<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
<classpathentry kind="lib" path="lib/min-jaba-client-2.0.jar" sourcepath="/clustengine2"/>
- <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
+ <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar" sourcepath="/Users/jimp/Documents/e6-workspace-new/Jmol/src"/>
<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
+ <classpathentry kind="lib" path="lib/VARNAv3-9.jar" sourcepath="/Users/jimp/Documents/Jalview/VARNA/VARNAv3-9-src.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
- <classpathentry kind="lib" path="/Users/jimp/git/jalview_clean/lib/VARNAv3-9-dev.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="output" path="classes"/>
</classpath>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ant.AntBuilderLaunchConfigurationType">
+<booleanAttribute key="editedByExternalToolsMainTab" value="true"/>
+<booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="true"/>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/Jalview Release 2.7/build.xml"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="1"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
+<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
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+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/Jalview Release 2.7/lib" path="3" type="2"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/Jalview Release 2.7/utils" path="3" type="2"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry id="org.eclipse.ant.ui.classpathentry.antHome"> <memento default="true"/> </runtimeClasspathEntry> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry id="org.eclipse.ant.ui.classpathentry.extraClasspathEntries"> <memento/> </runtimeClasspathEntry> "/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
+<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
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+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.eclipse.ant.internal.launching.remote.InternalAntRunner"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="Jalview Release 2.7"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_ANT_TARGETS" value="buildindices,"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${workspace_loc:/Jalview Release 2.7/build.xml}"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
+<stringAttribute key="process_factory_id" value="org.eclipse.ant.ui.remoteAntProcessFactory"/>
+</launchConfiguration>
</projects>
<buildSpec>
<buildCommand>
- <name>org.eclipse.wst.common.project.facet.core.builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
- <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
- <triggers>full,incremental,</triggers>
+ <name>org.eclipse.wst.common.project.facet.core.builder</name>
<arguments>
- <dictionary>
- <key>LaunchConfigHandle</key>
- <value><project>/.externalToolBuilders/Jalview Release indices [Builder].launch</value>
- </dictionary>
</arguments>
</buildCommand>
<buildCommand>
<arguments>
<dictionary>
<key>LaunchConfigHandle</key>
- <value><project>/.externalToolBuilders/buildapplet [Builder].launch</value>
+ <value><project>/.externalToolBuilders/Jalview Release indices [Builder].launch</value>
</dictionary>
</arguments>
</buildCommand>
<!-- Webstart Image - looked for in resources/images -->
<property name="WebStartImage" value="JalviewLogo_big.png"/>
<!-- J2SE version needed for webstart launch -->
- <property name="j2sev" value="1.6+"/>
+<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
+ <property name="j2sev" value="1.7+"/>
<!-- build directory configuration -->
<property name="libDir" value="lib" />
<property name="resourceDir" value="resources" />
<property name="outputJar" value="jalview.jar" />
<!-- Jalview Applet JMol Jar Dependency -->
<property name="jmolJar" value="JmolApplet-12.2.4.jar" />
+ <property name="varnaJar" value="VARNAv3-9-dev.jar" />
<property name="jalviewLiteJar" value="jalviewApplet.jar" />
<!-- switch to indicate if we should obfuscate jalviewLite -->
<!--<property name="donotobfuscate" value="true"/> -->
<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
-->
<include name="${jmolJar}" />
+ <include name="${varnaJar}" />
</fileset>
</path>
--- /dev/null
+HEADER RNA 29-MAR-06 2GIS
+TITLE STRUCTURE OF THE S-ADENOSYLMETHIONINE RIBOSWITCH MRNA
+TITLE 2 REGULATORY ELEMENT
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: SAM-I RIBOSWITCH;
+COMPND 3 CHAIN: A;
+COMPND 4 ENGINEERED: YES
+SOURCE MOL_ID: 1;
+SOURCE 2 SYNTHETIC: YES;
+SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS ENGINEERED BASED ON THE
+SOURCE 4 SAM-I RIBOSWITCH FROM THE METF-METH OPERON IN
+SOURCE 5 THERMOANAEROBACTER TENGCONGENSIS
+KEYWDS MRNA, RIBOSWITCH, S-ADENOSYLMETHIONINE, SAM, RNA-LIGAND
+KEYWDS 2 COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR R.K.MONTANGE,R.T.BATEY
+REVDAT 2 24-FEB-09 2GIS 1 VERSN
+REVDAT 1 04-JUL-06 2GIS 0
+JRNL AUTH R.K.MONTANGE,R.T.BATEY
+JRNL TITL STRUCTURE OF THE S-ADENOSYLMETHIONINE RIBOSWITCH
+JRNL TITL 2 REGULATORY MRNA ELEMENT.
+JRNL REF NATURE V. 441 1172 2006
+JRNL REFN ISSN 0028-0836
+JRNL PMID 16810258
+JRNL DOI 10.1038/NATURE04819
+REMARK 1
+REMARK 2
+REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
+REMARK 3
+REMARK 3 REFINEMENT.
+REMARK 3 PROGRAM : CNS 1.1
+REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
+REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
+REMARK 3 : READ,RICE,SIMONSON,WARREN
+REMARK 3
+REMARK 3 REFINEMENT TARGET : ENGH & HUBER
+REMARK 3
+REMARK 3 DATA USED IN REFINEMENT.
+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90
+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.32
+REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
+REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 441185.100
+REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
+REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3
+REMARK 3 NUMBER OF REFLECTIONS : 13415
+REMARK 3
+REMARK 3 FIT TO DATA USED IN REFINEMENT.
+REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
+REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
+REMARK 3 R VALUE (WORKING SET) : 0.266
+REMARK 3 FREE R VALUE : 0.289
+REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.400
+REMARK 3 FREE R VALUE TEST SET COUNT : 999
+REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009
+REMARK 3
+REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
+REMARK 3 TOTAL NUMBER OF BINS USED : 6
+REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90
+REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08
+REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.90
+REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2056
+REMARK 3 BIN R VALUE (WORKING SET) : 0.4270
+REMARK 3 BIN FREE R VALUE : 0.4160
+REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.30
+REMARK 3 BIN FREE R VALUE TEST SET COUNT : 162
+REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033
+REMARK 3
+REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK 3 PROTEIN ATOMS : 0
+REMARK 3 NUCLEIC ACID ATOMS : 2029
+REMARK 3 HETEROGEN ATOMS : 57
+REMARK 3 SOLVENT ATOMS : 88
+REMARK 3
+REMARK 3 B VALUES.
+REMARK 3 FROM WILSON PLOT (A**2) : 139.30
+REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.60
+REMARK 3 OVERALL ANISOTROPIC B VALUE.
+REMARK 3 B11 (A**2) : 11.87000
+REMARK 3 B22 (A**2) : 11.87000
+REMARK 3 B33 (A**2) : -23.74000
+REMARK 3 B12 (A**2) : 0.00000
+REMARK 3 B13 (A**2) : 0.00000
+REMARK 3 B23 (A**2) : 0.00000
+REMARK 3
+REMARK 3 ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39
+REMARK 3 ESD FROM SIGMAA (A) : 0.39
+REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
+REMARK 3
+REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48
+REMARK 3 ESD FROM C-V SIGMAA (A) : 0.35
+REMARK 3
+REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
+REMARK 3 BOND LENGTHS (A) : 0.010
+REMARK 3 BOND ANGLES (DEGREES) : 1.60
+REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.30
+REMARK 3 IMPROPER ANGLES (DEGREES) : 2.31
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
+REMARK 3 MAIN-CHAIN BOND (A**2) : 1.380 ; 1.500
+REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.560 ; 2.000
+REMARK 3 SIDE-CHAIN BOND (A**2) : 1.630 ; 2.000
+REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.610 ; 2.500
+REMARK 3
+REMARK 3 BULK SOLVENT MODELING.
+REMARK 3 METHOD USED : FLAT MODEL
+REMARK 3 KSOL : 0.88
+REMARK 3 BSOL : 300.00
+REMARK 3
+REMARK 3 NCS MODEL : NULL
+REMARK 3
+REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
+REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
+REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
+REMARK 3
+REMARK 3 PARAMETER FILE 1 : DNA-RNA_REP.PARAM
+REMARK 3 PARAMETER FILE 2 : ION2.PARAM
+REMARK 3 PARAMETER FILE 3 : SAM3.PARAM
+REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM
+REMARK 3 PARAMETER FILE 5 : NULL
+REMARK 3 TOPOLOGY FILE 1 : DNA-RNA_REP.TOP
+REMARK 3 TOPOLOGY FILE 2 : ION2.TOP
+REMARK 3 TOPOLOGY FILE 3 : SAM3.TOP
+REMARK 3 TOPOLOGY FILE 4 : WATER_REP.TOP
+REMARK 3 TOPOLOGY FILE 5 : NULL
+REMARK 3
+REMARK 3 OTHER REFINEMENT REMARKS: NULL
+REMARK 4
+REMARK 4 2GIS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-06.
+REMARK 100 THE RCSB ID CODE IS RCSB037170.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
+REMARK 200 DATE OF DATA COLLECTION : 11-NOV-05
+REMARK 200 TEMPERATURE (KELVIN) : 100
+REMARK 200 PH : NULL
+REMARK 200 NUMBER OF CRYSTALS USED : 1
+REMARK 200
+REMARK 200 SYNCHROTRON (Y/N) : Y
+REMARK 200 RADIATION SOURCE : ALS
+REMARK 200 BEAMLINE : 8.2.1
+REMARK 200 X-RAY GENERATOR MODEL : NULL
+REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
+REMARK 200 WAVELENGTH OR RANGE (A) : 1.10532, 1.10573
+REMARK 200 MONOCHROMATOR : NULL
+REMARK 200 OPTICS : NULL
+REMARK 200
+REMARK 200 DETECTOR TYPE : CCD
+REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
+REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BOS
+REMARK 200 DATA SCALING SOFTWARE : D*TREK
+REMARK 200
+REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14940
+REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
+REMARK 200 RESOLUTION RANGE LOW (A) : 49.320
+REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
+REMARK 200 DATA REDUNDANCY : 14.640
+REMARK 200 R MERGE (I) : 0.07200
+REMARK 200 R SYM (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08
+REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
+REMARK 200 DATA REDUNDANCY IN SHELL : 11.74
+REMARK 200 R MERGE FOR SHELL (I) : 0.42600
+REMARK 200 R SYM FOR SHELL (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: MAD
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
+REMARK 200 SOFTWARE USED: CNS
+REMARK 200 STARTING MODEL: NULL
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS (%): 52.20
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
+REMARK 290
+REMARK 290 SYMOP SYMMETRY
+REMARK 290 NNNMMM OPERATOR
+REMARK 290 1555 X,Y,Z
+REMARK 290 2555 -X,-Y,Z+1/2
+REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
+REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
+REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
+REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
+REMARK 290 7555 Y,X,-Z
+REMARK 290 8555 -Y,-X,-Z+1/2
+REMARK 290
+REMARK 290 WHERE NNN -> OPERATOR NUMBER
+REMARK 290 MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.48350
+REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.45050
+REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 119.22525
+REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.45050
+REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.74175
+REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.45050
+REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 119.22525
+REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.45050
+REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.74175
+REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
+REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.48350
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
+REMARK 300 BURIED SURFACE AREA.
