other = (Result) obj;
- if (obj == null)
- return false;
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
public synchronized boolean equals(java.lang.Object obj)
{
- if (!(obj instanceof Secstructpred))
+ if (obj == null)
{
return false;
}
- Secstructpred other = (Secstructpred) obj;
- if (obj == null)
+ if (!(obj instanceof Secstructpred))
{
return false;
}
+ Secstructpred other = (Secstructpred) obj;
if (this == obj)
{
return true;
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
+ if (obj == null)
+ {
+ return false;
+ }
if (!(obj instanceof SeqSearchResult))
+ {
return false;
+ }
SeqSearchResult other = (SeqSearchResult) obj;
- if (obj == null)
- return false;
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
+ if (obj == null)
+ {
+ return false;
+ }
if (!(obj instanceof Sequence))
+ {
return false;
+ }
Sequence other = (Sequence) obj;
- if (obj == null)
- return false;
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
+ if (obj == null)
+ {
+ return false;
+ }
if (!(obj instanceof SequenceSet))
+ {
return false;
+ }
SequenceSet other = (SequenceSet) obj;
- if (obj == null)
- return false;
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
private java.lang.Object __equalsCalc = null;
+ @Override
public synchronized boolean equals(java.lang.Object obj)
{
+ if (obj == null)
+ {
+ return false;
+ }
if (!(obj instanceof WsJobId))
+ {
return false;
+ }
WsJobId other = (WsJobId) obj;
- if (obj == null)
- return false;
if (this == obj)
+ {
return true;
+ }
if (__equalsCalc != null)
{
return (__equalsCalc == obj);
private boolean __hashCodeCalc = false;
+ @Override
public synchronized int hashCode()
{
if (__hashCodeCalc)
--- /dev/null
+
+package jalview.analysis;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
+
+import org.junit.Test;
+
+public class AAFrequencyTest
+{
+ private static final String C = AAFrequency.MAXCOUNT;
+
+ private static final String R = AAFrequency.MAXRESIDUE;
+
+ private static final String G = AAFrequency.PID_GAPS;
+
+ private static final String N = AAFrequency.PID_NOGAPS;
+
+ private static final String P = AAFrequency.PROFILE;
+
+ @Test
+ public void testCalculate_noProfile()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "CAGT");
+ SequenceI seq2 = new Sequence("Seq2", "CACT");
+ SequenceI seq3 = new Sequence("Seq3", "C--G");
+ SequenceI seq4 = new Sequence("Seq4", "CA-t");
+ SequenceI[] seqs = new SequenceI[]
+ { seq1, seq2, seq3, seq4 };
+ Hashtable[] result = new Hashtable[seq1.getLength()];
+
+ AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
+
+ // col 0 is 100% C
+ Hashtable col = result[0];
+ assertEquals(100f, (Float) col.get(G), 0.0001f);
+ assertEquals(100f, (Float) col.get(N), 0.0001f);
+ assertEquals(4, col.get(C));
+ assertEquals("C", col.get(R));
+ assertNull(col.get(P));
+
+ // col 1 is 75% A
+ col = result[1];
+ assertEquals(75f, (Float) col.get(G), 0.0001f);
+ assertEquals(100f, (Float) col.get(N), 0.0001f);
+ assertEquals(3, col.get(C));
+ assertEquals("A", col.get(R));
+
+ // col 2 is 50% G 50% C or 25/25 counting gaps
+ col = result[2];
+ assertEquals(25f, (Float) col.get(G), 0.0001f);
+ assertEquals(50f, (Float) col.get(N), 0.0001f);
+ assertEquals(1, col.get(C));
+ assertEquals("CG", col.get(R));
+
+ // col 3 is 75% T 25% G
+ col = result[3];
+ assertEquals(75f, (Float) col.get(G), 0.0001f);
+ assertEquals(75f, (Float) col.get(N), 0.0001f);
+ assertEquals(3, col.get(C));
+ assertEquals("T", col.get(R));
+ }
+
+ @Test
+ public void testCalculate_withProfile()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "CAGT");
+ SequenceI seq2 = new Sequence("Seq2", "CACT");
+ SequenceI seq3 = new Sequence("Seq3", "C--G");
+ SequenceI seq4 = new Sequence("Seq4", "CA-t");
+ SequenceI[] seqs = new SequenceI[]
+ { seq1, seq2, seq3, seq4 };
+ Hashtable[] result = new Hashtable[seq1.getLength()];
+
+ AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+ int[][] profile = (int[][]) result[0].get(P);
+ assertEquals(4, profile[0]['C']);
+ assertEquals(4, profile[1][0]); // no of seqs
+ assertEquals(4, profile[1][1]); // nongapped in column
+
+ profile = (int[][]) result[1].get(P);
+ assertEquals(3, profile[0]['A']);
+ assertEquals(4, profile[1][0]);
+ assertEquals(3, profile[1][1]);
+
+ profile = (int[][]) result[2].get(P);
+ assertEquals(1, profile[0]['G']);
+ assertEquals(1, profile[0]['C']);
+ assertEquals(4, profile[1][0]);
+ assertEquals(2, profile[1][1]);
+
+ profile = (int[][]) result[3].get(P);
+ assertEquals(3, profile[0]['T']);
+ assertEquals(1, profile[0]['G']);
+ assertEquals(4, profile[1][0]);
+ assertEquals(4, profile[1][1]);
+ }
+
+ @Test
+ public void testCalculate_withProfileTiming()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "CAGT");
+ SequenceI seq2 = new Sequence("Seq2", "CACT");
+ SequenceI seq3 = new Sequence("Seq3", "C--G");
+ SequenceI seq4 = new Sequence("Seq4", "CA-t");
+ SequenceI[] seqs = new SequenceI[]
+ { seq1, seq2, seq3, seq4 };
+ Hashtable[] result = new Hashtable[seq1.getLength()];
+
+ // ensure class loaded and initialized
+ AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+ int reps = 100000;
+ long start = System.currentTimeMillis();
+ for (int i = 0; i < reps; i++)
+ {
+ AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+ }
+ System.out.println(System.currentTimeMillis() - start);
+ }
+
+ @Test
+ public void testGetPercentageFormat()
+ {
+ assertNull(AAFrequency.getPercentageFormat(0));
+ assertNull(AAFrequency.getPercentageFormat(99));
+ assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
+ assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
+ assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
+ assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());
+ }
+}
*/
package jalview.analysis;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
import org.junit.Test;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
+import jalview.util.MapList;
public class AlignmentUtilsTests
{
+ // @formatter:off
+ private static final String TEST_DATA =
+ "# STOCKHOLM 1.0\n" +
+ "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
+ "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
+ "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
+ "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
+ "#=GR D.melanogaster.1 SS ................((((\n" +
+ "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
+ "#=GR D.melanogaster.2 SS ................((((\n" +
+ "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
+ "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
+ "//";
+
+ private static final String AA_SEQS_1 =
+ ">Seq1Name\n" +
+ "K-QY--L\n" +
+ ">Seq2Name\n" +
+ "-R-FP-W-\n";
+
+ private static final String CDNA_SEQS_1 =
+ ">Seq1Name\n" +
+ "AC-GG--CUC-CAA-CT\n" +
+ ">Seq2Name\n" +
+ "-CG-TTA--ACG---AAGT\n";
+
+ private static final String CDNA_SEQS_2 =
+ ">Seq1Name\n" +
+ "GCTCGUCGTACT\n" +
+ ">Seq2Name\n" +
+ "GGGTCAGGCAGT\n";
+ // @formatter:on
+
public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
+
@Test
public void testExpandFlanks()
{
assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));
}
}
+ }
}
+
+ /**
+ * Test method that returns a map of lists of sequences by sequence name.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testGetSequencesByName() throws IOException
+ {
+ final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
+ + ">Seq1Name\nABCD\n";
+ AlignmentI al = loadAlignment(data, "FASTA");
+ Map<String, List<SequenceI>> map = AlignmentUtils
+ .getSequencesByName(al);
+ assertEquals(2, map.keySet().size());
+ assertEquals(2, map.get("Seq1Name").size());
+ assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
+ assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
+ assertEquals(1, map.get("Seq2Name").size());
+ assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
+ }
+ /**
+ * Helper method to load an alignment and ensure dataset sequences are set up.
+ *
+ * @param data
+ * @param format TODO
+ * @return
+ * @throws IOException
+ */
+ protected AlignmentI loadAlignment(final String data, String format) throws IOException
+ {
+ Alignment a = new FormatAdapter().readFile(data,
+ AppletFormatAdapter.PASTE, format);
+ a.setDataset(null);
+ return a;
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for the case where we have no sequence
+ * cross-references, so mappings are made first-served 1-1 where sequences
+ * translate.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna_noXrefs() throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
+ dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
+ cdna.setDataset(null);
+
+ assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+
+ // 3 mappings made, each from 1 to 1 sequence
+ assertEquals(3, protein.getCodonFrames().size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
+
+ // V12345 mapped to A22222
+ AlignedCodonFrame acf = protein.getCodonFrame(
+ protein.getSequenceAt(0)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ Mapping[] protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ MapList mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
+ assertEquals(1, mapList.getFromRanges().size());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // V12346 mapped to A33333
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // V12347 mapped to A11111
+ acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // no mapping involving the 'extra' A44444
+ assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
+ }
+
+ /**
+ * Test for the alignSequenceAs method that takes two sequences and a mapping.
+ */
+ @Test
+ public void testAlignSequenceAs_withMapping_noIntrons()
+ {
+ MapList map = new MapList(new int[]
+ { 1, 6 }, new int[]
+ { 1, 2 }, 3, 1);
+
+ /*
+ * No existing gaps in dna:
+ */
+ checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
+ "---GGG---AAA");
+
+ /*
+ * Now introduce gaps in dna but ignore them when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
+ "---GGG---AAA");
+
+ /*
+ * Now include gaps in dna when realigning. First retaining 'mapped' gaps
+ * only, i.e. those within the exon region.
+ */
+ checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
+ "---G-G--G---A--A-A");
+
+ /*
+ * Include all gaps in dna when realigning (within and without the exon
+ * region). The leading gap, and the gaps between codons, are subsumed by
+ * the protein alignment gap.
+ */
+ checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", true, true, map,
+ "---G-GG---AA-A-");
+
+ /*
+ * Include only unmapped gaps in dna when realigning (outside the exon
+ * region). The leading gap, and the gaps between codons, are subsumed by
+ * the protein alignment gap.
+ */
+ checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
+ "---GGG---AAA-");
+ }
+
+ /**
+ * Test for the alignSequenceAs method that takes two sequences and a mapping.
+ */
+ @Test
+ public void testAlignSequenceAs_withMapping_withIntrons()
+ {
+ /*
+ * Exons at codon 2 (AAA) and 4 (TTT)
+ */
+ MapList map = new MapList(new int[]
+ { 4, 6, 10, 12 }, new int[]
+ { 1, 2 }, 3, 1);
+
+ /*
+ * Simple case: no gaps in dna
+ */
+ checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
+ "GGG---AAACCCTTTGGG");
+
+ /*
+ * Add gaps to dna - but ignore when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
+ false, false, map, "GGG---AAACCCTTTGGG");
+
+ /*
+ * Add gaps to dna - include within exons only when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, false, map, "GGG---A--A---ACCCT-TTGGG");
+
+ /*
+ * Include gaps outside exons only when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
+
+ /*
+ * Include gaps following first intron if we are 'preserving mapped gaps'
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+
+ /*
+ * Include all gaps in dna when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+ }
+
+ /**
+ * Test for the case where not all of the protein sequence is mapped to cDNA.
+ */
+ @Test
+ public void testAlignSequenceAs_withMapping_withUnmappedProtein()
+ {
+
+ /*
+ * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
+ */
+ final MapList map = new MapList(new int[]
+ { 4, 6, 10, 12 }, new int[]
+ { 1, 1, 3, 3 }, 3, 1);
+
+
+ /*
+ * Expect alignment does nothing (aborts realignment). Change this test
+ * first if different behaviour wanted.
+ */
+ checkAlignSequenceAs("GGGAAACCCTTTGGG", "-A-L-P-", false,
+ false, map, "GGGAAACCCTTTGGG");
+ }
+
+ /**
+ * Helper method that performs and verifies the method under test.
+ *
+ * @param dnaSeq
+ * @param proteinSeq
+ * @param preserveMappedGaps
+ * @param preserveUnmappedGaps
+ * @param map
+ * @param expected
+ */
+ protected void checkAlignSequenceAs(final String dnaSeq,
+ final String proteinSeq, final boolean preserveMappedGaps,
+ final boolean preserveUnmappedGaps, MapList map,
+ final String expected)
+ {
+ SequenceI dna = new Sequence("Seq1", dnaSeq);
+ dna.createDatasetSequence();
+ SequenceI protein = new Sequence("Seq1", proteinSeq);
+ protein.createDatasetSequence();
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+
+ AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-',
+ preserveMappedGaps, preserveUnmappedGaps);
+ assertEquals(expected, dna.getSequenceAsString());
+ }
+
+ /**
+ * Test for the alignSequenceAs method where we preserve gaps in introns only.
+ */
+ @Test
+ public void testAlignSequenceAs_keepIntronGapsOnly()
+ {
+
+ /*
+ * Intron GGGAAA followed by exon CCCTTT
+ */
+ MapList map = new MapList(new int[]
+ { 7, 12 }, new int[]
+ { 1, 2 }, 3, 1);
+
+ checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL",
+ false, true, map, "GG-G-AA-ACCCTTT");
+ }
+
+ /**
+ * Test for the method that generates an aligned translated sequence from one
+ * mapping.
+ */
+ @Test
+ public void testGetAlignedTranslation_dnaLikeProtein()
+ {
+ // dna alignment will be replaced
+ SequenceI dna = new Sequence("Seq1", "T-G-CC-A--T-TAC-CAG-");
+ dna.createDatasetSequence();
+ // protein alignment will be 'applied' to dna
+ SequenceI protein = new Sequence("Seq1", "-CH-Y--Q-");
+ protein.createDatasetSequence();
+ MapList map = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+
+ final SequenceI aligned = AlignmentUtils
+ .getAlignedTranslation(protein, '-', acf);
+ assertEquals("---TGCCAT---TAC------CAG---", aligned.getSequenceAsString());
+ assertSame(aligned.getDatasetSequence(), dna.getDatasetSequence());
+ }
+
+ /**
+ * Test the method that realigns protein to match mapped codon alignment.
+ */
+ @Test
+ public void testAlignProteinAsDna()
+ {
+ // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
+ SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
+ // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
+ SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
+ // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
+ SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
+ AlignmentI dna = new Alignment(new SequenceI[]
+ { dna1, dna2, dna3 });
+ dna.setDataset(null);
+
+ // protein alignment will be realigned like dna
+ SequenceI prot1 = new Sequence("Seq1", "CHYQ");
+ SequenceI prot2 = new Sequence("Seq2", "CHYQ");
+ SequenceI prot3 = new Sequence("Seq3", "CHYQ");
+ AlignmentI protein = new Alignment(new SequenceI[]
+ { prot1, prot2, prot3 });
+ protein.setDataset(null);
+
+ MapList map = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
+ acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
+ acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
+ protein.setCodonFrames(Collections.singleton(acf));
+
+ /*
+ * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
+ * [8,9,10] [10,11,12] [11,12,13]
+ */
+ AlignmentUtils.alignProteinAsDna(protein, dna);
+ assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
+ assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
+ assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
+ }
+
+ /**
+ * Test the method that tests whether a CDNA sequence translates to a protein
+ * sequence
+ */
+ @Test
+ public void testTranslatesAs()
+ {
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPKG".toCharArray()));
+ // with start codon
+ assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
+ 3, "FPKG".toCharArray()));
+ // with stop codon1
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
+ 0, "FPKG".toCharArray()));
+ // with stop codon2
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
+ 0, "FPKG".toCharArray()));
+ // with stop codon3
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
+ 0, "FPKG".toCharArray()));
+ // with start and stop codon1
+ assertTrue(AlignmentUtils.translatesAs(
+ "atgtttcccaaaggtaa".toCharArray(), 3, "FPKG".toCharArray()));
+ // with start and stop codon2
+ assertTrue(AlignmentUtils.translatesAs(
+ "atgtttcccaaaggtag".toCharArray(), 3, "FPKG".toCharArray()));
+ // with start and stop codon3
+ assertTrue(AlignmentUtils.translatesAs(
+ "atgtttcccaaaggtga".toCharArray(), 3, "FPKG".toCharArray()));
+
+ // wrong protein
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
+ 0,
+ "FPMG".toCharArray()));
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
+ * stop codons in addition to the protein coding sequence.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna_withStartAndStopCodons()
+ throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ // start + SAR:
+ dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
+ // = EIQ + stop
+ dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
+ // = start +EIQ + stop
+ dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
+ cdna.setDataset(null);
+
+ assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+
+ // 3 mappings made, each from 1 to 1 sequence
+ assertEquals(3, protein.getCodonFrames().size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
+
+ // V12345 mapped from A22222
+ AlignedCodonFrame acf = protein.getCodonFrame(
+ protein.getSequenceAt(0)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ Mapping[] protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ MapList mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
+ assertEquals(1, mapList.getFromRanges().size());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // V12346 mapped from A33333 starting position 4
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
+ assertEquals(1, mapList.getFromRanges().size());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // V12347 mapped to A11111 starting position 4
+ acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
+ assertEquals(1, mapList.getFromRanges().size());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // no mapping involving the 'extra' A44444
+ assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for the case where we have some sequence
+ * cross-references. Verify that 1-to-many mappings are made where
+ * cross-references exist and sequences are mappable.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna_withXrefs() throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
+ dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
+ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
+ cdna.setDataset(null);
+
+ // Xref A22222 to V12345 (should get mapped)
+ dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
+ // Xref V12345 to A44444 (should get mapped)
+ protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
+ // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
+ dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
+ // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
+ // it should get paired up with the unmapped A33333
+ // A11111 should be mapped to V12347
+ // A55555 is spare and has no xref so is not mapped
+
+ assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+
+ // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
+ assertEquals(3, protein.getCodonFrames().size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
+
+ // one mapping for each of the first 4 cDNA sequences
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
+
+ // V12345 mapped to A22222 and A44444
+ AlignedCodonFrame acf = protein.getCodonFrame(
+ protein.getSequenceAt(0)).get(0);
+ assertEquals(2, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
+ acf.getdnaSeqs()[1]);
+
+ // V12346 mapped to A33333
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // V12347 mapped to A11111
+ acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // no mapping involving the 'extra' A55555
+ assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for the case where we have some sequence
+ * cross-references. Verify that once we have made an xref mapping we don't
+ * also map un-xrefd sequeces.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna_prioritiseXrefs() throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ AlignmentI protein = new Alignment(
+ protseqs.toArray(new SequenceI[protseqs.size()]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
+ .size()]));
+ cdna.setDataset(null);
+
+ // Xref A22222 to V12345 (should get mapped)
+ // A11111 should then be mapped to the unmapped V12346
+ dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
+
+ assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+
+ // 2 protein mappings made
+ assertEquals(2, protein.getCodonFrames().size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+
+ // one mapping for each of the cDNA sequences
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
+
+ // V12345 mapped to A22222
+ AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
+ .get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+
+ // V12346 mapped to A11111
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ }
+
+ /**
+ * Test the method that shows or hides sequence annotations by type(s) and
+ * selection group.