+REMARK 350
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
+REMARK 500 O2' A A 20 O4' G A 21 2.13
+REMARK 500 O2' A A 20 OP2 G A 21 2.18
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
+REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
+REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
+REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
+REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
+REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
+REMARK 500
+REMARK 500 DISTANCE CUTOFF:
+REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
+REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
+REMARK 500 N3 IRI A 201 N3 IRI A 201 7555 1.02
+REMARK 500 IR IRI A 201 N3 IRI A 201 7555 2.10
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
+REMARK 500 G A 1 P G A 1 OP3 -0.078
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
+REMARK 500 A A 9 C2' - C3' - O3' ANGL. DEV. = 12.3 DEGREES
+REMARK 500 A A 33 C2' - C3' - O3' ANGL. DEV. = 12.6 DEGREES
+REMARK 500 G A 50 C4' - C3' - O3' ANGL. DEV. = 13.7 DEGREES
+REMARK 500 G A 50 C2' - C3' - O3' ANGL. DEV. = 10.0 DEGREES
+REMARK 500 G A 50 N9 - C1' - C2' ANGL. DEV. = -8.2 DEGREES
+REMARK 500 U A 63 C2' - C3' - O3' ANGL. DEV. = 15.3 DEGREES
+REMARK 500 G A 74 C4' - C3' - O3' ANGL. DEV. = 12.7 DEGREES
+REMARK 500 G A 74 C2' - C3' - O3' ANGL. DEV. = 11.3 DEGREES
+REMARK 500 G A 74 N9 - C1' - C2' ANGL. DEV. = -7.3 DEGREES
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: PLANAR GROUPS
+REMARK 500
+REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
+REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
+REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
+REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
+REMARK 500 AN RMSD GREATER THAN THIS VALUE
+REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 M RES CSSEQI RMS TYPE
+REMARK 500 G A 19 0.05 SIDE_CHAIN
+REMARK 500 G A 35 0.06 SIDE_CHAIN
+REMARK 500 G A 50 0.07 SIDE_CHAIN
+REMARK 500 U A 67 0.08 SIDE_CHAIN
+REMARK 500 G A 74 0.08 SIDE_CHAIN
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 620
+REMARK 620 METAL COORDINATION
+REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
+REMARK 620
+REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
+REMARK 620 MG A 205 MG
+REMARK 620 N RES CSSEQI ATOM
+REMARK 620 1 A A 10 OP2
+REMARK 620 2 U A 63 O3' 95.0
+REMARK 620 3 U A 64 OP2 133.2 53.2
+REMARK 620 N 1 2
+REMARK 620
+REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
+REMARK 620 MG A 206 MG
+REMARK 620 N RES CSSEQI ATOM
+REMARK 620 1 A A 84 O5'
+REMARK 620 2 A A 84 O3' 115.5
+REMARK 620 3 A A 85 OP2 130.4 63.5
+REMARK 620 4 A A 84 OP1 62.8 164.4 130.5
+REMARK 620 N 1 2 3
+REMARK 800
+REMARK 800 SITE
+REMARK 800 SITE_IDENTIFIER: AC1
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 205
+REMARK 800 SITE_IDENTIFIER: AC2
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 206
+REMARK 800 SITE_IDENTIFIER: AC3
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 201
+REMARK 800 SITE_IDENTIFIER: AC4
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 202
+REMARK 800 SITE_IDENTIFIER: AC5
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 203
+REMARK 800 SITE_IDENTIFIER: AC6
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 204
+REMARK 800 SITE_IDENTIFIER: AC7
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 301
+DBREF 2GIS A 1 94 PDB 2GIS 2GIS 1 94
+SEQRES 1 A 94 G G C U U A U C A A G A G
+SEQRES 2 A 94 A G G U G G A G G G A C U
+SEQRES 3 A 94 G G C C C G A U G A A A C
+SEQRES 4 A 94 C C G G C A A C C A G A A
+SEQRES 5 A 94 A U G G U G C C A A U U C
+SEQRES 6 A 94 C U G C A G C G G A A A C
+SEQRES 7 A 94 G U U G A A A G A U G A G
+SEQRES 8 A 94 C C A
+HET MG A 205 1
+HET MG A 206 1
+HET IRI A 201 7
+HET IRI A 202 7
+HET IRI A 203 7
+HET IRI A 204 7
+HET SAM A 301 27
+HETNAM MG MAGNESIUM ION
+HETNAM IRI IRIDIUM HEXAMMINE ION
+HETNAM SAM S-ADENOSYLMETHIONINE
+FORMUL 2 MG 2(MG 2+)
+FORMUL 4 IRI 4(H18 IR N6 3+)
+FORMUL 8 SAM C15 H22 N6 O5 S
+FORMUL 9 HOH *88(H2 O)
+LINK MG MG A 205 OP2 A A 10 1555 1555 2.88
+LINK MG MG A 205 O3' U A 63 1555 1555 2.88
+LINK MG MG A 205 OP2 U A 64 1555 1555 2.42
+LINK MG MG A 206 O5' A A 84 1555 1555 1.93
+LINK MG MG A 206 O3' A A 84 1555 1555 2.35
+LINK MG MG A 206 OP2 A A 85 1555 1555 2.46
+LINK MG MG A 206 OP1 A A 84 1555 1555 2.71
+SITE 1 AC1 4 A A 9 A A 10 U A 63 U A 64
+SITE 1 AC2 2 A A 84 A A 85
+SITE 1 AC3 5 C A 31 G A 32 A A 33 U A 34
+SITE 2 AC3 5 HOH A 448
+SITE 1 AC4 6 G A 15 G A 16 U A 17 G A 18
+SITE 2 AC4 6 A A 36 A A 38
+SITE 1 AC5 6 G A 23 C A 25 U A 26 G A 27
+SITE 2 AC5 6 G A 28 C A 29
+SITE 1 AC6 6 U A 4 U A 5 A A 6 U A 88
+SITE 2 AC6 6 G A 89 HOH A 475
+SITE 1 AC7 11 U A 7 G A 11 A A 45 A A 46
+SITE 2 AC7 11 C A 47 U A 57 G A 58 C A 59
+SITE 3 AC7 11 U A 88 G A 89 HOH A 437
+CRYST1 62.901 62.901 158.967 90.00 90.00 90.00 P 43 21 2 8
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.015898 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.015898 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.006291 0.00000
+ATOM 1 OP3 G A 1 66.836 54.358 31.023 1.00 83.72 O
+ATOM 2 P G A 1 66.932 54.717 32.506 1.00 83.64 P
+ATOM 3 OP1 G A 1 68.009 55.754 32.789 1.00 83.61 O
+ATOM 4 OP2 G A 1 65.585 55.074 33.126 1.00 82.16 O
+ATOM 5 O5' G A 1 67.440 53.379 33.287 1.00 79.65 O
+ATOM 6 C5' G A 1 68.672 52.742 32.913 1.00 73.57 C
+ATOM 7 C4' G A 1 69.247 51.962 34.076 1.00 70.37 C
+ATOM 8 O4' G A 1 69.770 52.884 35.073 1.00 66.83 O
+ATOM 9 C3' G A 1 68.269 51.092 34.851 1.00 68.85 C
+ATOM 10 O3' G A 1 68.072 49.836 34.215 1.00 68.87 O
+ATOM 11 C2' G A 1 68.974 50.952 36.194 1.00 66.89 C
+ATOM 12 O2' G A 1 70.032 50.011 36.151 1.00 66.32 O
+ATOM 13 C1' G A 1 69.560 52.353 36.371 1.00 64.13 C
+ATOM 14 N9 G A 1 68.630 53.226 37.076 1.00 60.62 N
+ATOM 15 C8 G A 1 67.918 54.269 36.547 1.00 60.07 C
+ATOM 16 N7 G A 1 67.123 54.838 37.412 1.00 59.30 N
+ATOM 17 C5 G A 1 67.331 54.130 38.585 1.00 57.00 C
+ATOM 18 C6 G A 1 66.738 54.282 39.860 1.00 55.77 C
+ATOM 19 O6 G A 1 65.881 55.106 40.221 1.00 56.93 O
+ATOM 20 N1 G A 1 67.233 53.352 40.767 1.00 54.01 N
+ATOM 21 C2 G A 1 68.178 52.396 40.480 1.00 55.22 C
+ATOM 22 N2 G A 1 68.526 51.581 41.489 1.00 54.38 N
+ATOM 23 N3 G A 1 68.740 52.247 39.288 1.00 56.29 N
+ATOM 24 C4 G A 1 68.270 53.140 38.397 1.00 57.86 C
+ATOM 25 P G A 2 66.612 49.156 34.222 1.00 69.18 P
+ATOM 26 OP1 G A 2 66.706 47.977 33.323 1.00 70.02 O
+ATOM 27 OP2 G A 2 65.566 50.194 33.985 1.00 68.86 O
+ATOM 28 O5' G A 2 66.442 48.597 35.701 1.00 66.97 O
+ATOM 29 C5' G A 2 67.276 47.544 36.152 1.00 62.30 C
+ATOM 30 C4' G A 2 67.252 47.457 37.651 1.00 59.60 C
+ATOM 31 O4' G A 2 67.506 48.784 38.198 1.00 56.42 O
+ATOM 32 C3' G A 2 65.898 47.105 38.233 1.00 59.17 C
+ATOM 33 O3' G A 2 65.645 45.711 38.175 1.00 60.55 O
+ATOM 34 C2' G A 2 66.007 47.655 39.650 1.00 56.90 C
+ATOM 35 O2' G A 2 66.780 46.829 40.499 1.00 57.29 O
+ATOM 36 C1' G A 2 66.787 48.946 39.405 1.00 54.02 C
+ATOM 37 N9 G A 2 65.942 50.127 39.299 1.00 50.64 N
+ATOM 38 C8 G A 2 65.753 50.932 38.206 1.00 50.83 C
+ATOM 39 N7 G A 2 64.944 51.936 38.442 1.00 50.61 N
+ATOM 40 C5 G A 2 64.573 51.774 39.768 1.00 48.72 C
+ATOM 41 C6 G A 2 63.723 52.556 40.584 1.00 48.85 C
+ATOM 42 O6 G A 2 63.108 53.584 40.289 1.00 50.52 O
+ATOM 43 N1 G A 2 63.627 52.034 41.866 1.00 48.14 N
+ATOM 44 C2 G A 2 64.268 50.902 42.311 1.00 47.93 C
+ATOM 45 N2 G A 2 64.035 50.543 43.580 1.00 47.56 N
+ATOM 46 N3 G A 2 65.071 50.172 41.568 1.00 48.14 N
+ATOM 47 C4 G A 2 65.177 50.661 40.312 1.00 49.83 C
+ATOM 48 P C A 3 64.129 45.193 38.109 1.00 60.96 P
+ATOM 49 OP1 C A 3 64.118 43.738 37.817 1.00 60.20 O
+ATOM 50 OP2 C A 3 63.355 46.126 37.249 1.00 61.70 O
+ATOM 51 O5' C A 3 63.587 45.427 39.585 1.00 60.54 O
+ATOM 52 C5' C A 3 63.884 44.512 40.626 1.00 55.75 C
+ATOM 53 C4' C A 3 63.184 44.934 41.889 1.00 53.73 C
+ATOM 54 O4' C A 3 63.549 46.312 42.172 1.00 52.44 O
+ATOM 55 C3' C A 3 61.674 45.025 41.777 1.00 53.43 C
+ATOM 56 O3' C A 3 61.022 43.789 41.941 1.00 55.57 O
+ATOM 57 C2' C A 3 61.321 45.978 42.898 1.00 51.46 C
+ATOM 58 O2' C A 3 61.402 45.337 44.151 1.00 52.96 O
+ATOM 59 C1' C A 3 62.458 46.978 42.787 1.00 49.83 C
+ATOM 60 N1 C A 3 62.072 48.135 41.979 1.00 46.39 N
+ATOM 61 C2 C A 3 61.207 49.065 42.547 1.00 45.76 C
+ATOM 62 O2 C A 3 60.800 48.861 43.692 1.00 47.45 O
+ATOM 63 N3 C A 3 60.831 50.152 41.837 1.00 43.39 N
+ATOM 64 C4 C A 3 61.290 50.323 40.602 1.00 44.39 C
+ATOM 65 N4 C A 3 60.911 51.413 39.948 1.00 44.48 N
+ATOM 66 C5 C A 3 62.168 49.382 39.986 1.00 45.55 C
+ATOM 67 C6 C A 3 62.534 48.309 40.707 1.00 46.04 C
+ATOM 68 P U A 4 59.622 43.553 41.204 1.00 57.98 P
+ATOM 69 OP1 U A 4 59.364 42.082 41.244 1.00 57.52 O
+ATOM 70 OP2 U A 4 59.681 44.265 39.900 1.00 59.29 O
+ATOM 71 O5' U A 4 58.561 44.348 42.088 1.00 53.55 O
+ATOM 72 C5' U A 4 58.363 44.011 43.446 1.00 53.36 C
+ATOM 73 C4' U A 4 57.410 44.981 44.081 1.00 55.02 C
+ATOM 74 O4' U A 4 57.989 46.313 44.050 1.00 55.96 O
+ATOM 75 C3' U A 4 56.097 45.142 43.346 1.00 57.18 C
+ATOM 76 O3' U A 4 55.179 44.108 43.677 1.00 60.33 O
+ATOM 77 C2' U A 4 55.642 46.516 43.814 1.00 54.53 C
+ATOM 78 O2' U A 4 55.165 46.437 45.140 1.00 55.14 O
+ATOM 79 C1' U A 4 56.967 47.272 43.829 1.00 52.98 C
+ATOM 80 N1 U A 4 57.269 47.986 42.580 1.00 49.42 N
+ATOM 81 C2 U A 4 56.614 49.174 42.350 1.00 47.24 C
+ATOM 82 O2 U A 4 55.771 49.612 43.103 1.00 45.38 O
+ATOM 83 N3 U A 4 56.978 49.829 41.207 1.00 46.59 N
+ATOM 84 C4 U A 4 57.903 49.416 40.282 1.00 48.90 C
+ATOM 85 O4 U A 4 58.117 50.111 39.282 1.00 50.34 O
+ATOM 86 C5 U A 4 58.523 48.162 40.580 1.00 48.98 C
+ATOM 87 C6 U A 4 58.187 47.505 41.691 1.00 49.39 C
+ATOM 88 P U A 5 54.205 43.531 42.537 1.00 60.31 P
+ATOM 89 OP1 U A 5 53.567 42.301 43.067 1.00 60.80 O
+ATOM 90 OP2 U A 5 54.982 43.466 41.269 1.00 61.31 O
+ATOM 91 O5' U A 5 53.102 44.672 42.382 1.00 57.62 O
+ATOM 92 C5' U A 5 52.176 44.937 43.427 1.00 56.18 C
+ATOM 93 C4' U A 5 51.450 46.221 43.143 1.00 55.97 C
+ATOM 94 O4' U A 5 52.432 47.275 43.039 1.00 55.58 O
+ATOM 95 C3' U A 5 50.695 46.272 41.826 1.00 56.58 C
+ATOM 96 O3' U A 5 49.393 45.733 41.981 1.00 58.63 O
+ATOM 97 C2' U A 5 50.663 47.767 41.536 1.00 55.50 C
+ATOM 98 O2' U A 5 49.696 48.452 42.301 1.00 56.71 O
+ATOM 99 C1' U A 5 52.048 48.188 42.023 1.00 54.24 C
+ATOM 100 N1 U A 5 53.071 48.125 40.974 1.00 50.31 N
+ATOM 101 C2 U A 5 53.197 49.208 40.124 1.00 48.81 C
+ATOM 102 O2 U A 5 52.488 50.194 40.204 1.00 48.14 O
+ATOM 103 N3 U A 5 54.188 49.091 39.181 1.00 47.64 N
+ATOM 104 C4 U A 5 55.044 48.019 39.011 1.00 49.86 C
+ATOM 105 O4 U A 5 55.897 48.060 38.122 1.00 53.10 O
+ATOM 106 C5 U A 5 54.843 46.933 39.930 1.00 49.29 C
+ATOM 107 C6 U A 5 53.886 47.020 40.854 1.00 48.98 C
+ATOM 108 P A A 6 48.651 45.080 40.719 1.00 60.24 P
+ATOM 109 OP1 A A 6 47.527 44.256 41.233 1.00 60.47 O
+ATOM 110 OP2 A A 6 49.696 44.440 39.882 1.00 58.91 O
+ATOM 111 O5' A A 6 48.047 46.341 39.956 1.00 56.95 O
+ATOM 112 C5' A A 6 47.050 47.139 40.571 1.00 55.21 C
+ATOM 113 C4' A A 6 46.808 48.385 39.760 1.00 56.41 C
+ATOM 114 O4' A A 6 47.992 49.219 39.787 1.00 56.16 O
+ATOM 115 C3' A A 6 46.574 48.148 38.285 1.00 57.58 C
+ATOM 116 O3' A A 6 45.232 47.755 38.032 1.00 59.85 O
+ATOM 117 C2' A A 6 46.960 49.491 37.679 1.00 55.59 C
+ATOM 118 O2' A A 6 45.980 50.474 37.905 1.00 56.04 O
+ATOM 119 C1' A A 6 48.163 49.859 38.536 1.00 53.99 C
+ATOM 120 N9 A A 6 49.425 49.404 37.958 1.00 52.37 N
+ATOM 121 C8 A A 6 50.091 48.223 38.172 1.00 52.73 C
+ATOM 122 N7 A A 6 51.212 48.119 37.495 1.00 50.40 N
+ATOM 123 C5 A A 6 51.282 49.309 36.791 1.00 48.95 C
+ATOM 124 C6 A A 6 52.220 49.810 35.895 1.00 49.10 C
+ATOM 125 N6 A A 6 53.319 49.157 35.543 1.00 49.07 N
+ATOM 126 N1 A A 6 51.991 51.030 35.360 1.00 49.55 N
+ATOM 127 C2 A A 6 50.892 51.689 35.721 1.00 49.92 C
+ATOM 128 N3 A A 6 49.936 51.324 36.564 1.00 51.13 N
+ATOM 129 C4 A A 6 50.192 50.108 37.068 1.00 50.04 C
+ATOM 130 P U A 7 44.942 46.678 36.880 1.00 60.77 P
+ATOM 131 OP1 U A 7 43.556 46.166 37.041 1.00 62.34 O
+ATOM 132 OP2 U A 7 46.083 45.727 36.862 1.00 60.86 O
+ATOM 133 O5' U A 7 45.014 47.576 35.575 1.00 58.27 O
+ATOM 134 C5' U A 7 44.309 48.807 35.537 1.00 56.31 C
+ATOM 135 C4' U A 7 44.796 49.660 34.396 1.00 55.63 C
+ATOM 136 O4' U A 7 46.124 50.175 34.690 1.00 53.71 O
+ATOM 137 C3' U A 7 44.989 48.897 33.106 1.00 55.41 C
+ATOM 138 O3' U A 7 43.761 48.723 32.432 1.00 57.39 O
+ATOM 139 C2' U A 7 45.975 49.781 32.356 1.00 54.03 C
+ATOM 140 O2' U A 7 45.344 50.895 31.752 1.00 54.05 O
+ATOM 141 C1' U A 7 46.877 50.253 33.497 1.00 51.60 C
+ATOM 142 N1 U A 7 48.069 49.414 33.644 1.00 48.98 N
+ATOM 143 C2 U A 7 49.147 49.744 32.880 1.00 47.41 C
+ATOM 144 O2 U A 7 49.125 50.684 32.101 1.00 50.13 O
+ATOM 145 N3 U A 7 50.245 48.941 33.048 1.00 44.70 N
+ATOM 146 C4 U A 7 50.360 47.854 33.884 1.00 44.88 C
+ATOM 147 O4 U A 7 51.421 47.226 33.925 1.00 43.14 O
+ATOM 148 C5 U A 7 49.192 47.568 34.642 1.00 45.41 C
+ATOM 149 C6 U A 7 48.109 48.343 34.502 1.00 48.51 C
+ATOM 150 P C A 8 43.662 47.638 31.261 1.00 59.85 P
+ATOM 151 OP1 C A 8 42.278 47.710 30.723 1.00 61.02 O
+ATOM 152 OP2 C A 8 44.188 46.346 31.770 1.00 59.29 O
+ATOM 153 O5' C A 8 44.678 48.182 30.158 1.00 58.48 O
+ATOM 154 C5' C A 8 44.351 49.334 29.392 1.00 56.82 C
+ATOM 155 C4' C A 8 45.288 49.473 28.222 1.00 58.23 C
+ATOM 156 O4' C A 8 46.602 49.835 28.707 1.00 57.92 O
+ATOM 157 C3' C A 8 45.519 48.211 27.410 1.00 58.66 C
+ATOM 158 O3' C A 8 44.512 48.077 26.413 1.00 61.50 O
+ATOM 159 C2' C A 8 46.870 48.491 26.771 1.00 57.69 C
+ATOM 160 O2' C A 8 46.744 49.342 25.647 1.00 56.83 O
+ATOM 161 C1' C A 8 47.593 49.232 27.896 1.00 56.12 C