+ */
+ @Test
+ public void testShowOrHideSequenceAnnotations()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "AAA");
+ SequenceI seq2 = new Sequence("Seq2", "BBB");
+ SequenceI seq3 = new Sequence("Seq3", "CCC");
+ Annotation[] anns = new Annotation[]
+ { new Annotation(2f) };
+ AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
+ anns);
+ ann1.setSequenceRef(seq1);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
+ anns);
+ ann2.setSequenceRef(seq2);
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
+ anns);
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
+ ann4.setSequenceRef(seq1);
+ AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
+ ann5.setSequenceRef(seq2);
+ AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
+ AlignmentI al = new Alignment(new SequenceI[] {seq1, seq2, seq3});
+ al.addAnnotation(ann1); // Structure for Seq1
+ al.addAnnotation(ann2); // Structure for Seq2
+ al.addAnnotation(ann3); // Structure for no sequence
+ al.addAnnotation(ann4); // Temp for seq1
+ al.addAnnotation(ann5); // Temp for seq2
+ al.addAnnotation(ann6); // Temp for no sequence
+ List<String> types = new ArrayList<String>();
+ List<SequenceI> scope = new ArrayList<SequenceI>();
+
+ /*
+ * Set all sequence related Structure to hidden (ann1, ann2)
+ */
+ types.add("Structure");
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
+ false);
+ assertFalse(ann1.visible);
+ assertFalse(ann2.visible);
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertTrue(ann4.visible); // not Structure, not affected
+ assertTrue(ann5.visible); // "
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set Temp in {seq1, seq3} to hidden
+ */
+ types.clear();
+ types.add("Temp");
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
+ false);
+ assertFalse(ann1.visible); // unchanged
+ assertFalse(ann2.visible); // unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible); // Temp for seq1 hidden
+ assertTrue(ann5.visible); // not in scope, not affected
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set Temp in all sequences to hidden
+ */
+ types.clear();
+ types.add("Temp");
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
+ false);
+ assertFalse(ann1.visible); // unchanged
+ assertFalse(ann2.visible); // unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible); // Temp for seq1 hidden
+ assertFalse(ann5.visible); // Temp for seq2 hidden
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set all types in {seq1, seq3} to visible
+ */
+ types.clear();
+ scope.clear();
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
+ true);
+ assertTrue(ann1.visible); // Structure for seq1 set visible
+ assertFalse(ann2.visible); // not in scope, unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertTrue(ann4.visible); // Temp for seq1 set visible
+ assertFalse(ann5.visible); // not in scope, unchanged
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set all types in all scope to hidden
+ */
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
+ false);
+ assertFalse(ann1.visible);
+ assertFalse(ann2.visible);
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible);
+ assertFalse(ann5.visible);
+ assertTrue(ann6.visible); // not sequence-related, not affected
}
}
--- /dev/null
+package jalview.analysis;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+
+import org.junit.Test;
+
+public class CodingUtilsTest
+{
+
+ @Test
+ public void testDecodeCodon()
+ {
+ assertTrue(Arrays.equals(new char[]
+ { 'A', 'A', 'A' }, CodingUtils.decodeCodon(0)));
+ assertTrue(Arrays.equals(new char[]
+ { 'A', 'A', 'C' }, CodingUtils.decodeCodon(1)));
+ assertTrue(Arrays.equals(new char[]
+ { 'A', 'A', 'G' }, CodingUtils.decodeCodon(2)));
+ assertTrue(Arrays.equals(new char[]
+ { 'A', 'A', 'T' }, CodingUtils.decodeCodon(3)));
+ assertTrue(Arrays.equals(new char[]
+ { 'A', 'C', 'A' }, CodingUtils.decodeCodon(4)));
+ assertTrue(Arrays.equals(new char[]
+ { 'C', 'A', 'A' }, CodingUtils.decodeCodon(16)));
+ assertTrue(Arrays.equals(new char[]
+ { 'G', 'G', 'G' }, CodingUtils.decodeCodon(42)));
+ assertTrue(Arrays.equals(new char[]
+ { 'T', 'T', 'T' }, CodingUtils.decodeCodon(63)));
+ }
+
+ @Test
+ public void testDecodeNucleotide()
+ {
+ assertEquals('A', CodingUtils.decodeNucleotide(0));
+ assertEquals('C', CodingUtils.decodeNucleotide(1));
+ assertEquals('G', CodingUtils.decodeNucleotide(2));
+ assertEquals('T', CodingUtils.decodeNucleotide(3));
+ assertEquals('0', CodingUtils.decodeNucleotide(4));
+ }
+
+ @Test
+ public void testEncodeCodon()
+ {
+ assertTrue(CodingUtils.encodeCodon('Z') < 0);
+ assertEquals(0, CodingUtils.encodeCodon('a'));
+ assertEquals(0, CodingUtils.encodeCodon('A'));
+ assertEquals(1, CodingUtils.encodeCodon('c'));
+ assertEquals(1, CodingUtils.encodeCodon('C'));
+ assertEquals(2, CodingUtils.encodeCodon('g'));
+ assertEquals(2, CodingUtils.encodeCodon('G'));
+ assertEquals(3, CodingUtils.encodeCodon('t'));
+ assertEquals(3, CodingUtils.encodeCodon('T'));
+ assertEquals(3, CodingUtils.encodeCodon('u'));
+ assertEquals(3, CodingUtils.encodeCodon('U'));
+
+ assertEquals(-1, CodingUtils.encodeCodon(null));
+ assertEquals(0, CodingUtils.encodeCodon(new char[]
+ { 'A', 'A', 'A' }));
+ assertEquals(1, CodingUtils.encodeCodon(new char[]
+ { 'A', 'A', 'C' }));
+ assertEquals(2, CodingUtils.encodeCodon(new char[]
+ { 'A', 'A', 'G' }));
+ assertEquals(3, CodingUtils.encodeCodon(new char[]
+ { 'A', 'A', 'T' }));
+ assertEquals(4, CodingUtils.encodeCodon(new char[]
+ { 'A', 'C', 'A' }));
+ assertEquals(16, CodingUtils.encodeCodon(new char[]
+ { 'C', 'A', 'A' }));
+ assertEquals(42, CodingUtils.encodeCodon(new char[]
+ { 'G', 'G', 'G' }));
+ assertEquals(63, CodingUtils.encodeCodon(new char[]
+ { 'T', 'T', 'T' }));
+ }
+
+}
--- /dev/null
+package jalview.analysis;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Test;
+
+public class CrossRefTest
+{
+
+ /**
+ * Tests for the method that checks if one sequence cross-references another
+ */
+ @Test
+ public void testHasCrossRef()
+ {
+ assertFalse(CrossRef.hasCrossRef(null, null));
+ SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
+ assertFalse(CrossRef.hasCrossRef(seq1, null));
+ assertFalse(CrossRef.hasCrossRef(null, seq1));
+ SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
+ assertFalse(CrossRef.hasCrossRef(seq1, seq2));
+
+ // different ref
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
+ assertFalse(CrossRef.hasCrossRef(seq1, seq2));
+
+ // case-insensitive; version number is ignored
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
+ assertTrue(CrossRef.hasCrossRef(seq1, seq2));
+
+ // right case!
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(CrossRef.hasCrossRef(seq1, seq2));
+ // test is one-way only
+ assertFalse(CrossRef.hasCrossRef(seq2, seq1));
+ }
+
+ /**
+ * Tests for the method that checks if either sequence cross-references the
+ * other
+ */
+ @Test
+ public void testHaveCrossRef()
+ {
+ assertFalse(CrossRef.hasCrossRef(null, null));
+ SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
+ assertFalse(CrossRef.haveCrossRef(seq1, null));
+ assertFalse(CrossRef.haveCrossRef(null, seq1));
+ SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
+ assertFalse(CrossRef.haveCrossRef(seq1, seq2));
+
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(CrossRef.haveCrossRef(seq1, seq2));
+ // next is true for haveCrossRef, false for hasCrossRef
+ assertTrue(CrossRef.haveCrossRef(seq2, seq1));
+
+ // now the other way round
+ seq1.setDBRef(null);
+ seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
+ assertTrue(CrossRef.haveCrossRef(seq1, seq2));
+ assertTrue(CrossRef.haveCrossRef(seq2, seq1));
+
+ // now both ways
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(CrossRef.haveCrossRef(seq1, seq2));
+ assertTrue(CrossRef.haveCrossRef(seq2, seq1));
+ }
+}
--- /dev/null
+package jalview.analysis;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+
+import java.util.Arrays;
+import java.util.Random;
+
+/**
+ * Generates, and outputs in Fasta format, a random DNA alignment for given
+ * sequence length and count. Will regenerate the same alignment each time if
+ * the same random seed is used (so may be used for reproducible unit tests).
+ * Not guaranteed to reproduce the same results between versions, as the rules
+ * may get tweaked to produce more 'realistic' results.
+ *
+ * Arguments:
+ * <ul>
+ * <li>length (number of bases in each sequence)</li>
+ * <li>height (number of sequences)</li>
+ * <li>a whole number random seed</li>
+ * <li>percentage of gaps to include (0-100)</li>
+ * <li>percentage chance of variation of each position (0-100)</li>
+ * </ul>
+ *
+ * @author gmcarstairs
+ *
+ */
+public class DnaAlignmentGenerator
+{
+ private static final char GAP = '-';
+
+ private static final char ZERO = '0';
+
+ private static final char[] BASES = new char[]
+ { 'G', 'T', 'C', 'A' };
+
+ private Random random;
+
+ /**
+ * Outputs a DNA 'alignment' where each position is a random choice from
+ * 'GTCA-'.
+ *
+ * @param args
+ */
+ public static void main(String[] args)
+ {
+ if (args.length != 5)
+ {
+ usage();
+ return;
+ }
+ int width = Integer.parseInt(args[0]);
+ int height = Integer.parseInt(args[1]);
+ long randomSeed = Long.valueOf(args[2]);
+ int gapPercentage = Integer.valueOf(args[3]);
+ int changePercentage = Integer.valueOf(args[4]);
+ AlignmentI al = new DnaAlignmentGenerator().generate(width, height,
+ randomSeed, gapPercentage, changePercentage);
+
+ System.out.println("; " + height + " sequences of " + width
+ + " bases with " + gapPercentage + "% gaps and "
+ + changePercentage + "% mutations (random seed = " + randomSeed
+ + ")");
+ System.out.println(new FastaFile().print(al.getSequencesArray()));
+ }
+
+ /**
+ * Print parameter help.
+ */
+ private static void usage()
+ {
+ System.out.println("Usage:");
+ System.out.println("arg0: number of (non-gap) bases per sequence");
+ System.out.println("arg1: number sequences");
+ System.out
+ .println("arg2: an integer as random seed (same seed = same results)");
+ System.out.println("arg3: percentage of gaps to (randomly) generate");
+ System.out
+ .println("arg4: percentage of 'mutations' to (randomly) generate");
+ System.out.println("Example: DnaAlignmentGenerator 12 15 387 10 5");
+ System.out
+ .println("- 15 sequences of 12 bases each, approx 10% gaps and 5% mutations, random seed = 387");
+
+ }
+
+ /**
+ * Default constructor
+ */
+ public DnaAlignmentGenerator()
+ {
+
+ }
+
+ /**
+ * Outputs a DNA 'alignment' of given width and height, where each position is
+ * a random choice from 'GTCA-'.
+ *
+ * @param width
+ * @param height
+ * @param randomSeed
+ * @param changePercentage
+ * @param gapPercentage
+ */
+ public AlignmentI generate(int width, int height, long randomSeed,
+ int gapPercentage, int changePercentage)
+ {
+ SequenceI[] seqs = new SequenceI[height];
+ random = new Random(randomSeed);
+ seqs[0] = generateSequence(1, width, gapPercentage);
+ for (int seqno = 1; seqno < height; seqno++)
+ {
+ seqs[seqno] = generateAnotherSequence(seqs[0].getSequence(),
+ seqno + 1, width, changePercentage);
+ }
+ AlignmentI al = new Alignment(seqs);
+ return al;
+ }
+
+ /**
+ * Outputs a DNA 'sequence' of given length, with some random gaps included.
+ *
+ * @param seqno
+ * @param length
+ * @param gapPercentage
+ */
+ private SequenceI generateSequence(int seqno, int length,
+ int gapPercentage)
+ {
+ StringBuilder seq = new StringBuilder(length);
+
+ /*
+ * Loop till we've added 'length' bases (excluding gaps)
+ */
+ for (int count = 0; count < length;)
+ {
+ boolean addGap = random.nextInt(100) < gapPercentage;
+ char c = addGap ? GAP : BASES[random.nextInt(Integer.MAX_VALUE) % 4];
+ seq.append(c);
+ if (!addGap)
+ {
+ count++;
+ }
+ }
+ final String seqName = "SEQ" + seqno;
+ final String seqString = seq.toString();
+ SequenceI sq = new Sequence(seqName, seqString);
+ sq.createDatasetSequence();
+ return sq;
+ }
+
+ /**
+ * Generate a sequence approximately aligned to the first one.
+ *
+ * @param ds
+ * @param seqno
+ * @param width
+ * number of bases
+ * @param changePercentage
+ * @return
+ */
+ private SequenceI generateAnotherSequence(char[] ds, int seqno,
+ int width, int changePercentage)
+ {
+ int length = ds.length;
+ char[] seq = new char[length];
+ Arrays.fill(seq, ZERO);
+ int gapsWanted = length - width;
+ int gapsAdded = 0;
+
+ /*
+ * First 'randomly' mimic gaps in model sequence.
+ */
+ for (int pos = 0; pos < length; pos++)
+ {
+ if (ds[pos] == GAP)
+ {
+ /*
+ * Add a gap at the same position with changePercentage likelihood
+ */
+ seq[pos] = randomCharacter(GAP, changePercentage);
+ if (seq[pos] == GAP)
+ {
+ gapsAdded++;
+ }
+ }
+ }
+
+ /*
+ * Next scatter any remaining gaps (if any) at random. This gives an even
+ * distribution.
+ */
+ while (gapsAdded < gapsWanted)
+ {
+ boolean added = false;
+ while (!added)
+ {
+ int pos = random.nextInt(length);
+ if (seq[pos] != GAP)
+ {
+ seq[pos] = GAP;
+ added = true;
+ gapsAdded++;
+ }
+ }
+ }
+
+ /*
+ * Finally fill in the rest with randomly mutated bases.
+ */
+ for (int pos = 0; pos < length; pos++)
+ {
+ if (seq[pos] == ZERO)
+ {
+ char c = randomCharacter(ds[pos], changePercentage);
+ seq[pos] = c;
+ }
+ }
+ final String seqName = "SEQ" + seqno;
+ final String seqString = new String(seq);
+ SequenceI sq = new Sequence(seqName, seqString);
+ sq.createDatasetSequence();
+ return sq;
+ }
+
+ /**
+ * Returns a random character that is changePercentage% likely to match the
+ * given type (as base or gap).
+ *
+ * @param changePercentage
+ *
+ * @param c
+ * @return
+ */
+ private char randomCharacter(char c, int changePercentage)
+ {
+ final boolean mutation = random.nextInt(100) < changePercentage;
+
+ if (!mutation)
+ {
+ return c;
+ }
+
+ char newchar = c;
+ while (newchar == c)
+ {
+ newchar = BASES[random.nextInt(Integer.MAX_VALUE) % 4];
+ }
+ return newchar;
+ }
+}
--- /dev/null
+package jalview.analysis;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignedCodon;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.io.FormatAdapter;
+
+import java.io.IOException;
+
+import org.junit.Test;
+
+public class DnaTest
+{
+ // @formatter:off
+ // AA encoding codons as ordered on the Jalview help page Amino Acid Table
+ private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
+ + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
+ + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
+ + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
+ + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
+ + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
+ + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
+ + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
+ + "TAC" + "TAA" + "TAG" + "TGA";
+
+ private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
+ + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
+ + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
+ + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
+ + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
+ + ">gi|27804621|gb|AY178912.1|/1-259\n"
+ + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
+ + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
+ + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
+ + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
+ + ">gi|27804623|gb|AY178913.1|/1-259\n"
+ + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
+ + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
+ + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
+ + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
+ + ">gi|27804627|gb|AY178915.1|/1-260\n"
+ + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
+ + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
+ + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
+ + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
+ + ">gi|27804631|gb|AY178917.1|/1-261\n"
+ + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
+ + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
+ + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
+ + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
+ + ">gi|27804635|gb|AY178919.1|/1-261\n"
+ + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
+ + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
+ + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
+ + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
+ + ">gi|27804641|gb|AY178922.1|/1-261\n"
+ + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
+ + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
+ + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
+ + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
+ + ">gi|27804647|gb|AY178925.1|/1-261\n"
+ + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
+ + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
+ + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
+ + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
+ + ">gi|27804649|gb|AY178926.1|/1-261\n"
+ + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
+ + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
+ + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
+ + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
+ + ">gi|27804653|gb|AY178928.1|/1-261\n"
+ + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
+ + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
+ + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
+ + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
+ + ">gi|27804659|gb|AY178931.1|/1-261\n"
+ + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
+ + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
+ + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
+ + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
+ // @formatter:on
+
+ /**
+ * Corner case for this test is the presence of codons after codons that were
+ * not translated.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testTranslateCdna_withUntranslatableCodons()
+ throws IOException
+ {
+ AlignmentI alf = new FormatAdapter().readFile(
+ JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
+ "FASTA");
+ ColumnSelection cs = new ColumnSelection();
+ AlignViewportI av = new AlignViewport(alf, cs);
+ Dna dna = new Dna(av, new int[]
+ { 0, alf.getWidth() - 1 });
+ AlignmentI translated = dna.translateCdna();
+ assertNotNull("Couldn't do a full width translation of test data.",
+ translated);
+ }
+
+ /**
+ * Test variant in which 15 column blocks at a time are translated (the rest
+ * hidden).
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
+ throws IOException
+ {
+ AlignmentI alf = new FormatAdapter().readFile(
+ JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
+ "FASTA");
+ int vwidth = 15;
+ for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
+ {
+ ColumnSelection cs = new ColumnSelection();
+ if (ipos > 0)
+ {
+ cs.hideColumns(0, ipos - 1);
+ }
+ cs.hideColumns(ipos + vwidth, alf.getWidth());
+ int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
+ AlignViewportI av = new AlignViewport(alf, cs);
+ Dna dna = new Dna(av, vcontigs);
+ AlignmentI transAlf = dna.translateCdna();
+
+ assertTrue("Translation failed (ipos=" + ipos
+ + ") No alignment data.", transAlf != null);
+ assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
+ transAlf.getHeight() > 0);
+ assertTrue("Translation failed (ipos=" + ipos + ") Translated "
+ + transAlf.getHeight() + " sequences from " + alf.getHeight()
+ + " sequences", alf.getHeight() == transAlf.getHeight());
+ }
+ }
+
+ /**
+ * Test simple translation to Amino Acids (with STOP codons translated to X).
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testTranslateCdna_simple() throws IOException
+ {
+ AlignmentI alf = new FormatAdapter().readFile(fasta,
+ FormatAdapter.PASTE, "FASTA");
+ ColumnSelection cs = new ColumnSelection();
+ AlignViewportI av = new AlignViewport(alf, cs);
+ Dna dna = new Dna(av, new int[]
+ { 0, alf.getWidth() - 1 });
+ AlignmentI translated = dna.translateCdna();
+ String aa = translated.getSequenceAt(0).getSequenceAsString();
+ assertEquals(
+ "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYYXXX",
+ aa);
+ }
+
+ /**
+ * Test translation excluding hidden columns.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testTranslateCdna_hiddenColumns() throws IOException
+ {
+ AlignmentI alf = new FormatAdapter().readFile(fasta,
+ FormatAdapter.PASTE, "FASTA");
+ ColumnSelection cs = new jalview.datamodel.ColumnSelection();
+ cs.hideColumns(6, 14); // hide codons 3/4/5
+ cs.hideColumns(24, 35); // hide codons 9-12
+ cs.hideColumns(177, 191); // hide codons 60-64
+ AlignViewportI av = new AlignViewport(alf, cs);
+ Dna dna = new Dna(av, new int[]
+ { 0, alf.getWidth() - 1 });
+ AlignmentI translated = dna.translateCdna();
+ String aa = translated.getSequenceAt(0).getSequenceAsString();
+ assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
+ }
+
+ /**
+ * Use this test to help debug into any cases of interest.
+ */
+ @Test
+ public void testCompareCodonPos_oneOnly()
+ {
+ assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
+ }
+
+ /**
+ * Tests for method that compares 'alignment' of two codon position triplets.
+ */
+ @Test
+ public void testCompareCodonPos()
+ {
+ /*
+ * Returns 0 for any null argument
+ */
+ assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
+ assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
+
+ /*
+ * Work through 27 combinations. First 9 cases where first position matches.
+ */
+ assertMatches("AAA", "GGG"); // 2 and 3 match
+ assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
+ assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
+ assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
+ assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
+ assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
+ assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
+ assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
+ assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
+
+ /*
+ * 9 cases where first position is shifted in first sequence.
+ */
+ assertFollows("-AAA", "G-GG"); // 2 and 3 match
+ assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
+ // 'enclosing' case: pick first to start precedes
+ assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
+ assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
+ assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
+ // 'enclosing' case: pick first to start precedes
+ assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
+ assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
+ assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
+ assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
+
+ /*
+ * 9 cases where first position is shifted in second sequence.
+ */
+ assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
+ assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
+ assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
+ assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
+ // 'enclosing' case with middle base deciding:
+ assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
+ assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
+ assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
+ assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
+ assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
+ }
+
+ /**
+ * This test generates a random cDNA alignment and its translation, then
+ * reorders the cDNA and retranslates, and verifies that the translations are
+ * the same (apart from ordering).