+ATOM 162 N1 C A 8 48.418 48.363 28.744 1.00 53.94 N
+ATOM 163 C2 C A 8 49.783 48.292 28.489 1.00 52.97 C
+ATOM 164 O2 C A 8 50.251 48.967 27.565 1.00 54.92 O
+ATOM 165 N3 C A 8 50.560 47.493 29.251 1.00 50.44 N
+ATOM 166 C4 C A 8 50.013 46.784 30.242 1.00 49.28 C
+ATOM 167 N4 C A 8 50.812 46.013 30.966 1.00 47.57 N
+ATOM 168 C5 C A 8 48.619 46.840 30.530 1.00 50.26 C
+ATOM 169 C6 C A 8 47.865 47.635 29.762 1.00 52.95 C
+ATOM 170 P A A 9 44.220 46.636 25.756 1.00 62.39 P
+ATOM 171 OP1 A A 9 43.364 45.868 26.691 1.00 62.54 O
+ATOM 172 OP2 A A 9 45.505 46.055 25.302 1.00 62.79 O
+ATOM 173 O5' A A 9 43.321 46.991 24.492 1.00 64.20 O
+ATOM 174 C5' A A 9 43.849 46.942 23.173 1.00 69.12 C
+ATOM 175 C4' A A 9 42.837 47.488 22.188 1.00 71.94 C
+ATOM 176 O4' A A 9 41.791 46.511 21.961 1.00 74.83 O
+ATOM 177 C3' A A 9 42.121 48.739 22.656 1.00 71.21 C
+ATOM 178 O3' A A 9 42.375 49.964 21.965 1.00 68.03 O
+ATOM 179 C2' A A 9 40.779 48.297 23.235 1.00 73.66 C
+ATOM 180 O2' A A 9 39.714 49.146 22.861 1.00 73.60 O
+ATOM 181 C1' A A 9 40.588 46.912 22.594 1.00 77.57 C
+ATOM 182 N9 A A 9 40.229 45.843 23.530 1.00 83.33 N
+ATOM 183 C8 A A 9 40.530 45.749 24.869 1.00 84.98 C
+ATOM 184 N7 A A 9 40.113 44.636 25.429 1.00 87.16 N
+ATOM 185 C5 A A 9 39.485 43.954 24.394 1.00 88.00 C
+ATOM 186 C6 A A 9 38.840 42.694 24.335 1.00 89.06 C
+ATOM 187 N6 A A 9 38.726 41.864 25.379 1.00 88.96 N
+ATOM 188 N1 A A 9 38.314 42.312 23.147 1.00 89.43 N
+ATOM 189 C2 A A 9 38.439 43.138 22.097 1.00 89.45 C
+ATOM 190 N3 A A 9 39.028 44.337 22.025 1.00 88.20 N
+ATOM 191 C4 A A 9 39.536 44.692 23.221 1.00 86.70 C
+ATOM 192 P A A 10 41.514 50.352 20.666 1.00 61.47 P
+ATOM 193 OP1 A A 10 40.725 49.160 20.325 1.00 65.15 O
+ATOM 194 OP2 A A 10 42.447 50.920 19.669 1.00 65.52 O
+ATOM 195 O5' A A 10 40.538 51.510 21.159 1.00 61.29 O
+ATOM 196 C5' A A 10 39.126 51.356 21.085 1.00 61.12 C
+ATOM 197 C4' A A 10 38.435 52.547 21.702 1.00 61.27 C
+ATOM 198 O4' A A 10 38.545 52.487 23.140 1.00 61.33 O
+ATOM 199 C3' A A 10 39.017 53.894 21.326 1.00 60.56 C
+ATOM 200 O3' A A 10 38.418 54.348 20.136 1.00 62.31 O
+ATOM 201 C2' A A 10 38.590 54.770 22.486 1.00 60.01 C
+ATOM 202 O2' A A 10 37.262 55.220 22.354 1.00 61.63 O
+ATOM 203 C1' A A 10 38.702 53.795 23.654 1.00 60.36 C
+ATOM 204 N9 A A 10 39.993 53.847 24.327 1.00 60.66 N
+ATOM 205 C8 A A 10 40.916 52.837 24.411 1.00 60.47 C
+ATOM 206 N7 A A 10 41.969 53.145 25.124 1.00 62.84 N
+ATOM 207 C5 A A 10 41.727 54.453 25.533 1.00 62.66 C
+ATOM 208 C6 A A 10 42.457 55.346 26.339 1.00 62.24 C
+ATOM 209 N6 A A 10 43.621 55.042 26.911 1.00 63.38 N
+ATOM 210 N1 A A 10 41.939 56.573 26.545 1.00 62.82 N
+ATOM 211 C2 A A 10 40.765 56.873 25.983 1.00 62.56 C
+ATOM 212 N3 A A 10 39.981 56.121 25.217 1.00 62.85 N
+ATOM 213 C4 A A 10 40.523 54.905 25.030 1.00 62.24 C
+ATOM 214 P G A 11 39.283 55.186 19.092 1.00 64.09 P
+ATOM 215 OP1 G A 11 38.517 55.279 17.830 1.00 67.46 O
+ATOM 216 OP2 G A 11 40.632 54.579 19.093 1.00 65.72 O
+ATOM 217 O5' G A 11 39.385 56.634 19.737 1.00 64.27 O
+ATOM 218 C5' G A 11 38.238 57.286 20.263 1.00 65.57 C
+ATOM 219 C4' G A 11 38.672 58.430 21.142 1.00 66.04 C
+ATOM 220 O4' G A 11 39.266 57.913 22.356 1.00 66.05 O
+ATOM 221 C3' G A 11 39.753 59.293 20.527 1.00 66.30 C
+ATOM 222 O3' G A 11 39.131 60.294 19.737 1.00 68.41 O
+ATOM 223 C2' G A 11 40.417 59.895 21.755 1.00 65.85 C
+ATOM 224 O2' G A 11 39.667 60.970 22.273 1.00 68.84 O
+ATOM 225 C1' G A 11 40.345 58.737 22.749 1.00 65.15 C
+ATOM 226 N9 G A 11 41.537 57.901 22.820 1.00 64.75 N
+ATOM 227 C8 G A 11 41.777 56.766 22.093 1.00 63.49 C
+ATOM 228 N7 G A 11 42.910 56.195 22.394 1.00 64.89 N
+ATOM 229 C5 G A 11 43.455 57.007 23.378 1.00 64.88 C
+ATOM 230 C6 G A 11 44.666 56.884 24.103 1.00 64.13 C
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+ATOM 235 N3 G A 11 42.807 59.069 24.535 1.00 65.84 N
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+ATOM 237 P A A 12 39.589 60.508 18.216 1.00 72.17 P
+ATOM 238 OP1 A A 12 38.441 61.088 17.469 1.00 72.28 O
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+ATOM 241 C5' A A 12 40.436 62.931 18.755 1.00 74.99 C
+ATOM 242 C4' A A 12 41.689 63.630 19.220 1.00 76.06 C
+ATOM 243 O4' A A 12 42.252 62.910 20.347 1.00 75.60 O
+ATOM 244 C3' A A 12 42.811 63.640 18.200 1.00 77.69 C
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+ATOM 246 C2' A A 12 44.049 63.806 19.063 1.00 76.03 C
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+ATOM 250 C8 A A 12 44.108 60.649 19.388 1.00 74.14 C
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+ATOM 253 C6 A A 12 46.096 59.060 21.819 1.00 74.42 C
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+ATOM 263 C5' G A 13 43.609 65.918 13.855 1.00 99.27 C
+ATOM 264 C4' G A 13 44.119 67.311 13.644 1.00103.14 C
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+ATOM 274 C5 G A 13 48.654 68.244 16.726 1.00104.42 C
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+ATOM 276 O6 G A 13 50.565 68.363 18.184 1.00102.76 O
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+ATOM 287 C4' A A 14 45.863 68.602 7.295 1.00117.25 C
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+ATOM 290 O3' A A 14 45.367 70.922 7.924 1.00115.58 O
+ATOM 291 C2' A A 14 43.702 69.579 6.645 1.00118.52 C
+ATOM 292 O2' A A 14 43.661 70.767 5.878 1.00117.82 O
+ATOM 293 C1' A A 14 44.122 68.423 5.730 1.00119.51 C
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+ATOM 295 C8 A A 14 43.339 66.006 5.934 1.00121.79 C
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+ATOM 298 C6 A A 14 40.141 65.887 4.464 1.00122.97 C
+ATOM 299 N6 A A 14 39.545 64.692 4.404 1.00123.09 N
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+ATOM 307 O5' G A 15 46.392 72.765 9.299 1.00110.78 O
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+ATOM 313 C2' G A 15 49.282 75.408 11.769 1.00102.62 C
+ATOM 314 O2' G A 15 48.760 76.718 11.867 1.00102.61 O
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+ATOM 317 C8 G A 15 48.919 71.930 12.610 1.00101.72 C
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+ATOM 319 C5 G A 15 50.453 71.971 14.085 1.00101.16 C
+ATOM 320 C6 G A 15 51.487 71.679 15.022 1.00101.10 C
+ATOM 321 O6 G A 15 51.994 70.575 15.304 1.00101.15 O
+ATOM 322 N1 G A 15 51.932 72.833 15.662 1.00100.41 N
+ATOM 323 C2 G A 15 51.449 74.098 15.432 1.00 99.93 C
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+ATOM 329 OP2 G A 16 51.725 74.492 9.095 1.00101.20 O
+ATOM 330 O5' G A 16 51.919 76.949 8.908 1.00100.66 O
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+ATOM 332 C4' G A 16 54.036 77.485 9.896 1.00100.56 C
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+ATOM 334 C3' G A 16 55.491 77.080 9.985 1.00101.38 C
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+ATOM 336 C2' G A 16 55.778 77.206 11.477 1.00100.28 C