+ */
+ @Test
+ public void testTranslateCdna_sequenceOrderIndependent()
+ {
+ /*
+ * Generate cDNA - 8 sequences of 12 bases each.
+ */
+ AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5);
+ ColumnSelection cs = new ColumnSelection();
+ AlignViewportI av = new AlignViewport(cdna, cs);
+ Dna dna = new Dna(av, new int[]
+ { 0, cdna.getWidth() - 1 });
+ AlignmentI translated = dna.translateCdna();
+
+ /*
+ * Jumble the cDNA sequences and translate.
+ */
+ SequenceI[] sorted = new SequenceI[cdna.getHeight()];
+ final int[] jumbler = new int[]
+ { 6, 7, 3, 4, 2, 0, 1, 5 };
+ int seqNo = 0;
+ for (int i : jumbler)
+ {
+ sorted[seqNo++] = cdna.getSequenceAt(i);
+ }
+ AlignmentI cdnaReordered = new Alignment(sorted);
+ av = new AlignViewport(cdnaReordered, cs);
+ dna = new Dna(av, new int[]
+ { 0, cdna.getWidth() - 1 });
+ AlignmentI translated2 = dna.translateCdna();
+
+ /*
+ * Check translated sequences are the same in both alignments.
+ */
+ System.out.println("Original");
+ System.out.println(translated.toString());
+ System.out.println("Sorted");
+ System.out.println(translated2.toString());
+
+ int sortedSequenceIndex = 0;
+ for (int originalSequenceIndex : jumbler)
+ {
+ final String translation1 = translated.getSequenceAt(
+ originalSequenceIndex).getSequenceAsString();
+ final String translation2 = translated2.getSequenceAt(sortedSequenceIndex)
+ .getSequenceAsString();
+ assertEquals(translation2, translation1);
+ sortedSequenceIndex++;
+ }
+ }
+
+ /**
+ * Test that all the cases in testCompareCodonPos have a 'symmetric'
+ * comparison (without checking the actual comparison result).
+ */
+ @Test
+ public void testCompareCodonPos_isSymmetric()
+ {
+ assertSymmetric("AAA", "GGG");
+ assertSymmetric("AA-A", "GGG");
+ assertSymmetric("AAA", "GG-G");
+ assertSymmetric("A-AA", "GG-G");
+ assertSymmetric("A-A-A", "GG-G");
+ assertSymmetric("A-AA", "GG--G");
+ assertSymmetric("AA-A", "G-GG");
+ assertSymmetric("AA--A", "G-GG");
+ assertSymmetric("AAA", "G-GG");
+ assertSymmetric("-AAA", "G-GG");
+ assertSymmetric("-AA-A", "G-GG");
+ assertSymmetric("-AAA", "G-G-G");
+ assertSymmetric("-A-AA", "G-G-G");
+ assertSymmetric("-A-A-A", "G-G-G");
+ assertSymmetric("-A-AA", "G-G--G");
+ assertSymmetric("-AA-A", "G--GG");
+ assertSymmetric("-AA--A", "G--GG");
+ assertSymmetric("-AAA", "G--GG");
+ assertSymmetric("A-AA", "-GGG");
+ assertSymmetric("A-A-A", "-GGG");
+ assertSymmetric("A-AA", "-GG-G");
+ assertSymmetric("A--AA", "-GG-G");
+ assertSymmetric("A--AA", "-GGG");
+ assertSymmetric("A--AA", "-GG--G");
+ assertSymmetric("AA-A", "-GGG");
+ assertSymmetric("AA--A", "-GGG");
+ assertSymmetric("AAA", "-GGG");
+ }
+
+ private void assertSymmetric(String codon1, String codon2)
+ {
+ assertEquals("Comparison of '" + codon1 + "' and '" + codon2
+ + " not symmetric", Integer.signum(compare(codon1, codon2)),
+ -Integer.signum(compare(codon2, codon1)));
+ }
+
+ /**
+ * Assert that the first sequence should map to the same position as the
+ * second in a translated alignment. Also checks that this is true if the
+ * order of the codons is reversed.
+ *
+ * @param codon1
+ * @param codon2
+ */
+ private void assertMatches(String codon1, String codon2)
+ {
+ assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
+ compare(codon1, codon2));
+ assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
+ compare(codon2, codon1));
+ }
+
+ /**
+ * Assert that the first sequence should precede the second in a translated
+ * alignment
+ *
+ * @param codon1
+ * @param codon2
+ */
+ private void assertPrecedes(String codon1, String codon2)
+ {
+ assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'",
+ -1, compare(codon1, codon2));
+ }
+
+ /**
+ * Assert that the first sequence should follow the second in a translated
+ * alignment
+ *
+ * @param codon1
+ * @param codon2
+ */
+ private void assertFollows(String codon1, String codon2)
+ {
+ assertEquals("Expected '" + codon1 + "' follows '" + codon2 + "'", 1,
+ compare(codon1, codon2));
+ }
+
+ /**
+ * Convert two nucleotide strings to base positions and pass to
+ * Dna.compareCodonPos, return the result.
+ *
+ * @param s1
+ * @param s2
+ * @return
+ */
+ private int compare(String s1, String s2)
+ {
+ final AlignedCodon cd1 = convertCodon(s1);
+ final AlignedCodon cd2 = convertCodon(s2);
+ System.out.println("K: " + s1 + " " + cd1.toString());
+ System.out.println("G: " + s2 + " " + cd2.toString());
+ System.out.println();
+ return Dna.compareCodonPos(cd1, cd2);
+ }
+
+ /**
+ * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
+ * should have exactly 3 non-gap characters, and use '-' for gaps.
+ *
+ * @param s
+ * @return
+ */
+ private AlignedCodon convertCodon(String s)
+ {
+ int[] codon = new int[3];
+ int i = 0;
+ for (int j = 0; j < s.length(); j++)
+ {
+ if (s.charAt(j) != '-')
+ {
+ codon[i++] = j;
+ }
+ }
+ return new AlignedCodon(codon[0], codon[1], codon[2]);
+ }
+
+ /**
+ * Weirdly, maybe worth a test to prove the helper method of this test class.
+ */
+ @Test
+ public void testConvertCodon()
+ {
+ assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
+ assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
+ assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
+ }
+}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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 3
- * of the License, or (at your option) any later version.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.analysis;
-
-import static org.junit.Assert.*;
-import jalview.datamodel.ColumnSelection;
-
-import java.io.IOException;
-
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-
-public class DnaTranslation
-{
-
- private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
- + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
- + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
- + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
- + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
- + ">gi|27804621|gb|AY178912.1|/1-259\n"
- + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
- + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
- + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
- + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
- + ">gi|27804623|gb|AY178913.1|/1-259\n"
- + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
- + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
- + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
- + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
- + ">gi|27804627|gb|AY178915.1|/1-260\n"
- + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
- + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
- + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
- + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
- + ">gi|27804631|gb|AY178917.1|/1-261\n"
- + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
- + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
- + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
- + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
- + ">gi|27804635|gb|AY178919.1|/1-261\n"
- + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
- + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
- + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
- + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
- + ">gi|27804641|gb|AY178922.1|/1-261\n"
- + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
- + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
- + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
- + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
- + ">gi|27804647|gb|AY178925.1|/1-261\n"
- + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
- + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
- + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
- + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
- + ">gi|27804649|gb|AY178926.1|/1-261\n"
- + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
- + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
- + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
- + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
- + ">gi|27804653|gb|AY178928.1|/1-261\n"
- + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
- + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
- + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
- + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
- + ">gi|27804659|gb|AY178931.1|/1-261\n"
- + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
- + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
- + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
- + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
-
- @Test
- public void translationWithUntranslatableCodonsTest()
- {
- // Corner case for this test is the presence of codons after codons that
- // were not translated.
- jalview.datamodel.AlignmentI alf = null;
- try
- {
- alf = new jalview.io.FormatAdapter().readFile(
- JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
- "FASTA");
- } catch (IOException x)
- {
- x.printStackTrace();
- fail("Unexpected IOException (" + x.getMessage()
- + ") - check test environment");
- }
- {
- // full translation
- ColumnSelection cs = new jalview.datamodel.ColumnSelection();
- assertNotNull("Couldn't do a full width translation of test data.",
- jalview.analysis.Dna.CdnaTranslate(
- alf.getSequencesArray(),
- cs.getVisibleSequenceStrings(0, alf.getWidth(),
- alf.getSequencesArray()), new int[]
- { 0, alf.getWidth() - 1 }, alf.getGapCharacter(),
- null, alf.getWidth(), null));
- }
- int vwidth = 15; // translate in 15 base stretches
- for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
- {
- ColumnSelection cs = new jalview.datamodel.ColumnSelection();
- if (ipos > 0)
- {
- cs.hideColumns(0, ipos - 1);
- }
- cs.hideColumns(ipos + vwidth, alf.getWidth());
- int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
- String[] sel = cs.getVisibleSequenceStrings(0, alf.getWidth(),
- alf.getSequencesArray());
- jalview.datamodel.AlignmentI transAlf = jalview.analysis.Dna
- .CdnaTranslate(alf.getSequencesArray(), sel, vcontigs,
- alf.getGapCharacter(), null, alf.getWidth(), null);
-
- assertTrue("Translation failed (ipos=" + ipos
- + ") No alignment data.", transAlf != null);
- assertTrue("Translation failed (ipos=" + ipos + ") Empty algnment.",
- transAlf.getHeight() > 0);
- assertTrue("Translation failed (ipos=" + ipos + ") Translated "
- + transAlf.getHeight() + " sequences from " + alf.getHeight()
- + " sequences", alf.getHeight() == transAlf.getHeight());
- }
-
- }
-}
*/
package jalview.analysis;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
}
}
+ @Test
+ public void testExtractGaps()
+ {
+ assertNull(AlignSeq.extractGaps(null, null));
+ assertNull(AlignSeq.extractGaps(". -", null));
+ assertNull(AlignSeq.extractGaps(null, "AB-C"));
+
+ assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
+ }
}
package jalview.commands;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertSame;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import java.util.Map;
+
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
testee = new EditCommand();
seqs = new SequenceI[4];
seqs[0] = new Sequence("seq0", "abcdefghjk");
+ seqs[0].setDatasetSequence(new Sequence("seq0ds", "abcdefghjk"));
seqs[1] = new Sequence("seq1", "fghjklmnopq");
+ seqs[1].setDatasetSequence(new Sequence("seq1ds", "fghjklmnopq"));
seqs[2] = new Sequence("seq2", "qrstuvwxyz");
+ seqs[2].setDatasetSequence(new Sequence("seq2ds", "qrstuvwxyz"));
seqs[3] = new Sequence("seq3", "1234567890");
+ seqs[3].setDatasetSequence(new Sequence("seq3ds", "1234567890"));
al = new Alignment(seqs);
al.setGapCharacter('?');
}
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
assertEquals("1234567890", seqs[3].getSequenceAsString());
seqs[1] = new Sequence("seq1", "fghjZXYnopq");
+ }
+
+ /**
+ * Test that the addEdit command correctly merges insert gap commands when
+ * possible.
+ */
+ @Test
+ public void testAddEdit_multipleInsertGap()
+ {
+ /*
+ * 3 insert gap in a row (aka mouse drag right):
+ */
+ Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[]
+ { seqs[0] }, 1, 1, al);
+ testee.addEdit(e);
+ SequenceI edited = new Sequence("seq0", "a?bcdefghjk");
+ edited.setDatasetSequence(seqs[0].getDatasetSequence());
+ e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[]
+ { edited }, 2, 1, al);
+ testee.addEdit(e);
+ edited = new Sequence("seq0", "a??bcdefghjk");
+ edited.setDatasetSequence(seqs[0].getDatasetSequence());
+ e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[]
+ { edited }, 3, 1, al);
+ testee.addEdit(e);
+ assertEquals(1, testee.getSize());
+ assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction());
+ assertEquals(1, testee.getEdit(0).getPosition());
+ assertEquals(3, testee.getEdit(0).getNumber());
+
+ /*
+ * Add a non-contiguous edit - should not be merged.
+ */
+ e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[]
+ { edited }, 5, 2, al);
+ testee.addEdit(e);
+ assertEquals(2, testee.getSize());
+ assertEquals(5, testee.getEdit(1).getPosition());
+ assertEquals(2, testee.getEdit(1).getNumber());
+
+ /*
+ * Add a Delete after the Insert - should not be merged.
+ */
+ e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
+ { edited }, 6, 2, al);
+ testee.addEdit(e);
+ assertEquals(3, testee.getSize());
+ assertEquals(Action.DELETE_GAP, testee.getEdit(2).getAction());
+ assertEquals(6, testee.getEdit(2).getPosition());
+ assertEquals(2, testee.getEdit(2).getNumber());
+ }
+
+ /**
+ * Test that the addEdit command correctly merges delete gap commands when
+ * possible.
+ */
+ @Test
+ public void testAddEdit_multipleDeleteGap()
+ {
+ /*
+ * 3 delete gap in a row (aka mouse drag left):
+ */
+ seqs[0].setSequence("a???bcdefghjk");
+ Edit e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
+ { seqs[0] }, 4, 1, al);
+ testee.addEdit(e);
+ assertEquals(1, testee.getSize());
+
+ SequenceI edited = new Sequence("seq0", "a??bcdefghjk");
+ edited.setDatasetSequence(seqs[0].getDatasetSequence());
+ e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
+ { edited }, 3, 1, al);
+ testee.addEdit(e);
+ assertEquals(1, testee.getSize());
+
+ edited = new Sequence("seq0", "a?bcdefghjk");
+ edited.setDatasetSequence(seqs[0].getDatasetSequence());
+ e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
+ { edited }, 2, 1, al);
+ testee.addEdit(e);
+ assertEquals(1, testee.getSize());
+ assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction());
+ assertEquals(2, testee.getEdit(0).getPosition());
+ assertEquals(3, testee.getEdit(0).getNumber());
+
+ /*
+ * Add a non-contiguous edit - should not be merged.
+ */
+ e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
+ { edited }, 2, 1, al);
+ testee.addEdit(e);
+ assertEquals(2, testee.getSize());
+ assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction());
+ assertEquals(2, testee.getEdit(1).getPosition());
+ assertEquals(1, testee.getEdit(1).getNumber());
+
+ /*
+ * Add an Insert after the Delete - should not be merged.
+ */
+ e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[]
+ { edited }, 1, 1, al);
+ testee.addEdit(e);
+ assertEquals(3, testee.getSize());
+ assertEquals(Action.INSERT_GAP, testee.getEdit(2).getAction());
+ assertEquals(1, testee.getEdit(2).getPosition());
+ assertEquals(1, testee.getEdit(2).getNumber());
+ }
+
+ /**
+ * Test that the addEdit command correctly handles 'remove gaps' edits for the
+ * case when they appear contiguous but are acting on different sequences.
+ * They should not be merged.
+ */
+ @Test
+ public void testAddEdit_removeAllGaps()
+ {
+ seqs[0].setSequence("a???bcdefghjk");
+ Edit e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
+ { seqs[0] }, 4, 1, al);
+ testee.addEdit(e);
+
+ seqs[1].setSequence("f??ghjklmnopq");
+ Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
+ { seqs[1] }, 3, 1, al);
+ testee.addEdit(e2);
+ assertEquals(2, testee.getSize());
+ assertSame(e, testee.getEdit(0));
+ assertSame(e2, testee.getEdit(1));
+ }
+
+ /**
+ * Test that the addEdit command correctly merges insert gap commands acting
+ * on a multi-sequence selection.
+ */
+ @Test
+ public void testAddEdit_groupInsertGaps()
+ {
+ /*
+ * 2 insert gap in a row (aka mouse drag right), on two sequences:
+ */
+ Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[]
+ { seqs[0], seqs[1] }, 1, 1, al);
+ testee.addEdit(e);
+ SequenceI seq1edited = new Sequence("seq0", "a?bcdefghjk");
+ seq1edited.setDatasetSequence(seqs[0].getDatasetSequence());
+ SequenceI seq2edited = new Sequence("seq1", "f?ghjklmnopq");
+ seq2edited.setDatasetSequence(seqs[1].getDatasetSequence());
+ e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[]
+ { seq1edited, seq2edited }, 2, 1, al);
+ testee.addEdit(e);
+
+ assertEquals(1, testee.getSize());
+ assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction());
+ assertEquals(1, testee.getEdit(0).getPosition());
+ assertEquals(2, testee.getEdit(0).getNumber());
+ assertEquals(seqs[0].getDatasetSequence(), testee.getEdit(0)
+ .getSequences()[0].getDatasetSequence());
+ assertEquals(seqs[1].getDatasetSequence(), testee.getEdit(0)
+ .getSequences()[1].getDatasetSequence());
+ }
+
+ /**
+ * Test for 'undoing' a series of gap insertions.
+ * <ul>
+ * <li>Start: ABCDEF insert 2 at pos 1</li>
+ * <li>next: A--BCDEF insert 1 at pos 4</li>
+ * <li>next: A--B-CDEF insert 2 at pos 0</li>
+ * <li>last: --A--B-CDEF</li>
+ * </ul>
+ */
+ @Test
+ public void testPriorState_multipleInserts()
+ {
+ EditCommand command = new EditCommand();
+ SequenceI seq = new Sequence("", "--A--B-CDEF");
+ SequenceI ds = new Sequence("", "ABCDEF");
+ seq.setDatasetSequence(ds);
+ SequenceI[] seqs = new SequenceI[]
+ { seq };
+ Edit e = command.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-');
+ command.addEdit(e);
+ e = command.new Edit(Action.INSERT_GAP, seqs, 4, 1, '-');
+ command.addEdit(e);
+ e = command.new Edit(Action.INSERT_GAP, seqs, 0, 2, '-');
+ command.addEdit(e);
+
+ Map<SequenceI, SequenceI> unwound = command.priorState(false);
+ assertEquals("ABCDEF", unwound.get(ds).getSequenceAsString());
+ }
+
+ /**
+ * Test for 'undoing' a series of gap deletions.
+ * <ul>
+ * <li>Start: A-B-C delete 1 at pos 1</li>
+ * <li>Next: AB-C delete 1 at pos 2</li>
+ * <li>End: ABC</li>
+ * </ul>
+ */
+ @Test
+ public void testPriorState_removeAllGaps()
+ {
+ EditCommand command = new EditCommand();
+ SequenceI seq = new Sequence("", "ABC");
+ SequenceI ds = new Sequence("", "ABC");
+ seq.setDatasetSequence(ds);
+ SequenceI[] seqs = new SequenceI[]
+ { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
+ command.addEdit(e);
+ e = command.new Edit(Action.DELETE_GAP, seqs, 2, 1, '-');
+ command.addEdit(e);
+
+ Map<SequenceI, SequenceI> unwound = command.priorState(false);
+ assertEquals("A-B-C", unwound.get(ds).getSequenceAsString());
+ }
+
+ /**
+ * Test for 'undoing' a single delete edit.
+ */
+ @Test
+ public void testPriorState_singleDelete()
+ {
+ EditCommand command = new EditCommand();
+ SequenceI seq = new Sequence("", "ABCDEF");
+ SequenceI ds = new Sequence("", "ABCDEF");
+ seq.setDatasetSequence(ds);
+ SequenceI[] seqs = new SequenceI[]
+ { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, seqs, 2, 2, '-');
+ command.addEdit(e);
+
+ Map<SequenceI, SequenceI> unwound = command.priorState(false);
+ assertEquals("AB--CDEF", unwound.get(ds).getSequenceAsString());
+ }
+
+ /**
+ * Test 'undoing' a single gap insertion edit command.
+ */
+ @Test
+ public void testPriorState_singleInsert()
+ {
+ EditCommand command = new EditCommand();
+ SequenceI seq = new Sequence("", "AB---CDEF");
+ SequenceI ds = new Sequence("", "ABCDEF");
+ seq.setDatasetSequence(ds);
+ SequenceI[] seqs = new SequenceI[]
+ { seq };
+ Edit e = command.new Edit(Action.INSERT_GAP, seqs, 2, 3, '-');
+ command.addEdit(e);
+
+ Map<SequenceI, SequenceI> unwound = command.priorState(false);
+ assertEquals("ABCDEF", unwound.get(ds).getSequenceAsString());
+ }
+
+ /**
+ * Test that mimics 'remove all gaps' action. This generates delete gap edits
+ * for contiguous gaps in each sequence separately.