+ATOM 337 O2' G A 16 56.066 78.524 11.885 1.00101.05 O
+ATOM 338 C1' G A 16 54.443 76.770 12.086 1.00 99.62 C
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+ATOM 340 C8 G A 16 53.508 74.423 12.025 1.00 97.73 C
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+ATOM 342 C5 G A 16 54.659 73.463 13.530 1.00 96.67 C
+ATOM 343 C6 G A 16 55.243 72.561 14.451 1.00 96.34 C
+ATOM 344 O6 G A 16 54.965 71.373 14.646 1.00 96.14 O
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+ATOM 350 P U A 17 57.613 77.465 8.504 1.00105.06 P
+ATOM 351 OP1 U A 17 58.306 78.633 7.898 1.00106.21 O
+ATOM 352 OP2 U A 17 57.264 76.299 7.656 1.00105.45 O
+ATOM 353 O5' U A 17 58.481 76.978 9.742 1.00104.29 O
+ATOM 354 C5' U A 17 59.030 77.934 10.631 1.00105.27 C
+ATOM 355 C4' U A 17 60.024 77.281 11.542 1.00106.09 C
+ATOM 356 O4' U A 17 59.313 76.526 12.556 1.00106.80 O
+ATOM 357 C3' U A 17 60.896 76.236 10.865 1.00106.38 C
+ATOM 358 O3' U A 17 61.999 76.794 10.166 1.00105.97 O
+ATOM 359 C2' U A 17 61.333 75.377 12.039 1.00107.09 C
+ATOM 360 O2' U A 17 62.390 75.956 12.777 1.00107.37 O
+ATOM 361 C1' U A 17 60.062 75.368 12.886 1.00107.53 C
+ATOM 362 N1 U A 17 59.249 74.171 12.641 1.00108.23 N
+ATOM 363 C2 U A 17 59.727 72.987 13.165 1.00108.78 C
+ATOM 364 O2 U A 17 60.774 72.918 13.788 1.00108.71 O
+ATOM 365 N3 U A 17 58.941 71.889 12.933 1.00109.36 N
+ATOM 366 C4 U A 17 57.756 71.849 12.242 1.00109.57 C
+ATOM 367 O4 U A 17 57.161 70.773 12.132 1.00109.52 O
+ATOM 368 C5 U A 17 57.327 73.116 11.719 1.00109.14 C
+ATOM 369 C6 U A 17 58.072 74.209 11.933 1.00108.45 C
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+ATOM 372 OP2 G A 18 61.283 75.919 7.968 1.00105.50 O
+ATOM 373 O5' G A 18 63.018 74.668 9.285 1.00103.99 O
+ATOM 374 C5' G A 18 64.021 74.559 10.291 1.00102.43 C
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+ATOM 378 O3' G A 18 65.928 72.132 9.335 1.00 99.74 O
+ATOM 379 C2' G A 18 64.031 70.830 10.098 1.00 99.32 C
+ATOM 380 O2' G A 18 64.952 70.220 10.976 1.00 98.70 O
+ATOM 381 C1' G A 18 62.774 71.261 10.858 1.00 99.21 C
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+ATOM 383 C8 G A 18 61.041 72.135 9.221 1.00 96.69 C
+ATOM 384 N7 G A 18 59.926 71.773 8.650 1.00 96.07 N
+ATOM 385 C5 G A 18 59.693 70.496 9.136 1.00 95.84 C
+ATOM 386 C6 G A 18 58.632 69.595 8.875 1.00 95.53 C
+ATOM 387 O6 G A 18 57.654 69.753 8.139 1.00 94.90 O
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+ATOM 390 N2 G A 18 59.815 66.907 10.994 1.00 95.41 N
+ATOM 391 N3 G A 18 60.830 68.947 10.676 1.00 95.69 N
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+ATOM 394 OP1 G A 19 67.023 74.021 8.096 1.00101.74 O
+ATOM 395 OP2 G A 19 65.531 72.332 6.866 1.00 99.87 O
+ATOM 396 O5' G A 19 67.784 71.666 7.719 1.00 98.72 O
+ATOM 397 C5' G A 19 67.715 70.548 6.836 1.00 95.36 C
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+ATOM 400 C3' G A 19 66.784 68.160 6.634 1.00 90.61 C
+ATOM 401 O3' G A 19 67.898 67.278 6.715 1.00 88.58 O
+ATOM 402 C2' G A 19 65.571 67.513 7.282 1.00 90.73 C
+ATOM 403 O2' G A 19 65.939 66.784 8.435 1.00 91.75 O
+ATOM 404 C1' G A 19 64.761 68.740 7.698 1.00 90.64 C
+ATOM 405 N9 G A 19 63.754 69.219 6.755 1.00 88.83 N
+ATOM 406 C8 G A 19 63.909 70.246 5.855 1.00 87.97 C
+ATOM 407 N7 G A 19 62.804 70.558 5.236 1.00 87.34 N
+ATOM 408 C5 G A 19 61.865 69.664 5.732 1.00 87.12 C
+ATOM 409 C6 G A 19 60.486 69.532 5.442 1.00 86.28 C
+ATOM 410 O6 G A 19 59.791 70.206 4.678 1.00 85.66 O
+ATOM 411 N1 G A 19 59.914 68.489 6.154 1.00 86.49 N
+ATOM 412 C2 G A 19 60.577 67.680 7.038 1.00 87.60 C
+ATOM 413 N2 G A 19 59.838 66.725 7.615 1.00 88.67 N
+ATOM 414 N3 G A 19 61.863 67.797 7.332 1.00 87.70 N
+ATOM 415 C4 G A 19 62.442 68.805 6.647 1.00 87.88 C
+ATOM 416 P A A 20 67.943 65.983 5.777 1.00 86.58 P
+ATOM 417 OP1 A A 20 69.331 65.483 5.704 1.00 86.40 O
+ATOM 418 OP2 A A 20 67.232 66.383 4.539 1.00 86.39 O
+ATOM 419 O5' A A 20 67.063 64.896 6.537 1.00 85.63 O
+ATOM 420 C5' A A 20 67.650 63.993 7.479 1.00 83.85 C
+ATOM 421 C4' A A 20 66.922 62.667 7.448 1.00 82.33 C
+ATOM 422 O4' A A 20 65.507 62.890 7.680 1.00 81.16 O
+ATOM 423 C3' A A 20 66.983 61.952 6.114 1.00 81.89 C
+ATOM 424 O3' A A 20 68.221 61.231 6.041 1.00 83.05 O
+ATOM 425 C2' A A 20 65.712 61.108 6.103 1.00 81.15 C
+ATOM 426 O2' A A 20 65.786 59.824 6.656 1.00 83.37 O
+ATOM 427 C1' A A 20 64.744 61.986 6.902 1.00 80.09 C
+ATOM 428 N9 A A 20 63.779 62.755 6.122 1.00 77.26 N
+ATOM 429 C8 A A 20 63.909 64.014 5.592 1.00 76.84 C
+ATOM 430 N7 A A 20 62.844 64.431 4.955 1.00 76.08 N
+ATOM 431 C5 A A 20 61.958 63.373 5.068 1.00 75.98 C
+ATOM 432 C6 A A 20 60.651 63.184 4.598 1.00 75.86 C
+ATOM 433 N6 A A 20 59.982 64.094 3.882 1.00 76.10 N
+ATOM 434 N1 A A 20 60.045 62.012 4.888 1.00 75.42 N
+ATOM 435 C2 A A 20 60.720 61.100 5.602 1.00 76.18 C
+ATOM 436 N3 A A 20 61.952 61.161 6.096 1.00 76.33 N
+ATOM 437 C4 A A 20 62.522 62.336 5.786 1.00 76.27 C
+ATOM 438 P G A 21 68.416 59.835 6.842 1.00 83.99 P
+ATOM 439 OP1 G A 21 69.871 59.617 7.084 1.00 82.93 O
+ATOM 440 OP2 G A 21 67.632 58.787 6.129 1.00 85.06 O
+ATOM 441 O5' G A 21 67.758 60.103 8.267 1.00 81.30 O
+ATOM 442 C5' G A 21 67.378 59.027 9.123 1.00 78.72 C
+ATOM 443 C4' G A 21 66.027 59.321 9.725 1.00 78.10 C
+ATOM 444 O4' G A 21 65.080 59.521 8.640 1.00 78.26 O
+ATOM 445 C3' G A 21 65.380 58.242 10.572 1.00 76.75 C
+ATOM 446 O3' G A 21 65.797 58.230 11.918 1.00 75.15 O
+ATOM 447 C2' G A 21 63.914 58.615 10.469 1.00 77.51 C
+ATOM 448 O2' G A 21 63.635 59.759 11.250 1.00 78.02 O
+ATOM 449 C1' G A 21 63.821 58.986 8.994 1.00 78.22 C
+ATOM 450 N9 G A 21 63.595 57.775 8.211 1.00 78.46 N
+ATOM 451 C8 G A 21 64.527 57.004 7.558 1.00 78.61 C
+ATOM 452 N7 G A 21 64.008 55.947 6.988 1.00 79.65 N
+ATOM 453 C5 G A 21 62.651 56.035 7.272 1.00 79.52 C
+ATOM 454 C6 G A 21 61.569 55.176 6.920 1.00 79.20 C
+ATOM 455 O6 G A 21 61.593 54.121 6.262 1.00 77.93 O
+ATOM 456 N1 G A 21 60.362 55.653 7.420 1.00 79.94 N
+ATOM 457 C2 G A 21 60.211 56.801 8.162 1.00 80.08 C
+ATOM 458 N2 G A 21 58.978 57.110 8.559 1.00 80.92 N
+ATOM 459 N3 G A 21 61.202 57.597 8.494 1.00 79.71 N
+ATOM 460 C4 G A 21 62.383 57.161 8.020 1.00 79.25 C
+ATOM 461 P G A 22 65.553 56.907 12.788 1.00 75.22 P
+ATOM 462 OP1 G A 22 66.079 57.154 14.161 1.00 76.23 O
+ATOM 463 OP2 G A 22 66.048 55.739 12.002 1.00 74.26 O
+ATOM 464 O5' G A 22 63.966 56.780 12.860 1.00 74.14 O
+ATOM 465 C5' G A 22 63.189 57.768 13.513 1.00 71.88 C
+ATOM 466 C4' G A 22 61.736 57.364 13.541 1.00 70.11 C
+ATOM 467 O4' G A 22 61.245 57.258 12.173 1.00 69.75 O
+ATOM 468 C3' G A 22 61.479 55.972 14.091 1.00 69.37 C
+ATOM 469 O3' G A 22 61.441 55.892 15.497 1.00 68.01 O
+ATOM 470 C2' G A 22 60.128 55.634 13.493 1.00 69.71 C
+ATOM 471 O2' G A 22 59.080 56.284 14.172 1.00 69.55 O