+ */
+ @Test
+ public void testPriorState_removeGapsMultipleSeqs()
+ {
+ EditCommand command = new EditCommand();
+ String original1 = "--ABC-DEF";
+ String original2 = "FG-HI--J";
+ String original3 = "M-NOPQ";
+
+ /*
+ * Two edits for the first sequence
+ */
+ SequenceI seq = new Sequence("", "ABC-DEF");
+ SequenceI ds1 = new Sequence("", "ABCDEF");
+ seq.setDatasetSequence(ds1);
+ SequenceI[] seqs = new SequenceI[]
+ { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, seqs, 0, 2, '-');
+ command.addEdit(e);
+ seq = new Sequence("", "ABCDEF");
+ seq.setDatasetSequence(ds1);
+ seqs = new SequenceI[]
+ { seq };
+ e = command.new Edit(Action.DELETE_GAP, seqs, 3, 1, '-');
+ command.addEdit(e);
+
+ /*
+ * Two edits for the second sequence
+ */
+ seq = new Sequence("", "FGHI--J");
+ SequenceI ds2 = new Sequence("", "FGHIJ");
+ seq.setDatasetSequence(ds2);
+ seqs = new SequenceI[]
+ { seq };
+ e = command.new Edit(Action.DELETE_GAP, seqs, 2, 1, '-');
+ command.addEdit(e);
+ seq = new Sequence("", "FGHIJ");
+ seq.setDatasetSequence(ds2);
+ seqs = new SequenceI[]
+ { seq };
+ e = command.new Edit(Action.DELETE_GAP, seqs, 4, 2, '-');
+ command.addEdit(e);
+
+ /*
+ * One edit for the third sequence.
+ */
+ seq = new Sequence("", "MNOPQ");
+ SequenceI ds3 = new Sequence("", "MNOPQ");
+ seq.setDatasetSequence(ds3);
+ seqs = new SequenceI[]
+ { seq };
+ e = command.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
+ command.addEdit(e);
+
+ Map<SequenceI, SequenceI> unwound = command.priorState(false);
+ assertEquals(original1, unwound.get(ds1).getSequenceAsString());
+ assertEquals(original2, unwound.get(ds2).getSequenceAsString());
+ assertEquals(original3, unwound.get(ds3).getSequenceAsString());
+ }
+
+ /**
+ * Test that mimics 'remove all gapped columns' action. This generates a
+ * series Delete Gap edits that each act on all sequences that share a gapped
+ * column region.
+ */
+ @Test
+ public void testPriorState_removeGappedCols()
+ {
+ EditCommand command = new EditCommand();
+ String original1 = "--ABC--DEF";
+ String original2 = "-G-HI--J";
+ String original3 = "-M-NO--PQ";
+
+ /*
+ * First edit deletes the first column.
+ */
+ SequenceI seq1 = new Sequence("", "-ABC--DEF");
+ SequenceI ds1 = new Sequence("", "ABCDEF");
+ seq1.setDatasetSequence(ds1);
+ SequenceI seq2 = new Sequence("", "G-HI--J");
+ SequenceI ds2 = new Sequence("", "GHIJ");
+ seq2.setDatasetSequence(ds2);
+ SequenceI seq3 = new Sequence("", "M-NO--PQ");
+ SequenceI ds3 = new Sequence("", "MNOPQ");
+ seq3.setDatasetSequence(ds3);
+ SequenceI[] seqs = new SequenceI[]
+ { seq1, seq2, seq3 };
+ Edit e = command.new Edit(Action.DELETE_GAP, seqs, 0, 1, '-');
+ command.addEdit(e);
+
+ /*
+ * Second edit deletes what is now columns 4 and 5.
+ */
+ seq1 = new Sequence("", "-ABCDEF");
+ seq1.setDatasetSequence(ds1);
+ seq2 = new Sequence("", "G-HIJ");
+ seq2.setDatasetSequence(ds2);
+ seq3 = new Sequence("", "M-NOPQ");
+ seq3.setDatasetSequence(ds3);
+ seqs = new SequenceI[]
+ { seq1, seq2, seq3 };
+ e = command.new Edit(Action.DELETE_GAP, seqs, 4, 2, '-');
+ command.addEdit(e);
+ Map<SequenceI, SequenceI> unwound = command.priorState(false);
+ assertEquals(original1, unwound.get(ds1).getSequenceAsString());
+ assertEquals(original2, unwound.get(ds2).getSequenceAsString());
+ assertEquals(original3, unwound.get(ds3).getSequenceAsString());
+ assertEquals(ds1, unwound.get(ds1).getDatasetSequence());
+ assertEquals(ds2, unwound.get(ds2).getDatasetSequence());
+ assertEquals(ds3, unwound.get(ds3).getDatasetSequence());
}
}
--- /dev/null
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import jalview.util.MapList;
+
+import java.util.Arrays;
+
+import org.junit.Test;
+
+public class AlignedCodonFrameTest
+{
+
+ /**
+ * Test the method that locates the first aligned sequence that has a mapping.
+ */
+ @Test
+ public void testFindAlignedSequence()
+ {
+ AlignmentI cdna = new Alignment(new SequenceI[]
+ {});
+ final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
+ seq1.createDatasetSequence();
+ cdna.addSequence(seq1);
+ final Sequence seq2 = new Sequence("Seq2", "-TA-GG-GG");
+ seq2.createDatasetSequence();
+ cdna.addSequence(seq2);
+
+ AlignmentI aa = new Alignment(new SequenceI[]
+ {});
+ final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ aseq1.createDatasetSequence();
+ aa.addSequence(aseq1);
+ final Sequence aseq2 = new Sequence("Seq2", "-LY-");
+ aseq2.createDatasetSequence();
+ aa.addSequence(aseq2);
+
+ /*
+ * Mapping from first DNA sequence to second AA sequence.
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ assertNull(acf.findAlignedSequence(seq1, aa));
+
+ MapList map = new MapList(new int[]
+ { 1, 6 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);
+
+ /*
+ * DNA seq1 maps to AA seq2
+ */
+ assertEquals(aa.getSequenceAt(1),
+ acf.findAlignedSequence(cdna
+ .getSequenceAt(0).getDatasetSequence(), aa));
+
+ assertEquals(cdna.getSequenceAt(0),
+ acf.findAlignedSequence(aa
+ .getSequenceAt(1).getDatasetSequence(), cdna));
+ }
+
+ /**
+ * Test the method that locates the mapped codon for a protein position.
+ */
+ @Test
+ public void testGetMappedRegion()
+ {
+ // introns lower case, exons upper case
+ final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
+ seq1.createDatasetSequence();
+ final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a");
+ seq2.createDatasetSequence();
+
+ final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ aseq1.createDatasetSequence();
+ final Sequence aseq2 = new Sequence("Seq2", "-LY-");
+ aseq2.createDatasetSequence();
+
+ /*
+ * First with no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ assertNull(acf.getMappedRegion(seq1, aseq1, 1));
+
+ /*
+ * Set up the mappings for the exons (upper-case bases)
+ */
+ MapList map = new MapList(new int[]
+ { 2, 4, 6, 6, 8, 9 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+ map = new MapList(new int[]
+ { 1, 2, 4, 5, 7, 8 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
+
+ assertEquals("[2, 4]",
+ Arrays.toString(acf.getMappedRegion(seq1, aseq1, 1)));
+ assertEquals("[6, 6, 8, 9]",
+ Arrays.toString(acf.getMappedRegion(seq1, aseq1, 2)));
+ assertEquals("[1, 2, 4, 4]",
+ Arrays.toString(acf.getMappedRegion(seq2, aseq2, 1)));
+ assertEquals("[5, 5, 7, 8]",
+ Arrays.toString(acf.getMappedRegion(seq2, aseq2, 2)));
+
+ /*
+ * No mapping from sequence 1 to sequence 2
+ */
+ assertNull(acf.getMappedRegion(seq1, aseq2, 1));
+ }
+
+ @Test
+ public void testGetMappedCodon()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
+ seq1.createDatasetSequence();
+ final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ aseq1.createDatasetSequence();
+
+ /*
+ * First with no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ assertNull(acf.getMappedCodon(seq1.getDatasetSequence(), 0));
+
+ /*
+ * Set up the mappings for the exons (upper-case bases)
+ */
+ MapList map = new MapList(new int[]
+ { 2, 4, 6, 6, 8, 9 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+
+ assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
+ aseq1.getDatasetSequence(), 1)));
+ assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
+ aseq1.getDatasetSequence(), 2)));
+ }
+}
--- /dev/null
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.fail;
+import jalview.util.MapList;
+
+import java.util.Iterator;
+
+import org.junit.Test;
+
+/**
+ * Unit tests for Mapping$AlignedCodonIterator
+ *
+ * @author gmcarstairs
+ *
+ */
+public class AlignedCodonIteratorTest
+{
+ /**
+ * Test normal case for iterating over aligned codons.
+ */
+ @Test
+ public void testNext()
+ {
+ SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
+ from.createDatasetSequence();
+ SequenceI to = new Sequence("Seq1", "-PQ-R-");
+ to.createDatasetSequence();
+ MapList map = new MapList(new int[]
+ { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[]
+ { 1, 3 }, 3, 1);
+ Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+ Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
+ AlignedCodon codon = codons.next();
+ assertEquals("[1, 3, 5]", codon.toString());
+ assertEquals("P", codon.product);
+ codon = codons.next();
+ assertEquals("[8, 10, 11]", codon.toString());
+ assertEquals("Q", codon.product);
+ codon = codons.next();
+ assertEquals("[13, 15, 17]", codon.toString());
+ assertEquals("R", codon.product);
+ assertFalse(codons.hasNext());
+ }
+
+ /**
+ * Test weird case where the mapping skips over a peptide.
+ */
+ @Test
+ public void testNext_unmappedPeptide()
+ {
+ SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
+ from.createDatasetSequence();
+ SequenceI to = new Sequence("Seq1", "-PQ-TR-");
+ to.createDatasetSequence();
+ MapList map = new MapList(new int[]
+ { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[]
+ { 1, 2, 4, 4 }, 3, 1);
+ Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+ Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
+ AlignedCodon codon = codons.next();
+ assertEquals("[1, 3, 5]", codon.toString());
+ assertEquals("P", codon.product);
+ codon = codons.next();
+ assertEquals("[8, 10, 11]", codon.toString());
+ assertEquals("Q", codon.product);
+ codon = codons.next();
+ assertEquals("[13, 15, 17]", codon.toString());
+ assertEquals("R", codon.product);
+ assertFalse(codons.hasNext());
+ }
+
+ /**
+ * Test for exception thrown for an incomplete codon.
+ */
+ @Test
+ public void testNext_incompleteCodon()
+ {
+ SequenceI from = new Sequence("Seq1", "-CgC-C-cCgTt");
+ from.createDatasetSequence();
+ SequenceI to = new Sequence("Seq1", "-PQ-R-");
+ to.createDatasetSequence();
+ MapList map = new MapList(new int[]
+ { 1, 1, 3, 4, 6, 6, 8, 8 }, new int[]
+ { 1, 3 }, 3, 1);
+ Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+ Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
+ AlignedCodon codon = codons.next();
+ assertEquals("[1, 3, 5]", codon.toString());
+ assertEquals("P", codon.product);
+ try
+ {
+ codon = codons.next();
+ fail("expected exception");
+ } catch (IncompleteCodonException e)
+ {
+ // expected
+ }
+ }
+
+ /**
+ * Test normal case for iterating over aligned codons.
+ */
+ @Test
+ public void testAnother()
+ {
+ SequenceI from = new Sequence("Seq1", "TGCCATTACCAG-");
+ from.createDatasetSequence();
+ SequenceI to = new Sequence("Seq1", "CHYQ");
+ to.createDatasetSequence();
+ MapList map = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1);
+ Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+ Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
+ AlignedCodon codon = codons.next();
+ assertEquals("[0, 1, 2]", codon.toString());
+ assertEquals("C", codon.product);
+ codon = codons.next();
+ assertEquals("[3, 4, 5]", codon.toString());
+ assertEquals("H", codon.product);
+ codon = codons.next();
+ assertEquals("[6, 7, 8]", codon.toString());
+ assertEquals("Y", codon.product);
+ codon = codons.next();
+ assertEquals("[9, 10, 11]", codon.toString());
+ assertEquals("Q", codon.product);
+ assertFalse(codons.hasNext());
+ }
+}
--- /dev/null
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+
+public class AlignedCodonTest
+{
+
+ @Test
+ public void testEquals()
+ {
+ AlignedCodon ac = new AlignedCodon(1, 3, 4);
+ assertTrue(ac.equals(null));
+ assertFalse(ac.equals("hello"));
+ assertFalse(ac.equals(new AlignedCodon(1, 3, 5)));
+ assertTrue(ac.equals(new AlignedCodon(1, 3, 4)));
+ assertTrue(ac.equals(ac));
+ }
+
+ @Test
+ public void testToString() {
+ AlignedCodon ac = new AlignedCodon(1, 3, 4);
+ assertEquals("[1, 3, 4]", ac.toString());
+ }
+}
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
+import jalview.util.MapList;
import java.io.IOException;
import java.util.Iterator;
"D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
"#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
"//";
+
+ private static final String AA_SEQS_1 =
+ ">Seq1Name\n" +
+ "K-QY--L\n" +
+ ">Seq2Name\n" +
+ "-R-FP-W-\n";
+
+ private static final String CDNA_SEQS_1 =
+ ">Seq1Name\n" +
+ "AC-GG--CUC-CAA-CT\n" +
+ ">Seq2Name\n" +
+ "-CG-TTA--ACG---AAGT\n";
+
+ private static final String CDNA_SEQS_2 =
+ ">Seq1Name\n" +
+ "GCTCGUCGTACT\n" +
+ ">Seq2Name\n" +
+ "GGGTCAGGCAGT\n";
// @formatter:on
+ private AlignmentI al;
- private Alignment al;
+ /**
+ * Helper method to load an alignment and ensure dataset sequences are set up.
+ *
+ * @param data
+ * @param format
+ * TODO
+ * @return
+ * @throws IOException
+ */
+ protected AlignmentI loadAlignment(final String data, String format)
+ throws IOException
+ {
+ Alignment a = new FormatAdapter().readFile(data,
+ AppletFormatAdapter.PASTE, format);
+ a.setDataset(null);
+ return a;
+ }
/*
* Read in Stockholm format test data including secondary structure
@Before
public void setUp() throws IOException
{
- al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
- AppletFormatAdapter.PASTE, "STH");
- for (int i = 0; i < al.getSequencesArray().length; ++i)
+ al = loadAlignment(TEST_DATA, "STH");
+ int i = 0;
+ for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
{
- al.addAnnotation(al.getSequenceAt(i).getAnnotation()[0]);
- al.getSequenceAt(i).getAnnotation()[0].setCalcId("CalcIdFor"
- + al.getSequenceAt(i).getName());
+ ann.setCalcId("CalcIdFor" + al.getSequenceAt(i).getName());
+ i++;
}
}
assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
assertFalse(iter.hasNext());
}
+
+ @Test
+ public void testDeleteAllAnnotations_includingAutocalculated()
+ {
+ AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
+ "Consensus", 0.5);
+ aa.autoCalculated = true;
+ al.addAnnotation(aa);
+ AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
+ assertEquals("Wrong number of annotations before deleting", 4,
+ anns.length);
+ al.deleteAllAnnotations(true);
+ assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
+ }
+
+ @Test
+ public void testDeleteAllAnnotations_excludingAutocalculated()
+ {
+ AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
+ "Consensus", 0.5);
+ aa.autoCalculated = true;
+ al.addAnnotation(aa);
+ AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
+ assertEquals("Wrong number of annotations before deleting", 4,
+ anns.length);
+ al.deleteAllAnnotations(false);
+ assertEquals("Not just one annotation left", 1,
+ al.getAlignmentAnnotation().length);
+ }
+
+ /**
+ * Tests for realigning as per a supplied alignment: Dna as Dna.
+ *
+ * Note: AlignedCodonFrame's state variables are named for protein-to-cDNA
+ * mapping, but can be exploited for a general 'sequence-to-sequence' mapping
+ * as here.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testAlignAs_dnaAsDna() throws IOException
+ {
+ // aligned cDNA:
+ AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
+ // unaligned cDNA:
+ AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA");
+
+ /*
+ * Make mappings between sequences. The 'aligned cDNA' is playing the role
+ * of what would normally be protein here.
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList ml = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 12 }, 1, 1);
+ acf.addMap(al2.getSequenceAt(0), al1.getSequenceAt(0), ml);
+ acf.addMap(al2.getSequenceAt(1), al1.getSequenceAt(1), ml);
+ al1.addCodonFrame(acf);
+
+ ((Alignment) al2).alignAs(al1, false, true);
+ assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0)
+ .getSequenceAsString());
+ assertEquals("-GG-GTC--AGG---CAGT", al2.getSequenceAt(1)
+ .getSequenceAsString());
+ }
+
+ /**
+ * Aligning protein from cDNA.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testAlignAs_proteinAsCdna() throws IOException
+ {
+ // see also AlignmentUtilsTests
+ AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
+ AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList ml = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1);
+ acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
+ acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
+ al2.addCodonFrame(acf);
+
+ ((Alignment) al2).alignAs(al1, false, true);
+ assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-R-F-P-W", al2.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Test aligning cdna as per protein alignment.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testAlignAs_cdnaAsProtein() throws IOException
+ {
+ /*
+ * Load alignments and add mappings for cDNA to protein
+ */
+ AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
+ AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList ml = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1);
+ acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
+ acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
+ al2.addCodonFrame(acf);
+
+ /*
+ * Realign DNA; currently keeping existing gaps in introns only
+ */
+ ((Alignment) al1).alignAs(al2, false, true);
+ assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
+ .getSequenceAsString());
+ assertEquals("---CGT---TAACGA---AGT", al1.getSequenceAt(1)
+ .getSequenceAsString());
+ }
+
+ /**
+ * Test aligning dna as per protein alignment, for the case where there are
+ * introns (i.e. some dna sites have no mapping from a peptide).
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
+ {
+ /*
+ * Load alignments and add mappings for cDNA to protein
+ */
+ String dna1 = "A-Aa-gG-GCC-cT-TT";
+ String dna2 = "c--CCGgg-TT--T-AA-A";
+ AlignmentI al1 = loadAlignment(">Seq1\n" + dna1 + "\n>Seq2\n" + dna2
+ + "\n", "FASTA");
+ AlignmentI al2 = loadAlignment(">Seq1\n-P--YK\n>Seq2\nG-T--F\n",
+ "FASTA");
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
+ // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
+ MapList ml1 = new MapList(new int[]
+ { 1, 2, 5, 8, 10, 12 }, new int[]
+ { 1, 3 }, 3, 1);
+ acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
+ MapList ml2 = new MapList(new int[]
+ { 2, 4, 7, 12 }, new int[]
+ { 1, 3 }, 3, 1);
+ acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
+ al2.addCodonFrame(acf);
+
+ /*
+ * Align ignoring gaps in dna introns and exons
+ */
+ ((Alignment) al1).alignAs(al2, false, false);
+ assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0)
+ .getSequenceAsString());
+ // note 1 gap in protein corresponds to 'gg-' in DNA (3 positions)
+ assertEquals("cCCGgg-TTT------AAA", al1.getSequenceAt(1)
+ .getSequenceAsString());
+
+ /*
+ * Reset and realign, preserving gaps in dna introns and exons
+ */
+ al1.getSequenceAt(0).setSequence(dna1);
+ al1.getSequenceAt(1).setSequence(dna2);
+ ((Alignment) al1).alignAs(al2, true, true);
+ // String dna1 = "A-Aa-gG-GCC-cT-TT";
+ // String dna2 = "c--CCGgg-TT--T-AA-A";
+ // assumption: we include 'the greater of' protein/dna gap lengths, not both
+ assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0)
+ .getSequenceAsString());
+ assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1)
+ .getSequenceAsString());
+ }
}
--- /dev/null
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.List;
+
+import org.junit.Test;
+
+public class ColumnSelectionTest
+{
+
+ @Test
+ public void testAddElement()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(2);
+ cs.addElement(5);
+ List<Integer> sel = cs.getSelected();
+ assertEquals(2, sel.size());
+ assertEquals(new Integer(2), sel.get(0));
+ assertEquals(new Integer(5), sel.get(1));
+ }
+
+ /**
+ * Test the remove method - in particular to verify that remove(int i) removes
+ * the element whose value is i, _NOT_ the i'th element.
+ */
+ @Test
+ public void testRemoveElement()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(2);
+ cs.addElement(5);
+
+ // removing elements not in the list has no effect
+ cs.removeElement(0);
+ cs.removeElement(1);
+ List<Integer> sel = cs.getSelected();
+ assertEquals(2, sel.size());
+ assertEquals(new Integer(2), sel.get(0));
+ assertEquals(new Integer(5), sel.get(1));
+
+ // removing an element in the list removes it
+ cs.removeElement(2);
+ assertEquals(1, sel.size());
+ assertEquals(new Integer(5), sel.get(0));
+ }
+}
--- /dev/null
+package jalview.datamodel;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import jalview.util.MapList;
+
+import org.junit.Test;
+
+public class DBRefEntryTest
+{
+
+ /**
+ * Tests for the method that compares equality of reference (but not mapping)
+ */
+ @Test
+ public void testEqualRef()
+ {
+ DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "V71633");
+ assertTrue(ref1.equalRef(ref1));
+ assertFalse(ref1.equalRef(null));
+
+ // comparison is not case sensitive
+ DBRefEntry ref2 = new DBRefEntry("uniprot", "1", "v71633");
+ assertTrue(ref1.equalRef(ref2));
+ assertTrue(ref2.equalRef(ref1));
+
+ // source, version and accessionid must match
+ assertFalse(ref1.equalRef(new DBRefEntry("UNIPRO", "1", "V71633")));
+ assertFalse(ref1.equalRef(new DBRefEntry("UNIPROT", "2", "V71633")));
+ assertFalse(ref1.equalRef(new DBRefEntry("UNIPROT", "1", "V71632")));
+
+ // presence of or differences in mappings are ignored
+ ref1.setMap(new Mapping(new MapList(new int[]
+ { 1, 3 }, new int[]
+ { 1, 1 }, 3, 1)));
+ assertTrue(ref1.equalRef(ref2));
+ assertTrue(ref2.equalRef(ref1));
+ ref1.setMap(new Mapping(new MapList(new int[]
+ { 1, 6 }, new int[]
+ { 1, 2 }, 3, 1)));
+ assertTrue(ref1.equalRef(ref2));
+ assertTrue(ref2.equalRef(ref1));
+ }
+}
--- /dev/null
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.Test;
+
+public class SearchResultsTest
+{
+
+ @Test
+ public void testToString()
+ {
+ SequenceI seq = new Sequence("", "abcdefghijklm");
+ SearchResults sr = new SearchResults();
+ sr.addResult(seq, 1, 1);
+ assertEquals("a", sr.toString());
+ sr.addResult(seq, 3, 5);
+ assertEquals("acde", sr.toString());
+
+ seq = new Sequence("", "pqrstuvwxy");
+ sr.addResult(seq, 6, 7);
+ assertEquals("acdeuv", sr.toString());
+ }
+}
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;
+import java.util.Arrays;
import java.util.List;
import org.junit.Before;
assertSame(annotation2, anns[1]);
}
+
+ @Test
+ public void testGetStartGetEnd()
+ {
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+
+ seq = new Sequence("test", "--AB-C-DEF--");
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+
+ seq = new Sequence("test", "----");
+ assertEquals(1, seq.getStart());
+ assertEquals(0, seq.getEnd()); // ??
+ }
+
+ /**
+ * Tests for the method that returns an alignment column position (base 1) for
+ * a given sequence position (base 1).
+ */
+ @Test
+ public void testFindIndex()
+ {
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ assertEquals(0, seq.findIndex(0));
+ assertEquals(1, seq.findIndex(1));
+ assertEquals(5, seq.findIndex(5));
+ assertEquals(6, seq.findIndex(6));
+ assertEquals(6, seq.findIndex(9));
+
+ seq = new Sequence("test", "-A--B-C-D-E-F--");
+ assertEquals(2, seq.findIndex(1));
+ assertEquals(5, seq.findIndex(2));
+ assertEquals(7, seq.findIndex(3));
+
+ // before start returns 0
+ assertEquals(0, seq.findIndex(0));
+ assertEquals(0, seq.findIndex(-1));
+
+ // beyond end returns last residue column
+ assertEquals(13, seq.findIndex(99));
+
+ }
+
+ /**
+ * Tests for the method that returns a dataset sequence position (base 1) for
+ * an aligned column position (base 0).
+ */
+ @Test
+ public void testFindPosition()
+ {
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ assertEquals(1, seq.findPosition(0));
+ assertEquals(6, seq.findPosition(5));
+ // assertEquals(-1, seq.findPosition(6)); // fails
+
+ seq = new Sequence("test", "AB-C-D--");
+ assertEquals(1, seq.findPosition(0));
+ assertEquals(2, seq.findPosition(1));
+ // gap position 'finds' residue to the right (not the left as per javadoc)
+ assertEquals(3, seq.findPosition(2));
+ assertEquals(3, seq.findPosition(3));
+ assertEquals(4, seq.findPosition(4));
+ assertEquals(4, seq.findPosition(5));
+ // returns 1 more than sequence length if off the end ?!?
+ assertEquals(5, seq.findPosition(6));
+ assertEquals(5, seq.findPosition(7));
+
+ seq = new Sequence("test", "--AB-C-DEF--");
+ assertEquals(1, seq.findPosition(0));
+ assertEquals(1, seq.findPosition(1));
+ assertEquals(1, seq.findPosition(2));
+ assertEquals(2, seq.findPosition(3));
+ assertEquals(3, seq.findPosition(4));
+ assertEquals(3, seq.findPosition(5));
+ assertEquals(4, seq.findPosition(6));
+ assertEquals(4, seq.findPosition(7));
+ assertEquals(5, seq.findPosition(8));
+ assertEquals(6, seq.findPosition(9));
+ assertEquals(7, seq.findPosition(10));
+ assertEquals(7, seq.findPosition(11));
+ }
+
+ @Test
+ public void testDeleteChars()
+ {
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+ seq.deleteChars(2, 3);
+ assertEquals("ABDEF", seq.getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(5, seq.getEnd());
+
+ seq = new Sequence("test", "ABCDEF");
+ seq.deleteChars(0, 2);
+ assertEquals("CDEF", seq.getSequenceAsString());
+ assertEquals(3, seq.getStart());
+ assertEquals(6, seq.getEnd());
+ }
+
+ @Test
+ public void testInsertCharAt()
+ {
+ // non-static methods:
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ seq.insertCharAt(0, 'z');
+ assertEquals("zABCDEF", seq.getSequenceAsString());
+ seq.insertCharAt(2, 2, 'x');
+ assertEquals("zAxxBCDEF", seq.getSequenceAsString());
+ // for static method see StringUtilsTest
+ }
+
+ /**
+ * Test the method that returns an array of aligned sequence positions where
+ * the array index is the data sequence position (both base 0).
+ */
+ @Test
+ public void testGapMap()
+ {
+ SequenceI seq = new Sequence("test", "-A--B-CD-E--F-");
+ seq.createDatasetSequence();
+ assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(seq.gapMap()));
+ }
+
+ /**
+ * Test the method that gets sequence features, either from the sequence or
+ * its dataset.
+ */
+ @Test
+ public void testGetSequenceFeatures()
+ {
+ SequenceI seq = new Sequence("test", "GATCAT");
+ seq.createDatasetSequence();
+
+ assertNull(seq.getSequenceFeatures());
+
+ /*
+ * SequenceFeature on sequence
+ */
+ SequenceFeature sf = new SequenceFeature();
+ seq.addSequenceFeature(sf);
+ SequenceFeature[] sfs = seq.getSequenceFeatures();
+ assertEquals(1, sfs.length);
+ assertSame(sf, sfs[0]);
+
+ /*
+ * SequenceFeature on sequence and dataset sequence; returns that on
+ * sequence
+ */
+ SequenceFeature sf2 = new SequenceFeature();
+ seq.getDatasetSequence().addSequenceFeature(sf2);
+ sfs = seq.getSequenceFeatures();
+ assertEquals(1, sfs.length);
+ assertSame(sf, sfs[0]);
+
+ /*
+ * SequenceFeature on dataset sequence only
+ */
+ seq.setSequenceFeatures(null);
+ sfs = seq.getSequenceFeatures();
+ assertEquals(1, sfs.length);
+ assertSame(sf2, sfs[0]);
+
+ /*
+ * Corrupt case - no SequenceFeature, dataset's dataset is the original
+ * sequence. Test shows no infinite loop results.
+ */
+ seq.getDatasetSequence().setSequenceFeatures(null);
+ seq.getDatasetSequence().setDatasetSequence(seq); // loop!
+ assertNull(seq.getSequenceFeatures());
+ }
}
package jalview.ext.paradise;
import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.FastaFile;
-import jalview.io.FormatAdapter;
import java.io.BufferedReader;
import java.io.File;
import org.junit.Test;
import MCview.PDBfile;
-
import compbio.util.FileUtil;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
public class TestAnnotate3D
{
sb.append(line + "\n");
}
assertTrue("No data returned by Annotate3D", sb.length() > 0);
- AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ final String lines = sb.toString();
+ AlignmentI al = new FormatAdapter().readFile(lines,
FormatAdapter.PASTE, "RNAML");
if (al == null || al.getHeight() == 0)
{
- System.out.println(sb.toString());
+ System.out.println(lines);
}
assertTrue("No alignment returned.", al != null);
assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
String sq_ = new String(sq.getSequence()).toLowerCase();
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
- if (new String(_struseq.getSequence()).toLowerCase().equals(
+ final String lowerCase = new String(_struseq.getSequence()).toLowerCase();
+ if (lowerCase.equals(
sq_))
{
struseq = _struseq;
package jalview.ext.rbvi.chimera;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
-import java.util.Arrays;
import java.util.Collection;
import org.junit.Test;
-import ext.edu.ucsf.rbvi.strucviz2.*;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
public class ChimeraConnect
{
@Test
public void test()
{
- StructureManager csm;
+ StructureManager csm;
ext.edu.ucsf.rbvi.strucviz2.ChimeraManager cm = new ChimeraManager(csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
- assertTrue("Couldn't launch chimera",cm.launchChimera(csm.getChimeraPaths()));
+ assertTrue("Couldn't launch chimera",
+ cm.launchChimera(StructureManager.getChimeraPaths()));
int n=0;
while (n++<100)
{
package jalview.ext.rbvi.chimera;
import static org.junit.Assert.assertTrue;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.FormatAdapter;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
-
public class JalviewChimeraView
{
@AfterClass
public static void tearDownAfterClass() throws Exception
{
+ try
+ {
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ } catch (Exception e)
+ {
+ // ignore NullPointerException thrown by JMol
+ }
}
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
@Before
public void setUp() throws IOException
{
+ // pin down annotation sort order for test
+ Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name());
+ Cache.applicationProperties.setProperty(
+ Preferences.SHOW_AUTOCALC_ABOVE, Boolean.TRUE.toString());
+
AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
AppletFormatAdapter.PASTE, "FASTA");
af = new AlignFrame(al, 700, 500);
@Test
public void testSelectType_showForSelected()
{
+ // sequences 1 and 2 have annotations IUPred and Jmol
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
setSelected(selectedSequencesCheckbox, true);
setSelected(hideCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
+
assertTrue(anns[5].visible); // JMol for seq3
assertFalse(anns[7].visible); // JMol for seq1
// ...now show them...
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
- assertFalse(anns[3].visible); // IUPRED
- assertTrue(anns[4].visible); // Beauty (not seq-related)
+ assertTrue(anns[3].visible); // Beauty (not seq-related)
+ assertFalse(anns[4].visible); // IUPRED
assertFalse(anns[5].visible); // JMol
assertFalse(anns[6].visible); // IUPRED
assertFalse(anns[7].visible); // JMol
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertEquals;
+
+import javax.swing.JScrollBar;
+
+import org.junit.Test;
+
+public class JvSwingUtilsTest
+{
+
+ @Test
+ public void testGetScrollBarProportion()
+ {
+ /*
+ * orientation, value, extent (width), min, max
+ */
+ JScrollBar sb = new JScrollBar(0, 125, 50, 0, 450);
+
+ /*
+ * operating range is 25 - 425 (400 wide) so value 125 is 100/400ths of this
+ * range
+ */
+ assertEquals(0.25f, JvSwingUtils.getScrollBarProportion(sb), 0.001f);
+ }
+
+ @Test
+ public void testGetScrollValueForProportion()
+ {
+ /*
+ * orientation, value, extent (width), min, max
+ */
+ JScrollBar sb = new JScrollBar(0, 125, 50, 0, 450);
+
+ /*
+ * operating range is 25 - 425 (400 wide) so value 125 is a quarter of this
+ * range
+ */
+ assertEquals(125, JvSwingUtils.getScrollValueForProportion(sb, 0.25f));
+ }
+}
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertTrue;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JTextField;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBSearchPanelTest
+{
+
+ @Before
+ public void setUp() throws Exception
+ {
+ }
+
+ @After
+ public void tearDown() throws Exception
+ {
+ }
+
+ @Test
+ public void populateCmbSearchTargetOptionsTest()
+ {
+ PDBSearchPanel searchPanel = new PDBSearchPanel(null);
+ assertTrue(searchPanel.getCmbSearchTarget().getItemCount() > 0);
+ searchPanel.populateCmbSearchTargetOptions();
+ }
+
+ @Test
+ public void txt_search_ActionPerformedTest()
+ {
+ PDBSearchPanel searchPanel = new PDBSearchPanel(null);
+ JInternalFrame mainFrame = searchPanel.getMainFrame();
+ JTextField txt_search = searchPanel.getTxtSearch();
+
+ assertTrue(mainFrame.getTitle().length() == 20);
+ assertTrue(mainFrame.getTitle()
+ .equalsIgnoreCase("PDB Sequence Fetcher"));
+
+ txt_search.setText("ABC");
+
+ assertTrue(mainFrame.getTitle().length() > 20);
+ assertTrue(!mainFrame.getTitle().equalsIgnoreCase(
+ "PDB Sequence Fetcher"));
+ }
+}
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Component;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JPanel;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PaintRefresherTest
+{
+ // TODO would prefer PaintRefresher to be a single rather than static
+ @Before
+ public void setUp()
+ {
+ PaintRefresher.components.clear();
+ }
+
+ @After
+ public void tearDown()
+ {
+ PaintRefresher.components.clear();
+ }
+
+ @Test
+ public void testRegister()
+ {
+ JPanel jp = new JPanel();
+ JPanel jp2 = new JPanel();
+ JPanel jp3 = new JPanel();
+ JPanel jp4 = new JPanel();
+ PaintRefresher.Register(jp, "22");
+ PaintRefresher.Register(jp, "22");
+ PaintRefresher.Register(jp2, "22");
+ PaintRefresher.Register(jp3, "33");
+ PaintRefresher.Register(jp3, "44");
+ PaintRefresher.Register(jp4, "44");
+
+ Map<String, List<Component>> registered = PaintRefresher.components;
+ assertEquals(3, registered.size());
+ assertEquals(2, registered.get("22").size());
+ assertEquals(1, registered.get("33").size());
+ assertEquals(2, registered.get("44").size());
+ assertTrue(registered.get("22").contains(jp));
+ assertTrue(registered.get("22").contains(jp2));
+ assertTrue(registered.get("33").contains(jp3));
+ assertTrue(registered.get("44").contains(jp3));
+ assertTrue(registered.get("44").contains(jp4));
+ }
+
+ @Test
+ public void testRemoveComponent()
+ {
+ Map<String, List<Component>> registered = PaintRefresher.components;
+
+ // no error with an empty PaintRefresher
+ JPanel jp = new JPanel();
+ JPanel jp2 = new JPanel();
+ PaintRefresher.RemoveComponent(jp);
+ assertTrue(registered.isEmpty());
+
+ /*
+ * Add then remove one item
+ */
+ PaintRefresher.Register(jp, "11");
+ PaintRefresher.RemoveComponent(jp);
+ assertTrue(registered.isEmpty());
+
+ /*
+ * Add one item under two ids, then remove it. It is removed from both ids,
+ * and the now empty id is removed.
+ */
+ PaintRefresher.Register(jp, "11");
+ PaintRefresher.Register(jp, "22");
+ PaintRefresher.Register(jp2, "22");
+ PaintRefresher.RemoveComponent(jp);
+ // "11" is removed as now empty, only 22/jp2 left
+ assertEquals(1, registered.size());
+ assertEquals(1, registered.get("22").size());
+ assertTrue(registered.get("22").contains(jp2));
+ }
+
+ @Test
+ public void testGetAssociatedPanels()
+ {
+ SequenceI [] seqs = new SequenceI[]{new Sequence("", "ABC")};
+ Alignment al = new Alignment(seqs);
+
+ /*
+ * AlignFrame constructor has side-effects: AlignmentPanel is constructed,
+ * and SeqCanvas, IdPanel, AlignmentPanel are all registered under the
+ * sequence set id of the viewport.