+ATOM 472 C1' G A 22 60.269 56.226 12.097 1.00 70.83 C
+ATOM 473 N9 G A 22 60.698 55.184 11.167 1.00 71.65 N
+ATOM 474 C8 G A 22 61.942 54.973 10.631 1.00 71.65 C
+ATOM 475 N7 G A 22 61.995 53.916 9.865 1.00 72.21 N
+ATOM 476 C5 G A 22 60.704 53.408 9.890 1.00 71.92 C
+ATOM 477 C6 G A 22 60.149 52.278 9.247 1.00 71.25 C
+ATOM 478 O6 G A 22 60.704 51.471 8.496 1.00 71.85 O
+ATOM 479 N1 G A 22 58.797 52.130 9.550 1.00 71.46 N
+ATOM 480 C2 G A 22 58.071 52.964 10.362 1.00 71.45 C
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+ATOM 482 N3 G A 22 58.578 54.021 10.962 1.00 72.00 N
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+ATOM 485 OP1 G A 23 61.633 54.663 17.661 1.00 67.78 O
+ATOM 486 OP2 G A 23 62.665 53.751 15.493 1.00 67.92 O
+ATOM 487 O5' G A 23 60.178 53.745 15.842 1.00 66.55 O
+ATOM 488 C5' G A 23 58.959 54.370 16.209 1.00 66.95 C
+ATOM 489 C4' G A 23 57.770 53.491 15.901 1.00 66.33 C
+ATOM 490 O4' G A 23 57.553 53.426 14.460 1.00 66.90 O
+ATOM 491 C3' G A 23 57.922 52.034 16.291 1.00 66.34 C
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+ATOM 494 O2' G A 23 55.584 51.547 15.920 1.00 61.23 O
+ATOM 495 C1' G A 23 57.037 52.146 14.114 1.00 64.35 C
+ATOM 496 N9 G A 23 57.967 51.457 13.227 1.00 63.89 N
+ATOM 497 C8 G A 23 59.306 51.697 13.043 1.00 63.75 C
+ATOM 498 N7 G A 23 59.868 50.849 12.223 1.00 64.11 N
+ATOM 499 C5 G A 23 58.831 50.010 11.833 1.00 62.97 C
+ATOM 500 C6 G A 23 58.825 48.887 10.958 1.00 62.43 C
+ATOM 501 O6 G A 23 59.769 48.388 10.326 1.00 63.41 O
+ATOM 502 N1 G A 23 57.556 48.332 10.852 1.00 61.36 N
+ATOM 503 C2 G A 23 56.437 48.785 11.502 1.00 60.60 C
+ATOM 504 N2 G A 23 55.296 48.112 11.268 1.00 60.05 N
+ATOM 505 N3 G A 23 56.431 49.822 12.322 1.00 61.58 N
+ATOM 506 C4 G A 23 57.652 50.383 12.437 1.00 62.69 C
+ATOM 507 P A A 24 58.081 50.365 18.262 1.00 70.89 P
+ATOM 508 OP1 A A 24 58.882 49.647 17.244 1.00 73.17 O
+ATOM 509 OP2 A A 24 56.848 49.740 18.787 1.00 72.21 O
+ATOM 510 O5' A A 24 59.039 50.727 19.478 1.00 71.11 O
+ATOM 511 C5' A A 24 60.110 51.657 19.320 1.00 70.21 C
+ATOM 512 C4' A A 24 61.356 51.123 19.985 1.00 68.55 C
+ATOM 513 O4' A A 24 61.028 50.722 21.337 1.00 67.16 O
+ATOM 514 C3' A A 24 61.944 49.873 19.358 1.00 69.42 C
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+ATOM 516 C2' A A 24 62.695 49.249 20.531 1.00 67.92 C
+ATOM 517 O2' A A 24 63.935 49.871 20.803 1.00 69.68 O
+ATOM 518 C1' A A 24 61.752 49.558 21.688 1.00 64.41 C
+ATOM 519 N9 A A 24 60.780 48.506 21.963 1.00 60.75 N
+ATOM 520 C8 A A 24 59.468 48.471 21.572 1.00 59.22 C
+ATOM 521 N7 A A 24 58.812 47.425 22.015 1.00 59.13 N
+ATOM 522 C5 A A 24 59.761 46.720 22.737 1.00 58.33 C
+ATOM 523 C6 A A 24 59.689 45.530 23.474 1.00 58.17 C
+ATOM 524 N6 A A 24 58.567 44.818 23.625 1.00 58.76 N
+ATOM 525 N1 A A 24 60.816 45.090 24.067 1.00 58.32 N
+ATOM 526 C2 A A 24 61.931 45.814 23.930 1.00 60.28 C
+ATOM 527 N3 A A 24 62.122 46.959 23.277 1.00 61.00 N
+ATOM 528 C4 A A 24 60.983 47.364 22.697 1.00 60.30 C
+ATOM 529 P C A 25 63.295 49.164 17.228 1.00 72.52 P
+ATOM 530 OP1 C A 25 64.442 49.734 16.487 1.00 70.92 O
+ATOM 531 OP2 C A 25 62.101 48.674 16.477 1.00 74.42 O
+ATOM 532 O5' C A 25 63.825 47.968 18.134 1.00 71.83 O
+ATOM 533 C5' C A 25 65.165 47.952 18.598 1.00 72.62 C
+ATOM 534 C4' C A 25 65.485 46.606 19.185 1.00 74.39 C
+ATOM 535 O4' C A 25 64.558 46.356 20.273 1.00 73.10 O
+ATOM 536 C3' C A 25 65.263 45.426 18.250 1.00 76.56 C
+ATOM 537 O3' C A 25 66.392 45.192 17.419 1.00 81.10 O
+ATOM 538 C2' C A 25 65.043 44.274 19.223 1.00 74.88 C
+ATOM 539 O2' C A 25 66.249 43.738 19.735 1.00 75.19 O
+ATOM 540 C1' C A 25 64.261 44.972 20.335 1.00 72.77 C
+ATOM 541 N1 C A 25 62.813 44.801 20.227 1.00 71.71 N
+ATOM 542 C2 C A 25 62.260 43.662 20.760 1.00 71.83 C
+ATOM 543 O2 C A 25 63.013 42.827 21.270 1.00 73.95 O
+ATOM 544 N3 C A 25 60.927 43.481 20.711 1.00 70.88 N
+ATOM 545 C4 C A 25 60.155 44.391 20.139 1.00 69.84 C
+ATOM 546 N4 C A 25 58.841 44.155 20.123 1.00 70.13 N
+ATOM 547 C5 C A 25 60.695 45.576 19.562 1.00 69.41 C
+ATOM 548 C6 C A 25 62.022 45.740 19.626 1.00 70.68 C
+ATOM 549 P U A 26 66.238 44.250 16.126 1.00 85.16 P
+ATOM 550 OP1 U A 26 67.594 43.929 15.605 1.00 84.53 O
+ATOM 551 OP2 U A 26 65.243 44.884 15.235 1.00 85.22 O
+ATOM 552 O5' U A 26 65.582 42.908 16.686 1.00 83.10 O
+ATOM 553 C5' U A 26 66.404 41.853 17.168 1.00 83.06 C
+ATOM 554 C4' U A 26 65.751 40.520 16.911 1.00 82.90 C
+ATOM 555 O4' U A 26 64.618 40.350 17.795 1.00 83.33 O
+ATOM 556 C3' U A 26 65.164 40.371 15.525 1.00 82.05 C
+ATOM 557 O3' U A 26 66.184 39.990 14.616 1.00 81.59 O
+ATOM 558 C2' U A 26 64.113 39.289 15.737 1.00 82.83 C
+ATOM 559 O2' U A 26 64.643 37.983 15.780 1.00 83.21 O
+ATOM 560 C1' U A 26 63.594 39.639 17.129 1.00 83.33 C
+ATOM 561 N1 U A 26 62.387 40.475 17.115 1.00 84.07 N
+ATOM 562 C2 U A 26 61.168 39.833 17.084 1.00 84.45 C
+ATOM 563 O2 U A 26 61.060 38.619 17.070 1.00 84.31 O
+ATOM 564 N3 U A 26 60.076 40.662 17.073 1.00 84.96 N
+ATOM 565 C4 U A 26 60.082 42.039 17.090 1.00 85.37 C
+ATOM 566 O4 U A 26 59.012 42.648 17.081 1.00 85.84 O
+ATOM 567 C5 U A 26 61.383 42.627 17.120 1.00 84.60 C
+ATOM 568 C6 U A 26 62.465 41.842 17.132 1.00 84.27 C
+ATOM 569 P G A 27 66.132 40.515 13.104 1.00 81.65 P
+ATOM 570 OP1 G A 27 67.350 40.038 12.413 1.00 83.23 O
+ATOM 571 OP2 G A 27 65.837 41.963 13.132 1.00 82.55 O
+ATOM 572 O5' G A 27 64.885 39.731 12.503 1.00 80.51 O
+ATOM 573 C5' G A 27 64.935 38.317 12.376 1.00 78.28 C
+ATOM 574 C4' G A 27 63.552 37.741 12.178 1.00 77.67 C
+ATOM 575 O4' G A 27 62.747 38.009 13.362 1.00 77.49 O
+ATOM 576 C3' G A 27 62.728 38.306 11.023 1.00 76.44 C
+ATOM 577 O3' G A 27 63.058 37.664 9.795 1.00 75.91 O
+ATOM 578 C2' G A 27 61.311 37.972 11.470 1.00 76.07 C
+ATOM 579 O2' G A 27 61.007 36.613 11.242 1.00 74.28 O
+ATOM 580 C1' G A 27 61.397 38.227 12.979 1.00 76.21 C
+ATOM 581 N9 G A 27 61.016 39.598 13.319 1.00 74.43 N
+ATOM 582 C8 G A 27 61.838 40.697 13.410 1.00 74.12 C
+ATOM 583 N7 G A 27 61.190 41.800 13.682 1.00 73.38 N
+ATOM 584 C5 G A 27 59.863 41.404 13.788 1.00 72.40 C
+ATOM 585 C6 G A 27 58.695 42.162 14.067 1.00 71.55 C
+ATOM 586 O6 G A 27 58.592 43.386 14.280 1.00 70.85 O
+ATOM 587 N1 G A 27 57.559 41.356 14.086 1.00 70.35 N
+ATOM 588 C2 G A 27 57.544 40.002 13.863 1.00 70.15 C
+ATOM 589 N2 G A 27 56.350 39.400 13.926 1.00 68.30 N
+ATOM 590 N3 G A 27 58.623 39.288 13.598 1.00 71.70 N
+ATOM 591 C4 G A 27 59.740 40.047 13.577 1.00 72.98 C
+ATOM 592 P G A 28 62.365 38.133 8.409 1.00 76.89 P
+ATOM 593 OP1 G A 28 62.160 36.878 7.623 1.00 77.47 O
+ATOM 594 OP2 G A 28 63.124 39.269 7.796 1.00 75.40 O
+ATOM 595 O5' G A 28 60.924 38.672 8.823 1.00 76.26 O
+ATOM 596 C5' G A 28 60.164 39.487 7.926 1.00 73.92 C
+ATOM 597 C4' G A 28 58.705 39.462 8.314 1.00 71.92 C
+ATOM 598 O4' G A 28 58.573 39.835 9.714 1.00 71.54 O