+ */
+ AlignmentViewport av = new AlignViewport(al);
+ AlignFrame af = new AlignFrame(al, 4, 1);
+ AlignmentPanel ap1 = af.alignPanel;
+ AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId());
+ assertEquals(1, panels.length);
+ assertSame(ap1, panels[0]);
+
+ panels = PaintRefresher.getAssociatedPanels(av.getSequenceSetId() + 1);
+ assertEquals(0, panels.length);
+ }
+}
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FormatAdapter;
-import jalview.util.MessageManager;
import java.awt.Component;
import java.io.IOException;
import org.junit.Before;
import org.junit.Test;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
+
public class PopupMenuTest
{
// 4 sequences x 13 positions
List<SequenceI> seqs = new ArrayList<SequenceI>();
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertFalse(menu.isEnabled());
- assertEquals(
- MessageManager.getString("label.add_reference_annotations"),
- menu.getText());
// now try null list
menu.setEnabled(true);
- testee.configureReferenceAnnotationsMenu(menu, seqs);
+ testee.configureReferenceAnnotationsMenu(menu, null);
assertFalse(menu.isEnabled());
}
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.util.Vector;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class StructureChooserTest
+{
+ Sequence seq;
+
+ @Before
+ public void setUp() throws Exception
+ {
+ seq = new Sequence("Test_Seq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26);
+ seq.setDatasetSequence(seq);
+ for (int x = 1; x < 5; x++)
+ {
+ DBRefEntry dbRef = new DBRefEntry();
+ dbRef.setAccessionId("XYZ_" + x);
+ seq.addDBRef(dbRef);
+ }
+
+ PDBEntry dbRef = new PDBEntry();
+ dbRef.setId("1tim");
+
+ Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+ pdbIds.add(dbRef);
+
+ seq.setPDBId(pdbIds);
+ }
+
+ @After
+ public void tearDown() throws Exception
+ {
+ seq = null;
+ }
+
+
+
+ @Test
+ public void buildQueryTest()
+ {
+ assertEquals(
+ "1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
+ StructureChooser.buildQuery(seq));
+ }
+
+ @Test
+ public void populateFilterComboBoxTest()
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { seq };
+ StructureChooser sc = new StructureChooser(selectedSeqs, seq,
+ null);
+ sc.populateFilterComboBox();
+ int optionsSize = sc.getCmbFilterOption().getItemCount();
+ assertEquals(2, optionsSize); // if structures are not discovered then don't
+ // populate filter options
+
+ sc.setStructuresDiscovered(true);
+ sc.populateFilterComboBox();
+ optionsSize = sc.getCmbFilterOption().getItemCount();
+ assertTrue(optionsSize > 2); // if structures are found, filter options
+ // should be populated
+ }
+
+ @Test
+ public void fetchStructuresInfoTest()
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { seq };
+ StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+ sc.fetchStructuresMetaData();
+ assertTrue(sc.getDiscoveredStructuresSet() != null);
+ assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
+
+ }
+}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
import java.io.File;
import java.util.Vector;
}
}
+ /**
+ * Check sequence features have been added
+ */
+ @Test
+ public void checkPDBSequenceFeatures()
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ StructureMapping[] mappings = ssm.getMapping("1gaq");
+ // suspect we really want to make assertions on sequence features
+ // in these mappings' sequencess
+ /*
+ * 1GAQ/A
+ */
+ SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
+ assertEquals(296, sf.length);
+ assertEquals("RESNUM", sf[0].getType());
+ assertEquals("GLU:19 1gaqA", sf[0].getDescription());
+ assertEquals("RESNUM", sf[295].getType());
+ assertEquals("TYR:314 1gaqA", sf[295].getDescription());
+
+ /*
+ * 1GAQ/B
+ */
+ sf = al.getSequenceAt(1).getSequenceFeatures();
+ assertEquals(98, sf.length);
+ assertEquals("RESNUM", sf[0].getType());
+ assertEquals("ALA:1 1gaqB", sf[0].getDescription());
+ assertEquals("RESNUM", sf[97].getType());
+ assertEquals("ALA:98 1gaqB", sf[97].getDescription());
+
+ /*
+ * 1GAQ/C
+ */
+ sf = al.getSequenceAt(2).getSequenceFeatures();
+ assertEquals(296, sf.length);
+ assertEquals("RESNUM", sf[0].getType());
+ assertEquals("GLU:19 1gaqC", sf[0].getDescription());
+ assertEquals("RESNUM", sf[295].getType());
+ assertEquals("TYR:314 1gaqC", sf[295].getDescription());
+ }
+
@Test
public void checkAnnotationWiring()
{
package jalview.io;
-import static org.junit.Assert.*;
+import static org.junit.Assert.fail;
+import org.junit.Ignore;
import org.junit.Test;
public class HtmlFileTest
{
@Test
+ @Ignore
public void test()
{
fail("Not yet implemented");
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import jalview.api.AlignmentViewPanel;
+import jalview.api.ViewStyleI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import java.io.File;
import org.junit.AfterClass;
+import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
@Test
public void gatherViewsHere() throws Exception
{
- int origCount = Desktop.getAlignframes() == null ? 0 : Desktop
- .getAlignframes().length;
+ int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
+ .getAlignFrames().length;
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", FormatAdapter.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
assertTrue("Didn't gather the views in the example file.",
- Desktop.getAlignframes().length == 1 + origCount);
+ Desktop.getAlignFrames().length == 1 + origCount);
}
}
}
+
+ @Test
+ public void testCopyViewSettings() throws Exception
+ {
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ Assert.assertTrue("Didn't read in the example file correctly.", af != null);
+ AlignmentViewPanel sps = null, groups = null;
+ for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
+ {
+ if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+ {
+ sps = ap;
+ }
+ if (ap.getViewName().contains("MAFFT"))
+ {
+ groups = ap;
+ }
+ }
+ assertTrue("Couldn't find the structure view", sps != null);
+ assertTrue("Couldn't find the MAFFT view", groups != null);
+
+ ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
+ ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
+ Assert.assertFalse(structureStyle.sameStyle(groupStyle));
+
+ groups.getAlignViewport().setViewStyle(structureStyle);
+ Assert.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
+ .getViewStyle()));
+ Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
+ .getViewStyle()));
+
+ }
}
--- /dev/null
+{
+ "responseHeader": {
+ "status": 400,
+ "QTime": 0,
+ "params": {
+ "sort": "",
+ "fl": "pdb_id",
+ "q": "text:abc OR text:go:abc AND molecule_sequence:['' TO *]",
+ "wt": "json",
+ "rows": "100"
+ }
+ },
+ "error": {
+ "msg": "org.apache.solr.search.SyntaxError: Cannot parse 'text:abc OR text:go:abc AND molecule_sequence:['' TO *]': Encountered \" \":\" \": \"\" at line 1, column 19.",
+ "code": 400
+ }
+}
\ No newline at end of file
--- /dev/null
+{
+ "responseHeader": {
+ "status": 0,
+ "QTime": 0,
+ "params": {
+ "sort": "",
+ "fl": "molecule_type,pdb_id,genus,gene_name,title",
+ "q": "text:abc AND molecule_sequence:['' TO *]",
+ "wt": "json",
+ "rows": "100"
+ }
+ },
+ "response": {
+ "numFound": 931,
+ "start": 0,
+ "docs": [
+ {
+ "pdb_id": "3qf4",
+ "title": "Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "THEMA_03290",
+ "Tmari_0285",
+ "TM_0287"
+ ]
+ },
+ {
+ "pdb_id": "4wbs",
+ "title": "Crystal structure of an ABC transporter related protein from Burkholderia phymatum",
+ "genus": [
+ "Burkholderia"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "Bphy_0327"
+ ]
+ },
+ {
+ "pdb_id": "1hn0",
+ "title": "CRYSTAL STRUCTURE OF CHONDROITIN ABC LYASE I FROM PROTEUS VULGARIS AT 1.9 ANGSTROMS RESOLUTION",
+ "genus": [
+ "Proteus"
+ ],
+ "molecule_type": "Protein"
+ },
+ {
+ "pdb_id": "4a82",
+ "title": "Fitted model of staphylococcus aureus sav1866 model ABC transporter in the human cystic fibrosis transmembrane conductance regulator volume map EMD-1966.",
+ "genus": [
+ "Homo"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "SAV1866"
+ ]
+ },
+ {
+ "pdb_id": "3nh6",
+ "title": "Nucleotide Binding Domain of human ABCB6 (apo structure)",
+ "genus": [
+ "Homo"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "ABCB6",
+ "UMAT",
+ "MTABC3",
+ "PRP"
+ ]
+ },
+ {
+ "pdb_id": "2nq2",
+ "title": "An inward-facing conformation of a putative metal-chelate type ABC transporter.",
+ "genus": [
+ "Haemophilus"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "HI_1471"
+ ]
+ },
+ {
+ "pdb_id": "3s4u",
+ "title": "Crystal structure of open, unliganded E. coli PhnD H157A",
+ "genus": [
+ "Escherichia"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "phnD",
+ "UTI89_C4699"
+ ]
+ },
+ {
+ "pdb_id": "4q4a",
+ "title": "Improved model of AMP-PNP bound TM287/288",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "TM_0288"
+ ]
+ },
+ {
+ "pdb_id": "1oxs",
+ "title": "Crystal structure of GlcV, the ABC-ATPase of the glucose ABC transporter from Sulfolobus solfataricus",
+ "genus": [
+ "Sulfolobus"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "SSO2850"
+ ]
+ },
+ {
+ "pdb_id": "4q4j",
+ "title": "Structure of crosslinked TM287/288_S498C_S520C mutant",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "TM_0288"
+ ]
+ },
+ {
+ "pdb_id": "1oxt",
+ "title": "Crystal structure of GlcV, the ABC-ATPase of the glucose ABC transporter from Sulfolobus solfataricus",
+ "genus": [
+ "Sulfolobus"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "SSO2850"
+ ]
+ },
+ {
+ "pdb_id": "4q4h",
+ "title": "TM287/288 in its apo state",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "TM_0288"
+ ]
+ },
+ {
+ "pdb_id": "3qf4",
+ "title": "Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "TM_0288"
+ ]
+ },
+ {
+ "pdb_id": "2fgk",
+ "title": "Crystal structure of the ABC-cassette E631Q mutant of HlyB with bound ATP",
+ "genus": [
+ "Escherichia"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "hlyB"
+ ]
+ }
+ ]
+ }
+}
\ No newline at end of file
*/
package jalview.schemes;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
-import java.io.IOException;
import java.util.Map;
-import java.util.Vector;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
import org.junit.Test;
public class DnaCodonTests
// note - this test will be removed once the old codon table (including
// Vectors) is removed
String additional = "", failtrans = "", differentTr = "";
- for (Object aa : ResidueProperties.codonHash.keySet())
+ for (String amacid : ResidueProperties.codonHash.keySet())
{
- String amacid = (String) aa;
- for (Object codons : ((Vector) ResidueProperties.codonHash
- .get(amacid)))
+ for (String codon : ResidueProperties.codonHash.get(amacid))
{
- String codon = (String) codons;
String trans = ResidueProperties.codonTranslate(codon);
String oldtrans = ResidueProperties._codonTranslate(codon);
if (trans == null)
--- /dev/null
+package jalview.schemes;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import org.junit.Test;
+
+public class ResiduePropertiesTest
+{
+
+ /**
+ * Test 'standard' codon translations (no ambiguity codes)
+ */
+ @Test
+ public void testCodonTranslate()
+ {
+ // standard translation table order column 1/2/3/4
+ assertEquals("F", ResidueProperties.codonTranslate("TTT"));
+ assertEquals("F", ResidueProperties.codonTranslate("TTC"));
+ assertEquals("L", ResidueProperties.codonTranslate("TTA"));
+ assertEquals("L", ResidueProperties.codonTranslate("TTG"));
+ assertEquals("L", ResidueProperties.codonTranslate("CTT"));
+ assertEquals("L", ResidueProperties.codonTranslate("CTC"));
+ assertEquals("L", ResidueProperties.codonTranslate("CTA"));
+ assertEquals("L", ResidueProperties.codonTranslate("CTG"));
+ assertEquals("I", ResidueProperties.codonTranslate("ATT"));
+ assertEquals("I", ResidueProperties.codonTranslate("ATC"));
+ assertEquals("I", ResidueProperties.codonTranslate("ATA"));
+ assertEquals("M", ResidueProperties.codonTranslate("ATG"));
+ assertEquals("V", ResidueProperties.codonTranslate("GTT"));
+ assertEquals("V", ResidueProperties.codonTranslate("GTC"));
+ assertEquals("V", ResidueProperties.codonTranslate("GTA"));
+ assertEquals("V", ResidueProperties.codonTranslate("GTG"));
+ assertEquals("S", ResidueProperties.codonTranslate("TCT"));
+ assertEquals("S", ResidueProperties.codonTranslate("TCC"));
+ assertEquals("S", ResidueProperties.codonTranslate("TCA"));
+ assertEquals("S", ResidueProperties.codonTranslate("TCG"));
+ assertEquals("P", ResidueProperties.codonTranslate("CCT"));
+ assertEquals("P", ResidueProperties.codonTranslate("CCC"));
+ assertEquals("P", ResidueProperties.codonTranslate("CCA"));
+ assertEquals("P", ResidueProperties.codonTranslate("CCG"));
+ assertEquals("T", ResidueProperties.codonTranslate("ACT"));
+ assertEquals("T", ResidueProperties.codonTranslate("ACC"));
+ assertEquals("T", ResidueProperties.codonTranslate("ACA"));
+ assertEquals("T", ResidueProperties.codonTranslate("ACG"));
+ assertEquals("A", ResidueProperties.codonTranslate("GCT"));
+ assertEquals("A", ResidueProperties.codonTranslate("GCC"));
+ assertEquals("A", ResidueProperties.codonTranslate("GCA"));
+ assertEquals("A", ResidueProperties.codonTranslate("GCG"));
+ assertEquals("Y", ResidueProperties.codonTranslate("TAT"));
+ assertEquals("Y", ResidueProperties.codonTranslate("TAC"));
+ assertEquals("STOP", ResidueProperties.codonTranslate("TAA"));
+ assertEquals("STOP", ResidueProperties.codonTranslate("TAG"));
+ assertEquals("H", ResidueProperties.codonTranslate("CAT"));
+ assertEquals("H", ResidueProperties.codonTranslate("CAC"));
+ assertEquals("Q", ResidueProperties.codonTranslate("CAA"));
+ assertEquals("Q", ResidueProperties.codonTranslate("CAG"));
+ assertEquals("N", ResidueProperties.codonTranslate("AAT"));
+ assertEquals("N", ResidueProperties.codonTranslate("AAC"));
+ assertEquals("K", ResidueProperties.codonTranslate("AAA"));
+ assertEquals("K", ResidueProperties.codonTranslate("AAG"));
+ assertEquals("D", ResidueProperties.codonTranslate("GAT"));
+ assertEquals("D", ResidueProperties.codonTranslate("GAC"));
+ assertEquals("E", ResidueProperties.codonTranslate("GAA"));
+ assertEquals("E", ResidueProperties.codonTranslate("GAG"));
+ assertEquals("C", ResidueProperties.codonTranslate("TGT"));
+ assertEquals("C", ResidueProperties.codonTranslate("TGC"));
+ assertEquals("STOP", ResidueProperties.codonTranslate("TGA"));
+ assertEquals("W", ResidueProperties.codonTranslate("TGG"));
+ assertEquals("R", ResidueProperties.codonTranslate("CGT"));
+ assertEquals("R", ResidueProperties.codonTranslate("CGC"));
+ assertEquals("R", ResidueProperties.codonTranslate("CGA"));
+ assertEquals("R", ResidueProperties.codonTranslate("CGG"));
+ assertEquals("S", ResidueProperties.codonTranslate("AGT"));
+ assertEquals("S", ResidueProperties.codonTranslate("AGC"));
+ assertEquals("R", ResidueProperties.codonTranslate("AGA"));
+ assertEquals("R", ResidueProperties.codonTranslate("AGG"));
+ assertEquals("G", ResidueProperties.codonTranslate("GGT"));
+ assertEquals("G", ResidueProperties.codonTranslate("GGC"));
+ assertEquals("G", ResidueProperties.codonTranslate("GGA"));
+ assertEquals("G", ResidueProperties.codonTranslate("GGG"));
+ }
+
+ /**
+ * Test a sample of codon translations involving ambiguity codes. Should
+ * return a protein value where the ambiguity does not affect the translation.
+ */
+ @Test
+ public void testCodonTranslate_ambiguityCodes()
+ {
+ // Y is C or T
+ assertEquals("C", ResidueProperties.codonTranslate("TGY"));
+ // Phenylalanine first base variation
+ assertEquals("L", ResidueProperties.codonTranslate("YTA"));
+
+ // W is A or T
+ assertEquals("L", ResidueProperties.codonTranslate("CTW"));
+ assertNull(ResidueProperties.codonTranslate("TTW"));
+
+ // S is G or C
+ assertEquals("G", ResidueProperties.codonTranslate("GGS"));
+ assertNull(ResidueProperties.codonTranslate("ATS"));
+
+ // K is T or G
+ assertEquals("S", ResidueProperties.codonTranslate("TCK"));
+ assertNull(ResidueProperties.codonTranslate("ATK"));
+
+ // M is C or A
+ assertEquals("T", ResidueProperties.codonTranslate("ACM"));
+ // Arginine first base variation
+ assertEquals("R", ResidueProperties.codonTranslate("MGA"));
+ assertEquals("R", ResidueProperties.codonTranslate("MGG"));
+ assertNull(ResidueProperties.codonTranslate("TAM"));
+
+ // D is A, G or T
+ assertEquals("P", ResidueProperties.codonTranslate("CCD"));
+ assertNull(ResidueProperties.codonTranslate("AAD"));
+
+ // V is A, C or G
+ assertEquals("V", ResidueProperties.codonTranslate("GTV"));
+ assertNull(ResidueProperties.codonTranslate("TTV"));
+
+ // H is A, C or T
+ assertEquals("A", ResidueProperties.codonTranslate("GCH"));
+ assertEquals("I", ResidueProperties.codonTranslate("ATH"));
+ assertNull(ResidueProperties.codonTranslate("AGH"));
+
+ // B is C, G or T
+ assertEquals("P", ResidueProperties.codonTranslate("CCB"));
+ assertNull(ResidueProperties.codonTranslate("TAB"));
+
+ // R is A or G
+ // additional tests for JAL-1685 (resolved)
+ assertEquals("L", ResidueProperties.codonTranslate("CTR"));
+ assertEquals("V", ResidueProperties.codonTranslate("GTR"));
+ assertEquals("S", ResidueProperties.codonTranslate("TCR"));
+ assertEquals("P", ResidueProperties.codonTranslate("CCR"));
+ assertEquals("T", ResidueProperties.codonTranslate("ACR"));
+ assertEquals("A", ResidueProperties.codonTranslate("GCR"));
+ assertEquals("R", ResidueProperties.codonTranslate("CGR"));
+ assertEquals("G", ResidueProperties.codonTranslate("GGR"));
+ assertEquals("R", ResidueProperties.codonTranslate("AGR"));
+ assertEquals("E", ResidueProperties.codonTranslate("GAR"));
+ assertEquals("K", ResidueProperties.codonTranslate("AAR"));
+ assertEquals("L", ResidueProperties.codonTranslate("TTR"));
+ assertEquals("Q", ResidueProperties.codonTranslate("CAR"));
+ assertEquals("STOP", ResidueProperties.codonTranslate("TAR"));
+ assertEquals("STOP", ResidueProperties.codonTranslate("TRA"));
+ // Arginine first and third base ambiguity
+ assertEquals("R", ResidueProperties.codonTranslate("MGR"));
+ assertNull(ResidueProperties.codonTranslate("ATR"));
+
+ // N is any base; 8 proteins accept any base in 3rd position
+ assertEquals("L", ResidueProperties.codonTranslate("CTN"));
+ assertEquals("V", ResidueProperties.codonTranslate("GTN"));
+ assertEquals("S", ResidueProperties.codonTranslate("TCN"));
+ assertEquals("P", ResidueProperties.codonTranslate("CCN"));
+ assertEquals("T", ResidueProperties.codonTranslate("ACN"));
+ assertEquals("A", ResidueProperties.codonTranslate("GCN"));
+ assertEquals("R", ResidueProperties.codonTranslate("CGN"));
+ assertEquals("G", ResidueProperties.codonTranslate("GGN"));
+ assertNull(ResidueProperties.codonTranslate("ATN"));
+ assertNull(ResidueProperties.codonTranslate("ANT"));
+ assertNull(ResidueProperties.codonTranslate("NAT"));
+ assertNull(ResidueProperties.codonTranslate("ANN"));
+ assertNull(ResidueProperties.codonTranslate("NNA"));
+ assertNull(ResidueProperties.codonTranslate("NNN"));
+
+ // some random stuff
+ assertNull(ResidueProperties.codonTranslate("YWB"));
+ assertNull(ResidueProperties.codonTranslate("VHD"));
+ assertNull(ResidueProperties.codonTranslate("WSK"));
+ }
+}
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+
+import org.junit.Assert;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import MCview.PDBfile;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
-import org.junit.Assert;
-import org.junit.Test;
-
-import MCview.PDBfile;
-
public class Mapping
{
* msd numbering, not pdb res numbering.
*/
@Test
+ @Ignore
public void pdbEntryPositionMap() throws Exception
{
fail("This test intentionally left to fail");
}
@Test
+ @Ignore
public void testPDBentryMapping() throws Exception
{
fail("This test intentionally left to fail");
--- /dev/null
+package jalview.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.AlignedCodonFrame;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class StructureSelectionManagerTest
+{
+ private StructureSelectionManager ssm;
+
+ @Before
+ public void setUp()
+ {
+ ssm = new StructureSelectionManager();
+ }
+
+ @Test
+ public void testAddMapping()
+ {
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+
+ /*
+ * One mapping only.
+ */
+ ssm.addMapping(acf1);
+ assertEquals(1, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ assertEquals(1, ssm.seqMappingRefCounts.size());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
+
+ /*
+ * A second mapping.
+ */
+ ssm.addMapping(acf2);
+ assertEquals(2, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ assertTrue(ssm.seqmappings.contains(acf2));
+ assertEquals(2, ssm.seqMappingRefCounts.size());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+
+ /*
+ * A second reference to the first mapping.
+ */
+ ssm.addMapping(acf1);
+ assertEquals(2, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ assertTrue(ssm.seqmappings.contains(acf2));
+ assertEquals(2, ssm.seqMappingRefCounts.size());
+ assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+ }
+
+ @Test
+ public void testAddMappings()
+ {
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ AlignedCodonFrame acf3 = new AlignedCodonFrame();
+
+ Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
+ set1.add(acf1);
+ set1.add(acf2);
+ Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
+ set2.add(acf2);
+ set2.add(acf3);
+
+ /*
+ * Adding both sets adds acf2 twice and acf1 and acf3 once each.
+ */
+ ssm.addMappings(set1);
+ ssm.addMappings(set2);
+
+ assertEquals(3, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ assertTrue(ssm.seqmappings.contains(acf2));
+ assertTrue(ssm.seqmappings.contains(acf3));
+ assertEquals(3, ssm.seqMappingRefCounts.size());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
+ assertEquals(2, ssm.seqMappingRefCounts.get(acf2).intValue());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+ }
+
+ @Test
+ public void testRemoveMapping()
+ {
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ ssm.addMapping(acf1);
+
+ /*
+ * Add one and remove it.
+ */
+ ssm.removeMapping(acf1);
+ ssm.removeMapping(acf2);
+ assertEquals(0, ssm.seqmappings.size());
+ assertEquals(0, ssm.seqMappingRefCounts.size());
+
+ /*
+ * Add one twice and remove it once.
+ */
+ ssm.addMapping(acf1);
+ ssm.addMapping(acf2);
+ ssm.addMapping(acf1);
+ ssm.removeMapping(acf1);
+ assertEquals(2, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ assertTrue(ssm.seqmappings.contains(acf2));
+ assertEquals(2, ssm.seqMappingRefCounts.size());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+
+ /*
+ * Remove both once more to clear the set.