+ATOM 599 C3' G A 28 57.811 40.439 7.565 1.00 70.88 C
+ATOM 600 O3' G A 28 57.367 39.868 6.331 1.00 69.61 O
+ATOM 601 C2' G A 28 56.656 40.616 8.546 1.00 70.99 C
+ATOM 602 O2' G A 28 55.717 39.557 8.480 1.00 71.07 O
+ATOM 603 C1' G A 28 57.387 40.587 9.894 1.00 71.11 C
+ATOM 604 N9 G A 28 57.746 41.916 10.380 1.00 70.31 N
+ATOM 605 C8 G A 28 58.962 42.543 10.281 1.00 70.75 C
+ATOM 606 N7 G A 28 58.958 43.747 10.782 1.00 70.48 N
+ATOM 607 C5 G A 28 57.663 43.920 11.251 1.00 69.56 C
+ATOM 608 C6 G A 28 57.055 45.027 11.906 1.00 69.08 C
+ATOM 609 O6 G A 28 57.557 46.119 12.224 1.00 68.50 O
+ATOM 610 N1 G A 28 55.724 44.771 12.202 1.00 69.21 N
+ATOM 611 C2 G A 28 55.060 43.608 11.915 1.00 69.07 C
+ATOM 612 N2 G A 28 53.767 43.555 12.280 1.00 68.80 N
+ATOM 613 N3 G A 28 55.616 42.572 11.315 1.00 69.71 N
+ATOM 614 C4 G A 28 56.906 42.797 11.014 1.00 69.55 C
+ATOM 615 P C A 29 57.271 40.780 5.008 1.00 67.90 P
+ATOM 616 OP1 C A 29 56.896 39.914 3.864 1.00 70.57 O
+ATOM 617 OP2 C A 29 58.508 41.596 4.940 1.00 69.03 O
+ATOM 618 O5' C A 29 56.055 41.759 5.299 1.00 66.35 O
+ATOM 619 C5' C A 29 54.758 41.248 5.567 1.00 62.83 C
+ATOM 620 C4' C A 29 53.946 42.279 6.308 1.00 62.09 C
+ATOM 621 O4' C A 29 54.537 42.496 7.619 1.00 59.41 O
+ATOM 622 C3' C A 29 53.949 43.661 5.684 1.00 62.50 C
+ATOM 623 O3' C A 29 53.018 43.803 4.618 1.00 64.25 O
+ATOM 624 C2' C A 29 53.618 44.546 6.876 1.00 61.37 C
+ATOM 625 O2' C A 29 52.234 44.525 7.187 1.00 61.74 O
+ATOM 626 C1' C A 29 54.421 43.860 7.981 1.00 59.52 C
+ATOM 627 N1 C A 29 55.777 44.424 8.092 1.00 59.57 N
+ATOM 628 C2 C A 29 55.950 45.631 8.772 1.00 59.50 C
+ATOM 629 O2 C A 29 54.973 46.175 9.280 1.00 60.54 O
+ATOM 630 N3 C A 29 57.180 46.174 8.858 1.00 59.71 N
+ATOM 631 C4 C A 29 58.225 45.562 8.299 1.00 59.10 C
+ATOM 632 N4 C A 29 59.412 46.152 8.405 1.00 56.50 N
+ATOM 633 C5 C A 29 58.091 44.321 7.607 1.00 59.16 C
+ATOM 634 C6 C A 29 56.856 43.790 7.529 1.00 59.74 C
+ATOM 635 P C A 30 53.015 45.164 3.761 1.00 65.71 P
+ATOM 636 OP1 C A 30 51.995 45.078 2.682 1.00 66.48 O
+ATOM 637 OP2 C A 30 54.428 45.487 3.422 1.00 64.15 O
+ATOM 638 O5' C A 30 52.539 46.252 4.817 1.00 66.68 O
+ATOM 639 C5' C A 30 52.834 47.619 4.624 1.00 66.07 C
+ATOM 640 C4' C A 30 52.552 48.383 5.883 1.00 64.24 C
+ATOM 641 O4' C A 30 53.379 47.875 6.961 1.00 63.99 O
+ATOM 642 C3' C A 30 52.853 49.863 5.817 1.00 63.38 C
+ATOM 643 O3' C A 30 51.704 50.500 5.285 1.00 63.48 O
+ATOM 644 C2' C A 30 53.060 50.195 7.287 1.00 63.64 C
+ATOM 645 O2' C A 30 51.818 50.289 7.955 1.00 63.72 O
+ATOM 646 C1' C A 30 53.793 48.945 7.782 1.00 63.35 C
+ATOM 647 N1 C A 30 55.243 49.051 7.628 1.00 63.96 N
+ATOM 648 C2 C A 30 55.945 49.948 8.418 1.00 64.30 C
+ATOM 649 O2 C A 30 55.330 50.610 9.257 1.00 66.15 O
+ATOM 650 N3 C A 30 57.280 50.073 8.250 1.00 64.07 N
+ATOM 651 C4 C A 30 57.909 49.334 7.339 1.00 63.26 C
+ATOM 652 N4 C A 30 59.218 49.497 7.206 1.00 63.72 N
+ATOM 653 C5 C A 30 57.220 48.395 6.526 1.00 63.27 C
+ATOM 654 C6 C A 30 55.897 48.284 6.704 1.00 64.28 C
+ATOM 655 P C A 31 51.870 51.754 4.306 1.00 64.41 P
+ATOM 656 OP1 C A 31 50.528 52.130 3.784 1.00 63.20 O
+ATOM 657 OP2 C A 31 52.983 51.484 3.365 1.00 63.17 O
+ATOM 658 O5' C A 31 52.369 52.895 5.282 1.00 63.89 O
+ATOM 659 C5' C A 31 51.578 53.280 6.382 1.00 63.36 C
+ATOM 660 C4' C A 31 52.287 54.339 7.160 1.00 63.12 C
+ATOM 661 O4' C A 31 53.352 53.730 7.927 1.00 63.91 O
+ATOM 662 C3' C A 31 53.003 55.344 6.284 1.00 61.70 C
+ATOM 663 O3' C A 31 52.113 56.345 5.844 1.00 61.08 O
+ATOM 664 C2' C A 31 54.052 55.885 7.231 1.00 62.18 C
+ATOM 665 O2' C A 31 53.483 56.788 8.145 1.00 62.99 O
+ATOM 666 C1' C A 31 54.443 54.622 7.990 1.00 63.19 C
+ATOM 667 N1 C A 31 55.620 53.977 7.410 1.00 63.84 N
+ATOM 668 C2 C A 31 56.831 54.589 7.597 1.00 63.43 C
+ATOM 669 O2 C A 31 56.855 55.634 8.245 1.00 64.84 O
+ATOM 670 N3 C A 31 57.946 54.041 7.081 1.00 63.21 N
+ATOM 671 C4 C A 31 57.872 52.902 6.402 1.00 64.27 C
+ATOM 672 N4 C A 31 59.010 52.390 5.922 1.00 64.98 N
+ATOM 673 C5 C A 31 56.633 52.238 6.190 1.00 65.15 C
+ATOM 674 C6 C A 31 55.535 52.809 6.707 1.00 64.47 C
+ATOM 675 P G A 32 52.458 57.185 4.523 1.00 62.37 P
+ATOM 676 OP1 G A 32 51.396 58.213 4.397 1.00 60.41 O
+ATOM 677 OP2 G A 32 52.715 56.238 3.403 1.00 60.94 O
+ATOM 678 O5' G A 32 53.835 57.910 4.866 1.00 63.18 O
+ATOM 679 C5' G A 32 53.847 59.093 5.641 1.00 62.39 C
+ATOM 680 C4' G A 32 55.228 59.676 5.680 1.00 63.39 C
+ATOM 681 O4' G A 32 56.105 58.751 6.367 1.00 64.76 O
+ATOM 682 C3' G A 32 55.889 59.815 4.326 1.00 64.49 C
+ATOM 683 O3' G A 32 55.509 60.970 3.617 1.00 65.91 O
+ATOM 684 C2' G A 32 57.362 59.837 4.675 1.00 65.04 C
+ATOM 685 O2' G A 32 57.780 61.102 5.143 1.00 64.75 O
+ATOM 686 C1' G A 32 57.404 58.811 5.800 1.00 64.89 C
+ATOM 687 N9 G A 32 57.744 57.503 5.264 1.00 66.38 N
+ATOM 688 C8 G A 32 56.907 56.435 5.060 1.00 68.11 C
+ATOM 689 N7 G A 32 57.510 55.412 4.521 1.00 69.20 N
+ATOM 690 C5 G A 32 58.823 55.836 4.361 1.00 68.47 C
+ATOM 691 C6 G A 32 59.932 55.175 3.806 1.00 69.12 C
+ATOM 692 O6 G A 32 59.980 54.056 3.304 1.00 71.60 O
+ATOM 693 N1 G A 32 61.076 55.961 3.856 1.00 69.48 N
+ATOM 694 C2 G A 32 61.139 57.234 4.358 1.00 69.13 C
+ATOM 695 N2 G A 32 62.336 57.831 4.314 1.00 68.48 N
+ATOM 696 N3 G A 32 60.103 57.870 4.863 1.00 68.83 N
+ATOM 697 C4 G A 32 58.984 57.116 4.833 1.00 67.70 C
+ATOM 698 P A A 33 55.228 60.837 2.054 1.00 67.60 P
+ATOM 699 OP1 A A 33 53.763 60.625 1.905 1.00 65.92 O
+ATOM 700 OP2 A A 33 56.180 59.801 1.567 1.00 67.33 O
+ATOM 701 O5' A A 33 55.593 62.258 1.434 1.00 67.76 O
+ATOM 702 C5' A A 33 56.865 62.878 1.641 1.00 69.76 C
+ATOM 703 C4' A A 33 56.994 64.038 0.684 1.00 71.33 C
+ATOM 704 O4' A A 33 58.204 64.805 0.937 1.00 71.47 O
+ATOM 705 C3' A A 33 57.125 63.544 -0.740 1.00 72.06 C
+ATOM 706 O3' A A 33 56.034 63.736 -1.619 1.00 74.07 O
+ATOM 707 C2' A A 33 58.602 63.589 -1.112 1.00 71.79 C
+ATOM 708 O2' A A 33 58.810 64.058 -2.429 1.00 71.97 O
+ATOM 709 C1' A A 33 59.144 64.615 -0.110 1.00 70.81 C
+ATOM 710 N9 A A 33 60.441 64.313 0.492 1.00 69.50 N
+ATOM 711 C8 A A 33 61.506 65.166 0.616 1.00 69.12 C
+ATOM 712 N7 A A 33 62.547 64.634 1.211 1.00 68.67 N
+ATOM 713 C5 A A 33 62.140 63.340 1.497 1.00 68.66 C
+ATOM 714 C6 A A 33 62.789 62.260 2.126 1.00 67.48 C
+ATOM 715 N6 A A 33 64.024 62.321 2.622 1.00 67.34 N
+ATOM 716 N1 A A 33 62.112 61.104 2.236 1.00 66.36 N
+ATOM 717 C2 A A 33 60.863 61.047 1.756 1.00 68.99 C
+ATOM 718 N3 A A 33 60.140 61.993 1.155 1.00 68.41 N
+ATOM 719 C4 A A 33 60.845 63.127 1.054 1.00 69.05 C
+ATOM 720 P U A 34 55.824 65.152 -2.328 1.00 74.88 P
+ATOM 721 OP1 U A 34 55.020 64.908 -3.544 1.00 76.95 O
+ATOM 722 OP2 U A 34 57.139 65.818 -2.430 1.00 77.84 O
+ATOM 723 O5' U A 34 54.926 65.989 -1.318 1.00 78.42 O
+ATOM 724 C5' U A 34 54.185 65.351 -0.295 1.00 81.29 C