+ */
+ ssm.removeMapping(acf1);
+ ssm.removeMapping(acf2);
+ assertEquals(0, ssm.seqmappings.size());
+ assertEquals(0, ssm.seqMappingRefCounts.size());
+ }
+
+ @Test
+ public void testRemoveMappings()
+ {
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ AlignedCodonFrame acf3 = new AlignedCodonFrame();
+
+ /*
+ * Initial ref counts are 3/2/1:
+ */
+ ssm.addMapping(acf1);
+ ssm.addMapping(acf1);
+ ssm.addMapping(acf1);
+ ssm.addMapping(acf2);
+ ssm.addMapping(acf2);
+ ssm.addMapping(acf3);
+
+ Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
+ set1.add(acf1);
+ set1.add(acf2);
+ Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
+ set2.add(acf2);
+ set2.add(acf3);
+
+ /*
+ * Remove one ref each to acf1, acf2, counts are now 2/1/1:
+ */
+ ssm.removeMappings(set1);
+ assertEquals(3, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ assertTrue(ssm.seqmappings.contains(acf2));
+ assertTrue(ssm.seqmappings.contains(acf3));
+ assertEquals(3, ssm.seqMappingRefCounts.size());
+ assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+ assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+
+ /*
+ * Remove one ref each to acf2, acf3 - they are removed
+ */
+ ssm.removeMappings(set2);
+ assertEquals(1, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ assertEquals(1, ssm.seqMappingRefCounts.size());
+ assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
+ }
+}
--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Test;
+
+public class ComparisonTest
+{
+
+ @Test
+ public void testIsGap()
+ {
+ assertTrue(Comparison.isGap('-'));
+ assertTrue(Comparison.isGap('.'));
+ assertTrue(Comparison.isGap(' '));
+ assertFalse(Comparison.isGap('X'));
+ assertFalse(Comparison.isGap('x'));
+ assertFalse(Comparison.isGap('*'));
+ assertFalse(Comparison.isGap('G'));
+ }
+
+ /**
+ * Test for isNucleotide is that sequences in a dataset are more than 85%
+ * AGCTU. Test is not case-sensitive and ignores gaps.
+ */
+ @Test
+ public void testIsNucleotide() {
+ SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
+ assertFalse(Comparison.isNucleotide(new SequenceI[]
+ { seq }));
+
+ seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
+ assertFalse(Comparison.isNucleotide(new SequenceI[]
+ { seq }));
+
+ seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
+ assertTrue(Comparison.isNucleotide(new SequenceI[]
+ { seq }));
+
+ seq = new Sequence("eightyfivepercentgapped",
+ "--agc--tuA--GCPV-a---gct-uA-GC---UV");
+ assertFalse(Comparison.isNucleotide(new SequenceI[]
+ { seq }));
+
+ seq = new Sequence("nineypercentgapped",
+ "ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
+ assertTrue(Comparison.isNucleotide(new SequenceI[]
+ { seq }));
+
+ seq = new Sequence("allgap", "---------");
+ assertFalse(Comparison.isNucleotide(new SequenceI[]
+ { seq }));
+
+ seq = new Sequence("DNA", "ACTugGCCAG");
+ SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
+ assertTrue(Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 })); // 90% DNA
+ assertFalse(Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 })); // 80% DNA
+
+ seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
+ // 12/14 = 85.7%
+ assertTrue(Comparison.isNucleotide(new SequenceI[]
+ { seq }));
+
+ assertFalse(Comparison.isNucleotide(null));
+ }
+
+ /**
+ * Test percentage identity calculation for two sequences.
+ */
+ @Test
+ public void testPID_matchGaps()
+ {
+ String seq1 = "ABCDEF";
+ String seq2 = "abcdef";
+ assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
+
+ // comparison range defaults to length of first sequence
+ seq2 = "abcdefghijklmnopqrstuvwxyz";
+ assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
+
+ seq2 = "a---bcdef";
+ }
+}
--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class MapListTest
+{
+
+ @Test
+ public void testSomething()
+ {
+ MapList ml = new MapList(new int[]
+ { 1, 5, 10, 15, 25, 20 }, new int[]
+ { 51, 1 }, 1, 3);
+ MapList ml1 = new MapList(new int[]
+ { 1, 3, 17, 4 }, new int[]
+ { 51, 1 }, 1, 3);
+ MapList ml2 = new MapList(new int[]
+ { 1, 60 }, new int[]
+ { 1, 20 }, 3, 1);
+ // test internal consistency
+ int to[] = new int[51];
+ testMap(ml, 1, 60);
+ MapList mldna = new MapList(new int[]
+ { 2, 2, 6, 8, 12, 16 }, new int[]
+ { 1, 3 }, 3, 1);
+ int[] frm = mldna.locateInFrom(1, 1);
+ testLocateFrom(mldna, 1, 1, new int[]
+ { 2, 2, 6, 7 });
+ testMap(mldna, 1, 3);
+ /*
+ * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
+ * toofrom=ml.shiftFrom(too[0]);
+ * System.out.println("ShiftFrom("+from+")=="+too[0]+" %
+ * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
+ */
+ }
+
+ private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
+ {
+ int[] frm = mldna.locateInFrom(i, j);
+ Assert.assertEquals("Failed test locate from " + i + " to " + j,
+ Arrays.toString(frm), Arrays.toString(ks));
+ }
+
+ /**
+ * test routine. not incremental.
+ *
+ * @param ml
+ * @param fromS
+ * @param fromE
+ */
+ private void testMap(MapList ml, int fromS, int fromE)
+ {
+ // todo convert to JUnit style tests
+ for (int from = 1; from <= 25; from++)
+ {
+ int[] too = ml.shiftFrom(from);
+ System.out.print("ShiftFrom(" + from + ")==");
+ if (too == null)
+ {
+ System.out.print("NaN\n");
+ }
+ else
+ {
+ System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
+ System.out.print("\t+--+\t");
+ int[] toofrom = ml.shiftTo(too[0]);
+ if (toofrom != null)
+ {
+ if (toofrom[0] != from)
+ {
+ System.err.println("Mapping not reflexive:" + from + " "
+ + too[0] + "->" + toofrom[0]);
+ }
+ System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
+ + " % " + toofrom[1] + " (" + toofrom[2] + ")");
+ }
+ else
+ {
+ System.out.println("ShiftTo(" + too[0] + ")=="
+ + "NaN! - not Bijective Mapping!");
+ }
+ }
+ }
+ int mmap[][] = ml.makeFromMap();
+ System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
+ + mmap[0][2] + " " + mmap[0][3] + " ");
+ for (int i = 1; i <= mmap[1].length; i++)
+ {
+ if (mmap[1][i - 1] == -1)
+ {
+ System.out.print(i + "=XXX");
+
+ }
+ else
+ {
+ System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
+ }
+ if (i % 20 == 0)
+ {
+ System.out.print("\n");
+ }
+ else
+ {
+ System.out.print(",");
+ }
+ }
+ // test range function
+ System.out.print("\nTest locateInFrom\n");
+ {
+ int f = mmap[0][2], t = mmap[0][3];
+ while (f <= t)
+ {
+ System.out.println("Range " + f + " to " + t);
+ int rng[] = ml.locateInFrom(f, t);
+ if (rng != null)
+ {
+ for (int i = 0; i < rng.length; i++)
+ {
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\nReversed\n");
+ rng = ml.locateInFrom(t, f);
+ if (rng != null)
+ {
+ for (int i = 0; i < rng.length; i++)
+ {
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\n");
+ f++;
+ t--;
+ }
+ }
+ System.out.print("\n");
+ mmap = ml.makeToMap();
+ System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
+ + mmap[0][2] + " " + mmap[0][3] + " ");
+ for (int i = 1; i <= mmap[1].length; i++)
+ {
+ if (mmap[1][i - 1] == -1)
+ {
+ System.out.print(i + "=XXX");
+
+ }
+ else
+ {
+ System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
+ }
+ if (i % 20 == 0)
+ {
+ System.out.print("\n");
+ }
+ else
+ {
+ System.out.print(",");
+ }
+ }
+ System.out.print("\n");
+ // test range function
+ System.out.print("\nTest locateInTo\n");
+ {
+ int f = mmap[0][2], t = mmap[0][3];
+ while (f <= t)
+ {
+ System.out.println("Range " + f + " to " + t);
+ int rng[] = ml.locateInTo(f, t);
+ if (rng != null)
+ {
+ for (int i = 0; i < rng.length; i++)
+ {
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\nReversed\n");
+ rng = ml.locateInTo(t, f);
+ if (rng != null)
+ {
+ for (int i = 0; i < rng.length; i++)
+ {
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ f++;
+ t--;
+ System.out.print("\n");
+ }
+ }
+ }
+
+ /**
+ * Tests for method that locates ranges in the 'from' map for given range in
+ * the 'to' map.
+ */
+ @Test
+ public void testLocateInFrom_noIntrons()
+ {
+ /*
+ * Simple mapping with no introns
+ */
+ int[] codons = new int[]
+ { 1, 12 };
+ int[] protein = new int[]
+ { 1, 4 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+ assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
+ assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
+ assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
+ assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
+ assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
+ assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
+ assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
+ assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
+ assertEquals("[4, 12]", Arrays.toString(ml.locateInFrom(2, 4)));
+ assertEquals("[7, 12]", Arrays.toString(ml.locateInFrom(3, 4)));
+ assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
+
+ assertNull(ml.locateInFrom(0, 0));
+ assertNull(ml.locateInFrom(1, 5));
+ assertNull(ml.locateInFrom(-1, 1));
+ }
+
+ /**
+ * Tests for method that locates ranges in the 'from' map for given range in
+ * the 'to' map.
+ */
+ @Test
+ public void testLocateInFrom_withIntrons()
+ {
+ /*
+ * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
+ * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
+ */
+ int[] codons =
+ { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein =
+ { 1, 4 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+ assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
+ assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
+ assertEquals("[10, 10, 12, 12, 14, 14]",
+ Arrays.toString(ml.locateInFrom(3, 3)));
+ assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
+ }
+
+ /**
+ * Tests for method that locates ranges in the 'to' map for given range in the
+ * 'from' map.
+ */
+ @Test
+ public void testLocateInTo_noIntrons()
+ {
+ /*
+ * Simple mapping with no introns
+ */
+ int[] codons = new int[]
+ { 1, 12 };
+ int[] protein = new int[]
+ { 1, 4 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
+ assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
+ assertEquals("[3, 3]", Arrays.toString(ml.locateInTo(7, 9)));
+ assertEquals("[4, 4]", Arrays.toString(ml.locateInTo(10, 12)));
+ assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 6)));
+ assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(1, 9)));
+ assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 12)));
+ assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
+ assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(4, 12)));
+
+ /*
+ * A part codon is treated as if a whole one.
+ */
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
+ assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 4)));
+ assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(2, 8)));
+ assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
+ assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11)));
+
+ assertNull(ml.locateInTo(0, 0));
+ assertNull(ml.locateInTo(1, 13));
+ assertNull(ml.locateInTo(-1, 1));
+ }
+
+ /**
+ * Tests for method that locates ranges in the 'to' map for given range in the
+ * 'from' map.
+ */
+ @Test
+ public void testLocateInTo_withIntrons()
+ {
+ /*
+ * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
+ * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
+ */
+ int[] codons =
+ { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ /*
+ * Mapped proteins at positions 1, 3, 4, 6 in the sequence
+ */
+ int[] protein =
+ { 1, 1, 3, 4, 6, 6 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+
+ /*
+ * Can't map from an unmapped position
+ */
+ assertNull(ml.locateInTo(1, 2));
+ assertNull(ml.locateInTo(2, 4));
+ assertNull(ml.locateInTo(4, 4));
+
+ /*
+ * Valid range or subrange of codon1 maps to protein1.
+ */
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 3)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 5)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 3)));
+ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 5)));
+
+ // codon position 6 starts the next protein:
+ assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.locateInTo(3, 6)));
+
+ // codon positions 7 to 17 (part) cover proteins 2/3/4 at positions 3/4/6
+ assertEquals("[3, 4, 6, 6]", Arrays.toString(ml.locateInTo(7, 17)));
+
+ }
+
+ /**
+ * Test equals method.
+ */
+ @Test
+ public void testEquals()
+ {
+ int[] codons = new int[]
+ { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein = new int[]
+ { 1, 4 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+ MapList ml1 = new MapList(codons, protein, 3, 1); // same values
+ MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
+ MapList ml3 = new MapList(codons, protein, 3, 2); // toRatio differs
+ codons[2] = 4;
+ MapList ml6 = new MapList(codons, protein, 3, 1); // fromShifts differ
+ protein[1] = 3;
+ MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
+
+ assertTrue(ml.equals(ml));
+ assertTrue(ml.equals(ml1));
+ assertTrue(ml1.equals(ml));
+
+ assertFalse(ml.equals(null));
+ assertFalse(ml.equals("hello"));
+ assertFalse(ml.equals(ml2));
+ assertFalse(ml.equals(ml3));
+ assertFalse(ml.equals(ml6));
+ assertFalse(ml.equals(ml7));
+ assertFalse(ml6.equals(ml7));
+
+ try
+ {
+ MapList ml4 = new MapList(codons, null, 3, 1); // toShifts null
+ assertFalse(ml.equals(ml4));
+ } catch (NullPointerException e)
+ {
+ // actually thrown by constructor before equals can be called
+ }
+ try
+ {
+ MapList ml5 = new MapList(null, protein, 3, 1); // fromShifts null
+ assertFalse(ml.equals(ml5));
+ } catch (NullPointerException e)
+ {
+ // actually thrown by constructor before equals can be called
+ }
+ }
+
+ /**
+ * Test for the method that flattens a list of ranges into a single array.
+ */
+ @Test
+ public void testGetRanges()
+ {
+ List<int[]> ranges = new ArrayList<int[]>();
+ ranges.add(new int[]
+ { 2, 3 });
+ ranges.add(new int[]
+ { 5, 6 });
+ assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
+ }
+
+ /**
+ * Check state after construction
+ */
+ @Test
+ public void testConstructor()
+ {
+ int[] codons =
+ { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein =
+ { 1, 1, 3, 4, 6, 6 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+ assertEquals(3, ml.getFromRatio());
+ assertEquals(2, ml.getFromLowest());
+ assertEquals(18, ml.getFromHighest());
+ assertEquals(1, ml.getToLowest());
+ assertEquals(6, ml.getToHighest());
+ assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
+ prettyPrint(ml.getFromRanges()));
+ assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml.getToRanges()));
+
+ /*
+ * Also copy constructor
+ */
+ MapList ml2 = new MapList(ml);
+ assertEquals(3, ml2.getFromRatio());
+ assertEquals(2, ml2.getFromLowest());
+ assertEquals(18, ml2.getFromHighest());
+ assertEquals(1, ml2.getToLowest());
+ assertEquals(6, ml2.getToHighest());
+ assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
+ prettyPrint(ml2.getFromRanges()));
+ assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml2.getToRanges()));
+ }
+
+ /**
+ * Convert a List of {[i, j], [k, l], ...} to "[[i, j], [k, l], ...]"
+ *
+ * @param ranges
+ * @return
+ */
+ private String prettyPrint(List<int[]> ranges)
+ {
+ StringBuilder sb = new StringBuilder(ranges.size() * 5);
+ boolean first = true;
+ sb.append("{");
+ for (int[] range : ranges)
+ {
+ if (!first)
+ {
+ sb.append(", ");
+ }
+ sb.append(Arrays.toString(range));
+ first = false;
+ }
+ sb.append("}");
+ return sb.toString();
+ }
+
+ /**
+ * Test the method that creates an inverse mapping
+ */
+ @Test
+ public void testGetInverse()
+ {
+ int[] codons =
+ { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein =
+ { 1, 1, 3, 4, 6, 6 };
+
+ MapList ml = new MapList(codons, protein, 3, 1);
+ MapList ml2 = ml.getInverse();
+ assertEquals(ml.getFromRatio(), ml2.getToRatio());
+ assertEquals(ml.getFromRatio(), ml2.getToRatio());
+ assertEquals(ml.getToHighest(), ml2.getFromHighest());
+ assertEquals(ml.getFromHighest(), ml2.getToHighest());
+ assertEquals(prettyPrint(ml.getFromRanges()),
+ prettyPrint(ml2.getToRanges()));
+ assertEquals(prettyPrint(ml.getToRanges()),
+ prettyPrint(ml2.getFromRanges()));
+ }
+}
--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignViewport;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Set;
+
+import org.junit.Test;
+
+public class MappingUtilsTest
+{
+ private AlignViewportI dnaView;
+ private AlignViewportI proteinView;
+
+ /**
+ * Simple test of mapping with no intron involved.
+ */
+ @Test
+ public void testBuildSearchResults()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
+ seq1.createDatasetSequence();
+
+ final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ aseq1.createDatasetSequence();
+
+ /*
+ * Map dna bases 1-6 to protein residues 1-2
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[]
+ { 1, 6 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+ Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+
+ /*
+ * Check protein residue 1 maps to codon 1-3, 2 to codon 4-6
+ */
+ SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
+ assertEquals(1, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+
+ /*
+ * Check inverse mappings, from codons 1-3, 4-6 to protein 1, 2
+ */
+ for (int i = 1; i < 7; i++)
+ {
+ sr = MappingUtils.buildSearchResults(seq1, i, acfList);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(aseq1.getDatasetSequence(), m.getSequence());
+ int residue = i > 3 ? 2 : 1;
+ assertEquals(residue, m.getStart());
+ assertEquals(residue, m.getEnd());
+ }
+ }
+
+ /**
+ * Simple test of mapping with introns involved.
+ */
+ @Test
+ public void testBuildSearchResults_withIntro()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
+ seq1.createDatasetSequence();
+
+ final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ aseq1.createDatasetSequence();
+
+ /*
+ * Map dna bases [2, 4, 5], [7, 9, 11] to protein residues 1 and 2
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[]
+ { 2, 2, 4, 5, 7, 7, 9, 9, 11, 11 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+ Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+
+ /*
+ * Check protein residue 1 maps to [2, 4, 5]
+ */
+ SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
+ assertEquals(2, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(2, m.getStart());
+ assertEquals(2, m.getEnd());
+ m = sr.getResults().get(1);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(5, m.getEnd());
+
+ /*
+ * Check protein residue 2 maps to [7, 9, 11]
+ */
+ sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
+ assertEquals(3, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(7, m.getStart());
+ assertEquals(7, m.getEnd());
+ m = sr.getResults().get(1);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(9, m.getStart());
+ assertEquals(9, m.getEnd());
+ m = sr.getResults().get(2);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(11, m.getStart());
+ assertEquals(11, m.getEnd());
+
+ /*
+ * Check inverse mappings, from codons to protein
+ */
+ for (int i = 1; i < 14; i++)
+ {
+ sr = MappingUtils.buildSearchResults(seq1, i, acfList);
+ int residue = (i == 2 || i == 4 || i == 5) ? 1 : (i == 7 || i == 9
+ || i == 11 ? 2 : 0);
+ if (residue == 0)
+ {
+ assertEquals(0, sr.getResults().size());
+ continue;
+ }
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(aseq1.getDatasetSequence(), m.getSequence());
+ assertEquals(residue, m.getStart());
+ assertEquals(residue, m.getEnd());
+ }
+ }
+
+ /**
+ * Test mapping a sequence group.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapSequenceGroup() throws IOException
+ {
+ /*
+ * Set up dna and protein Seq1/2/3 with mappings (held on the protein
+ * viewport).
+ */
+ AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n",
+ "FASTA");
+ cdna.setDataset(null);
+ AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n",
+ "FASTA");
+ protein.setDataset(null);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[]
+ { 1, 3 }, new int[]
+ { 1, 1 }, 3, 1);
+ for (int seq = 0; seq < 3; seq++)
+ {
+ acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
+ .getSequenceAt(seq).getDatasetSequence(), map);
+ }
+ Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+
+ AlignViewportI dnaView = new AlignViewport(cdna);
+ AlignViewportI proteinView = new AlignViewport(protein);
+ protein.setCodonFrames(acfList);
+
+ /*
+ * Select Seq1 and Seq3 in the protein
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setColourText(true);
+ sg.setIdColour(Color.GREEN);
+ sg.setOutlineColour(Color.LIGHT_GRAY);
+ sg.addSequence(protein.getSequenceAt(0), false);
+ sg.addSequence(protein.getSequenceAt(2), false);
+
+ /*
+ * Verify the mapped sequence group in dna
+ */
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(2, mappedGroup.getSequences().size());
+ assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
+ assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(1));
+
+ /*
+ * Verify mapping sequence group from dna to protein
+ */
+ sg.clear();
+ sg.addSequence(cdna.getSequenceAt(1), false);
+ sg.addSequence(cdna.getSequenceAt(0), false);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(2, mappedGroup.getSequences().size());
+ assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0));
+ assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1));
+ }
+
+ /**
+ * Helper method to load an alignment and ensure dataset sequences are set up.
+ *
+ * @param data
+ * @param format
+ * TODO
+ * @return
+ * @throws IOException
+ */
+ protected AlignmentI loadAlignment(final String data, String format)
+ throws IOException
+ {
+ Alignment a = new FormatAdapter().readFile(data,
+ AppletFormatAdapter.PASTE, format);
+ a.setDataset(null);
+ return a;
+ }
+
+ /**
+ * Test mapping a column selection in protein to its dna equivalent
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapColumnSelection_proteinToDna() throws IOException
+ {
+ setupMappedAlignments();
+
+ ColumnSelection colsel = new ColumnSelection();
+
+ /*
+ * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
+ * in dna respectively, overall 0-4
+ */
+ colsel.addElement(0);
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
+ proteinView, dnaView);
+ assertEquals("[0, 1, 2, 3, 4]", cs.getSelected().toString());
+
+ /*
+ * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
+ */
+ colsel.clear();
+ colsel.addElement(1);
+ cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ assertEquals("[0, 1, 2, 3]", cs.getSelected().toString());
+
+ /*
+ * Column 2 in protein picks up gaps only - no mapping
+ */
+ colsel.clear();
+ colsel.addElement(2);
+ cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ assertEquals("[]", cs.getSelected().toString());
+
+ /*
+ * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
+ * 6-9, 6-10, 5-8 respectively, overall to 5-10
+ */
+ colsel.clear();
+ colsel.addElement(3);
+ cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ assertEquals("[5, 6, 7, 8, 9, 10]", cs.getSelected().toString());
+
+ /*
+ * Combine selection of columns 1 and 3 to get a discontiguous mapped
+ * selection
+ */
+ colsel.clear();
+ colsel.addElement(1);
+ colsel.addElement(3);
+ cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]", cs.getSelected()
+ .toString());
+ }
+
+ /**
+ * @throws IOException
+ */
+ protected void setupMappedAlignments() throws IOException
+ {
+ /*
+ * Set up dna and protein Seq1/2/3 with mappings (held on the protein
+ * viewport). Lower case for introns.
+ */
+ AlignmentI cdna = loadAlignment(">Seq1\nAC-GctGtC-T\n"
+ + ">Seq2\nTc-GA-G-T-Tc\n" + ">Seq3\nTtTT-AaCGg-\n",
+ "FASTA");
+ cdna.setDataset(null);
+ AlignmentI protein = loadAlignment(
+ ">Seq1\n-K-P\n>Seq2\nL--Q\n>Seq3\nG--S\n",
+ "FASTA");
+ protein.setDataset(null);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[]
+ { 1, 3, 6, 6, 8, 9 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein
+ .getSequenceAt(0).getDatasetSequence(), map);
+ map = new MapList(new int[]
+ { 1, 1, 3, 4, 5, 7 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
+ .getSequenceAt(1).getDatasetSequence(), map);
+ map = new MapList(new int[]
+ { 1, 1, 3, 4, 5, 5, 7, 8 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
+ .getSequenceAt(2).getDatasetSequence(), map);
+ Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+
+ dnaView = new AlignViewport(cdna);
+ proteinView = new AlignViewport(protein);
+ protein.setCodonFrames(acfList);
+ }
+
+ /**
+ * Test mapping a column selection in dna to its protein equivalent
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapColumnSelection_dnaToProtein() throws IOException
+ {
+ setupMappedAlignments();
+
+ ColumnSelection colsel = new ColumnSelection();
+
+ /*
+ * Column 0 in dna picks up first bases which map to residue 1, columns 0-1
+ * in protein.
+ */
+ colsel.addElement(0);
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, dnaView,
+ proteinView);
+ assertEquals("[0, 1]", cs.getSelected().toString());
+
+ /*
+ * Columns 3-5 in dna map to the first residues in protein Seq1, Seq2, and
+ * the first two in Seq3. Overall to columns 0, 1, 3 (col2 is all gaps).
+ */
+ colsel.addElement(3);
+ colsel.addElement(4);
+ colsel.addElement(5);
+ cs = MappingUtils.mapColumnSelection(colsel, dnaView, proteinView);
+ assertEquals("[0, 1, 3]", cs.getSelected().toString());
+ }
+
+ /**
+ * Tests for the method that converts a series of [start, end] ranges to
+ * single positions
+ */
+ @Test
+ public void testFlattenRanges()
+ {
+ assertEquals("[1, 2, 3, 4]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 4 })));
+ assertEquals("[1, 2, 3, 4]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 2, 3, 4 })));
+ assertEquals("[1, 2, 3, 4]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 1, 2, 2, 3, 3, 4, 4 })));
+ assertEquals("[1, 2, 3, 4, 7, 8, 9, 12]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 4, 7, 9, 12, 12 })));
+ // unpaired start position is ignored:
+ assertEquals("[1, 2, 3, 4, 7, 8, 9, 12]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[]
+ { 1, 4, 7, 9, 12, 12, 15 })));
+ }
+}
--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+
+public class QuickSortTest
+{
+ private static final String c1 = "Blue";
+
+ private static final String c2 = "Yellow";
+
+ private static final String c3 = "Orange";
+
+ private static final String c4 = "Green";
+
+ private Object[] things;
+
+ private final Object[] sortedThings = new Object[]
+ { c4, c2, c1, c3 };
+
+ @Before
+ public void setUp()
+ {
+ things = new Object[]
+ { c1, c2, c3, c4 };
+ }
+
+ @Test
+ public void testSort_byIntValues()
+ {
+ int[] values = new int[]
+ { 3, 2, 4, 1 };
+ QuickSort.sort(values, things);
+ assertTrue(Arrays.equals(new int[]
+ { 1, 2, 3, 4 }, values));
+ assertTrue(Arrays.equals(sortedThings, things));
+ }
+
+ @Test
+ public void testSort_byFloatValues()
+ {
+ float[] values = new float[]
+ { 3f, 2f, 4f, 1f };
+ QuickSort.sort(values, things);
+ assertTrue(Arrays.equals(new float[]
+ { 1f, 2f, 3f, 4f }, values));
+ assertTrue(Arrays.equals(sortedThings, things));
+ }
+
+ @Test
+ public void testSort_byDoubleValues()
+ {
+ double[] values = new double[]
+ { 3d, 2d, 4d, 1d };
+ QuickSort.sort(values, things);
+ assertTrue(Arrays.equals(new double[]
+ { 1d, 2d, 3d, 4d }, values));
+ assertTrue(Arrays.equals(sortedThings, things));
+ }
+
+ /**
+ * Sort by String is descending order, case-sensitive
+ */
+ @Test
+ public void testSort_byStringValues()
+ {
+ String[] values = new String[]
+ { "JOHN", "henry", "lucy", "ALISON" };
+ QuickSort.sort(values, things);
+ assertTrue(Arrays.equals(new String[]
+ { "lucy", "henry", "JOHN", "ALISON" }, values));
+ assertTrue(Arrays.equals(new Object[]
+ { c3, c2, c1, c4 }, things));
+ }
+
+ /**
+ * Test whether sort is stable i.e. equal values retain their mutual ordering.
+ */
+ @Test
+ @Ignore
+ public void testSort_withDuplicates()
+ {
+ int[] values = new int[]
+ { 3, 4, 2, 4, 1 };
+ Object [] things = new Object [] {"A", "X", "Y", "B", "Z"};
+ QuickSort.sort(values, things);
+ assertTrue(Arrays.equals(new int[]
+ { 1, 2, 3, 4, 4 }, values));
+ // this fails - do we care?
+ assertTrue(Arrays.equals(new Object[]
+ { "Z", "Y", "A", "X", "B" }, things));
+ }
+
+ /**
+ * Test that exercises sort with a mostly zero-valued sortby array. May be of
+ * interest to check the sort algorithm is efficient.
+ */
+ @Test
+ public void testSort_MostlyZeroValues()
+ {
+ char[] residues = new char[64];
+ for (int i = 0; i < 64; i++)
+ {
+ residues[i] = (char) i;
+ }
+ float[] counts = new float[64];
+ counts[43] = 16;
+ counts[59] = 7;
+ counts[62] = 2;
+ QuickSort.sort(counts, residues);
+ assertEquals(43, residues[63]);
+ assertEquals(59, residues[62]);
+ assertEquals(62, residues[61]);
+ }
+}
--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.Test;
+
+public class ShiftListTest
+{
+
+ @Test
+ public void testParseMap()
+ {
+ assertNull(ShiftList.parseMap(null));
+ assertNull(ShiftList.parseMap(new int[]
+ {}));
+
+ /*
+ * Gap map showing residues in aligned positions 2,3,6,8,9,10,12
+ */
+ int[] gm = new int[]
+ { 2, 3, 6, 8, 9, 10, 12 };
+ List<int[]> shifts = ShiftList.parseMap(gm).getShifts();
+ assertEquals(4, shifts.size());
+
+ // TODO are these results (which pass) correct??
+ assertEquals("[0, 2]", Arrays.toString(shifts.get(0)));
+ assertEquals("[4, 2]", Arrays.toString(shifts.get(1)));
+ assertEquals("[7, 1]", Arrays.toString(shifts.get(2)));
+ assertEquals("[11, 1]", Arrays.toString(shifts.get(3)));
+ }
+}
--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+
+import org.junit.Test;
+
+public class StringUtilsTest
+{
+
+ @Test
+ public void testInsertCharAt()
+ {
+ char[] c1 = "ABC".toCharArray();
+ char[] expected = new char[]
+ { 'A', 'B', 'C', 'w', 'w' };
+ assertTrue(Arrays.equals(expected,
+ StringUtils.insertCharAt(c1, 3, 2, 'w')));
+ expected = new char[]
+ { 'A', 'B', 'C', 'w', 'w' };
+ assertTrue(Arrays.equals(expected,
+ StringUtils.insertCharAt(c1, 4, 2, 'w')));
+ assertTrue(Arrays.equals(expected,
+ StringUtils.insertCharAt(c1, 5, 2, 'w')));
+ assertTrue(Arrays.equals(expected,
+ StringUtils.insertCharAt(c1, 6, 2, 'w')));
+ assertTrue(Arrays.equals(expected,
+ StringUtils.insertCharAt(c1, 7, 2, 'w')));
+ }
+
+ @Test
+ public void testDeleteChars()
+ {
+ char[] c1 = "ABC".toCharArray();
+
+ // delete second position
+ assertTrue(Arrays.equals(new char[]
+ { 'A', 'C' }, StringUtils.deleteChars(c1, 1, 2)));
+
+ // delete positions 1 and 2
+ assertTrue(Arrays.equals(new char[]
+ { 'C' }, StringUtils.deleteChars(c1, 0, 2)));
+
+ // delete positions 1-3
+ assertTrue(Arrays.equals(new char[]
+ {}, StringUtils.deleteChars(c1, 0, 3)));
+
+ // delete position 3
+ assertTrue(Arrays.equals(new char[]
+ { 'A', 'B' }, StringUtils.deleteChars(c1, 2, 3)));
+
+ // out of range deletion is ignore
+ assertTrue(Arrays.equals(c1, StringUtils.deleteChars(c1, 3, 4)));
+ }
+
+ @Test
+ public void testGetLastToken()
+ {
+ assertNull(StringUtils.getLastToken(null, null));
+ assertNull(StringUtils.getLastToken(null, "/"));
+ assertEquals("a", StringUtils.getLastToken("a", null));
+
+ assertEquals("abc", StringUtils.getLastToken("abc", "/"));
+ assertEquals("c", StringUtils.getLastToken("abc", "b"));
+ assertEquals("file1.dat", StringUtils.getLastToken(
+ "file://localhost:8080/data/examples/file1.dat", "/"));
+ }
+
+ @Test
+ public void testSeparatorListToArray()
+ {
+ String[] result = StringUtils.separatorListToArray(
+ "foo=',',min='foo',max='1,2,3',fa=','", ",");
+ assertEquals("[foo=',', min='foo', max='1,2,3', fa=',']",
+ Arrays.toString(result));
+ /*
+ * Comma nested in '' is not treated as delimiter; tokens are not trimmed
+ */
+ result = StringUtils.separatorListToArray("minsize='2', sep=','", ",");
+ assertEquals("[minsize='2', sep=',']", Arrays.toString(result));
+
+ /*
+ * String delimited by | containing a quoted | (should not be treated as
+ * delimiter)
+ */
+ assertEquals("[abc='|'d, ef, g]", Arrays.toString(StringUtils
+ .separatorListToArray("abc='|'d|ef|g", "|")));
+ }
+
+ @Test
+ public void testArrayToSeparatorList()
+ {
+ assertEquals("*", StringUtils.arrayToSeparatorList(null, "*"));
+ assertEquals("*", StringUtils.arrayToSeparatorList(new String[]
+ {}, "*"));
+ assertEquals("a*bc*cde", StringUtils.arrayToSeparatorList(new String[]
+ { "a", "bc", "cde" }, "*"));
+ assertEquals("a*cde", StringUtils.arrayToSeparatorList(new String[]
+ { "a", null, "cde" }, "*"));
+ assertEquals("a**cde", StringUtils.arrayToSeparatorList(new String[]
+ { "a", "", "cde" }, "*"));
+ // delimiter within token is not (yet) escaped
+ assertEquals("a*b*c*cde", StringUtils.arrayToSeparatorList(new String[]
+ { "a", "b*c", "cde" }, "*"));
+ }
+}
--- /dev/null
+package jalview.viewmodel.styles;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class TestviewStyle
+{
+
+ @Test
+ public void testSetterGetter()
+ {
+ ViewStyle orig = new ViewStyle();
+ orig.setCharHeight(23);
+ orig.setWrappedWidth(253);
+ orig.setWrapAlignment(true);
+ ViewStyle copy = new ViewStyle(orig);
+ orig.setWrapAlignment(false);
+ Assert.assertEquals(copy.getCharHeight(), orig.getCharHeight());
+ Assert.assertEquals(copy.getWrappedWidth(), orig.getWrappedWidth());
+ Assert.assertEquals(copy.getWrapAlignment(), !orig.getWrapAlignment());
+ }
+
+}
--- /dev/null
+package jalview.ws.dbsources;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBRestClientTest
+{
+
+ @Before
+ public void setUp() throws Exception
+ {
+ }
+
+ @After
+ public void tearDown() throws Exception
+ {
+ }
+
+ @Test
+ public void executeRequestTest()
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("text:");
+ request.setSearchTerm("abc");
+ request.setWantedFields(wantedFields);
+
+ PDBRestResponse response = new PDBRestClient().executeRequest(request);
+ assertTrue(response.getNumberOfItemsFound() > 99);
+ assertTrue(response.getSearchSummary() != null);
+ assertTrue(response.getSearchSummary().size() > 99);
+ }
+
+ @Test
+ public void getPDBDocFieldsAsCommaDelimitedStringTest()
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+ assertEquals("molecule_type,pdb_id,genus,gene_name,title",
+ PDBRestClient
+ .getPDBDocFieldsAsCommaDelimitedString(wantedFields));
+ }
+
+ @Test
+ public void parsePDBJsonExceptionStringTest()
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("text:");
+ request.setSearchTerm("abc");
+ request.setWantedFields(wantedFields);
+
+ String jsonErrorResponse = "";
+ try
+ {
+ jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+
+ String parsedErrorResponse = PDBRestClient
+ .parseJsonExceptionString(jsonErrorResponse);
+ String expectedErrorMsg = "org.apache.solr.search.SyntaxError: Cannot parse 'text:abc OR text:go:abc AND molecule_sequence:['' TO *]': Encountered \" \":\" \": \"\" at line 1, column 19.{\"q\":\"text:abc OR text:go:abc AND molecule_sequence:['' TO *]\",\"fl\":\"pdb_id\",\"sort\":\"\",\"rows\":\"100\",\"wt\":\"json\"}";
+
+ assertEquals(expectedErrorMsg, parsedErrorResponse);
+ }
+
+ @Test(expected = RuntimeException.class)
+ public void testForExpectedRuntimeException()
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.PDB_ID);
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setFieldToSearchBy("text:");
+ request.setSearchTerm("abc OR text:go:abc");
+ request.setWantedFields(wantedFields);
+ new PDBRestClient().executeRequest(request);
+ }
+
+ @Test
+ public void parsePDBJsonResponseTest()
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(false);
+ request.setWantedFields(wantedFields);
+
+ String jsonString = "";
+ try
+ {
+ jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ PDBRestResponse response = PDBRestClient.parsePDBJsonResponse(
+ jsonString, request);
+ assertTrue(response.getSearchSummary() != null);
+ assertTrue(response.getNumberOfItemsFound() == 931);
+ assertTrue(response.getSearchSummary().size() == 14);
+ }
+
+ @Test
+ public void getPDBIdColumIndexTest()
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ assertEquals(5, PDBRestClient.getPDBIdColumIndex(wantedFields, true));
+ assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false));
+ }
+
+ public String readJsonStringFromFile(String filePath) throws IOException
+ {
+ String fileContent;
+ BufferedReader br = new BufferedReader(new FileReader(filePath));
+ try
+ {
+ StringBuilder sb = new StringBuilder();
+ String line = br.readLine();
+
+ while (line != null)
+ {
+ sb.append(line);
+ sb.append(System.lineSeparator());
+ line = br.readLine();
+ }
+ fileContent = sb.toString();
+ } finally
+ {
+ br.close();
+ }
+ return fileContent;
+ }
+
+
+}
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import jalview.ws.jws2.Jws2Discoverer;
import java.util.Vector;
import org.junit.AfterClass;
import org.junit.BeforeClass;
+import org.junit.Ignore;
import org.junit.Test;
+import jalview.ws.jws2.Jws2Discoverer;
+
public class JalviewJabawsTestUtils
{
{ "http://localhost:8080/jabaws" };
@Test
+ @Ignore
public void testAnnotExport()
{
fail("Not yet implemented");
if (rnaalifoldws == null)
{
- fail("rnaalifoldws is null");
+ fail("no web service");
}
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
*/
package jalview.ws.rest;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
import java.util.Map;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.io.FileParse;
-import jalview.ws.rest.InputType;
-import jalview.ws.rest.params.SeqGroupIndexVector;
-
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
import org.junit.Test;
+import jalview.gui.AlignFrame;
+import jalview.util.StringUtils;
+
/**
* @author jimp
*
{
@Test
- public void testSeparatorListToArrayForRestServiceDescriptions()
- {
- assertTrue(
- "separatorListToArray is faulty.",
- RestServiceDescription.separatorListToArray(
- "foo=',',min='foo',max='1,2,3',fa=','", ",").length == 4);
- assertTrue("separatorListToArray is faulty.",
- RestServiceDescription.separatorListToArray(
- "minsize='2', sep=','", ",").length != 2); // probably
- // should come as
- // 2
- }
-
- @Test
public void testShmmrService()
{
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import jalview.analysis.CrossRef;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.util.DBRefUtils;
-import jalview.ws.SequenceFetcher;
import java.util.ArrayList;
import java.util.List;
import org.junit.BeforeClass;
import org.junit.Test;
+import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.util.DBRefUtils;
+import jalview.ws.SequenceFetcher;
+
/**
* @author jimp
*
@BeforeClass
public static void setUpBeforeClass() throws Exception
{
+ jalview.bin.Cache.initLogger();
}
/**
{
String retrievalId = "CAA23748"; // "V00488";
DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
- assertNotNull("Couldn't find the EMBL retrieval client",embl);
+ assertNotNull("Couldn't find the EMBL retrieval client", embl);
+ verifyProteinNucleotideXref(retrievalId, embl);
+ }
+
+ @Test
+ public void testEmblCDSUniprotProductRecovery() throws Exception
+ {
+ String retrievalId = "AAH29712";
+ DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+ DBRefSource.EMBLCDS).get(0);
+ assertNotNull("Couldn't find the EMBL retrieval client", embl);
+ verifyProteinNucleotideXref(retrievalId, embl);
+ }
+
+ private void verifyProteinNucleotideXref(String retrievalId,
+ DbSourceProxy embl) throws Exception
+ {
AlignmentI alsq = embl.getSequenceRecords(retrievalId);
assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
assertNotNull(dr);
assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
+ assertEquals("Expected cross refernce map to be one amino acid", dr[0]
+ .getMap().getMappedWidth(), 1);
+ assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
+ .getMap().getWidth(), 3);
AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
assertNotNull(
"Couldn't recover cross reference sequence from dataset. Was it ever added ?",
git://source.jalview.org / jalview.git / commitdiff