+ATOM 725 C4' U A 34 52.728 65.677 -0.440 1.00 83.18 C
+ATOM 726 O4' U A 34 52.277 65.244 -1.744 1.00 85.09 O
+ATOM 727 C3' U A 34 51.830 64.944 0.538 1.00 84.70 C
+ATOM 728 O3' U A 34 51.739 65.734 1.721 1.00 86.22 O
+ATOM 729 C2' U A 34 50.492 64.920 -0.195 1.00 85.34 C
+ATOM 730 O2' U A 34 49.750 66.116 -0.048 1.00 86.46 O
+ATOM 731 C1' U A 34 50.941 64.780 -1.652 1.00 85.85 C
+ATOM 732 N1 U A 34 50.856 63.449 -2.274 1.00 86.02 N
+ATOM 733 C2 U A 34 49.694 62.731 -2.110 1.00 86.35 C
+ATOM 734 O2 U A 34 48.760 63.134 -1.441 1.00 86.70 O
+ATOM 735 N3 U A 34 49.663 61.521 -2.759 1.00 86.83 N
+ATOM 736 C4 U A 34 50.662 60.967 -3.534 1.00 86.45 C
+ATOM 737 O4 U A 34 50.500 59.849 -4.031 1.00 85.04 O
+ATOM 738 C5 U A 34 51.837 61.771 -3.643 1.00 86.54 C
+ATOM 739 C6 U A 34 51.894 62.951 -3.021 1.00 85.75 C
+ATOM 740 P G A 35 52.152 65.101 3.133 1.00 86.03 P
+ATOM 741 OP1 G A 35 53.057 63.962 2.842 1.00 87.58 O
+ATOM 742 OP2 G A 35 50.900 64.870 3.900 1.00 86.93 O
+ATOM 743 O5' G A 35 52.992 66.243 3.851 1.00 82.44 O
+ATOM 744 C5' G A 35 53.697 65.970 5.055 1.00 82.21 C
+ATOM 745 C4' G A 35 54.954 65.202 4.743 1.00 80.34 C
+ATOM 746 O4' G A 35 55.443 65.620 3.455 1.00 81.24 O
+ATOM 747 C3' G A 35 56.105 65.432 5.709 1.00 80.16 C
+ATOM 748 O3' G A 35 56.017 64.446 6.733 1.00 78.85 O
+ATOM 749 C2' G A 35 57.326 65.138 4.843 1.00 81.09 C
+ATOM 750 O2' G A 35 57.613 63.762 4.756 1.00 84.00 O
+ATOM 751 C1' G A 35 56.852 65.607 3.468 1.00 81.14 C
+ATOM 752 N9 G A 35 57.345 66.850 2.883 1.00 80.09 N
+ATOM 753 C8 G A 35 56.599 67.774 2.191 1.00 79.74 C
+ATOM 754 N7 G A 35 57.324 68.703 1.637 1.00 79.94 N
+ATOM 755 C5 G A 35 58.624 68.394 2.016 1.00 78.91 C
+ATOM 756 C6 G A 35 59.843 69.026 1.693 1.00 78.16 C
+ATOM 757 O6 G A 35 60.033 70.005 0.961 1.00 79.05 O
+ATOM 758 N1 G A 35 60.919 68.399 2.305 1.00 76.96 N
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+ATOM 760 N2 G A 35 61.990 66.850 3.623 1.00 76.36 N
+ATOM 761 N3 G A 35 59.702 66.685 3.407 1.00 78.05 N
+ATOM 762 C4 G A 35 58.645 67.280 2.825 1.00 78.58 C
+ATOM 763 P A A 36 56.302 64.840 8.264 1.00 76.30 P
+ATOM 764 OP1 A A 36 54.975 64.874 8.942 1.00 75.67 O
+ATOM 765 OP2 A A 36 57.180 66.045 8.282 1.00 77.08 O
+ATOM 766 O5' A A 36 57.155 63.624 8.842 1.00 72.20 O
+ATOM 767 C5' A A 36 56.630 62.304 8.880 1.00 69.65 C
+ATOM 768 C4' A A 36 57.735 61.338 9.196 1.00 67.97 C
+ATOM 769 O4' A A 36 58.775 61.499 8.202 1.00 68.85 O
+ATOM 770 C3' A A 36 58.432 61.569 10.525 1.00 67.41 C
+ATOM 771 O3' A A 36 57.747 60.830 11.524 1.00 67.02 O
+ATOM 772 C2' A A 36 59.815 60.974 10.276 1.00 67.37 C
+ATOM 773 O2' A A 36 59.886 59.573 10.441 1.00 66.90 O
+ATOM 774 C1' A A 36 60.045 61.341 8.808 1.00 67.53 C
+ATOM 775 N9 A A 36 60.752 62.600 8.641 1.00 66.76 N
+ATOM 776 C8 A A 36 60.375 63.652 7.852 1.00 67.45 C
+ATOM 777 N7 A A 36 61.191 64.671 7.908 1.00 66.96 N
+ATOM 778 C5 A A 36 62.172 64.259 8.794 1.00 66.08 C
+ATOM 779 C6 A A 36 63.311 64.889 9.276 1.00 66.19 C
+ATOM 780 N6 A A 36 63.665 66.125 8.928 1.00 67.40 N
+ATOM 781 N1 A A 36 64.087 64.205 10.142 1.00 66.85 N
+ATOM 782 C2 A A 36 63.716 62.966 10.495 1.00 66.08 C
+ATOM 783 N3 A A 36 62.657 62.268 10.111 1.00 65.19 N
+ATOM 784 C4 A A 36 61.917 62.982 9.248 1.00 65.98 C
+ATOM 785 P A A 37 57.509 61.470 12.975 1.00 68.44 P
+ATOM 786 OP1 A A 37 56.864 60.414 13.806 1.00 68.71 O
+ATOM 787 OP2 A A 37 56.818 62.771 12.773 1.00 66.15 O
+ATOM 788 O5' A A 37 58.982 61.698 13.553 1.00 69.51 O
+ATOM 789 C5' A A 37 59.702 60.597 14.106 1.00 72.39 C
+ATOM 790 C4' A A 37 61.083 61.004 14.590 1.00 73.88 C
+ATOM 791 O4' A A 37 61.842 61.585 13.493 1.00 74.64 O
+ATOM 792 C3' A A 37 61.133 62.080 15.665 1.00 75.34 C
+ATOM 793 O3' A A 37 60.948 61.522 16.963 1.00 77.76 O
+ATOM 794 C2' A A 37 62.544 62.635 15.506 1.00 74.93 C
+ATOM 795 O2' A A 37 63.525 61.813 16.108 1.00 73.93 O
+ATOM 796 C1' A A 37 62.730 62.569 13.995 1.00 75.06 C
+ATOM 797 N9 A A 37 62.515 63.833 13.299 1.00 76.44 N
+ATOM 798 C8 A A 37 61.475 64.214 12.492 1.00 77.47 C
+ATOM 799 N7 A A 37 61.604 65.421 12.002 1.00 77.88 N
+ATOM 800 C5 A A 37 62.808 65.868 12.528 1.00 78.70 C
+ATOM 801 C6 A A 37 63.516 67.076 12.386 1.00 79.68 C
+ATOM 802 N6 A A 37 63.093 68.103 11.641 1.00 80.75 N
+ATOM 803 N1 A A 37 64.689 67.195 13.045 1.00 80.31 N
+ATOM 804 C2 A A 37 65.112 66.167 13.792 1.00 80.01 C
+ATOM 805 N3 A A 37 64.538 64.987 14.002 1.00 79.09 N
+ATOM 806 C4 A A 37 63.376 64.900 13.332 1.00 78.07 C
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+ATOM 808 OP1 A A 38 60.704 61.769 19.430 1.00 80.61 O
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+ATOM 815 O3' A A 38 62.076 66.412 20.583 1.00 84.40 O
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+ATOM 818 C1' A A 38 62.993 66.945 17.115 1.00 80.98 C
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+ATOM 1095 C1' A A 51 38.293 70.602 48.737 1.00 86.88 C
+ATOM 1096 N9 A A 51 39.245 71.707 48.758 1.00 82.36 N
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+ATOM 1102 N1 A A 51 39.199 75.530 47.539 1.00 76.02 N
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+ATOM 1107 OP1 A A 52 39.960 66.929 44.294 1.00 98.51 O
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+ATOM 1114 O3' A A 52 37.991 71.808 40.147 1.00105.83 O
+ATOM 1115 C2' A A 52 38.020 73.163 42.155 1.00101.22 C
+ATOM 1116 O2' A A 52 36.680 73.455 41.831 1.00102.17 O
+ATOM 1117 C1' A A 52 38.111 72.767 43.631 1.00 99.83 C
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+ATOM 1121 C5 A A 52 41.110 74.232 45.031 1.00 96.25 C
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+ATOM 1123 N6 A A 52 43.037 75.365 45.910 1.00 94.72 N
+ATOM 1124 N1 A A 52 41.481 76.527 44.657 1.00 95.37 N
+ATOM 1125 C2 A A 52 40.338 76.521 43.962 1.00 96.12 C
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+ATOM 1129 OP1 A A 53 37.810 72.491 37.721 1.00108.36 O
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+ATOM 1131 O5' A A 53 38.606 74.150 39.369 1.00107.46 O
+ATOM 1132 C5' A A 53 38.058 75.137 38.499 1.00107.85 C
+ATOM 1133 C4' A A 53 38.929 76.365 38.509 1.00108.27 C
+ATOM 1134 O4' A A 53 39.209 76.699 39.891 1.00108.81 O
+ATOM 1135 C3' A A 53 40.298 76.243 37.854 1.00108.40 C
+ATOM 1136 O3' A A 53 40.239 76.517 36.456 1.00107.76 O
+ATOM 1137 C2' A A 53 41.086 77.317 38.590 1.00108.67 C
+ATOM 1138 O2' A A 53 40.806 78.618 38.112 1.00108.67 O
+ATOM 1139 C1' A A 53 40.542 77.152 40.011 1.00109.27 C
+ATOM 1140 N9 A A 53 41.277 76.108 40.718 1.00109.89 N
+ATOM 1141 C8 A A 53 41.033 74.758 40.673 1.00110.42 C
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+ATOM 1143 C5 A A 53 42.720 74.990 41.938 1.00110.94 C
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+ATOM 1145 N6 A A 53 44.285 73.710 43.257 1.00112.10 N
+ATOM 1146 N1 A A 53 44.452 76.014 43.167 1.00111.76 N
+ATOM 1147 C2 A A 53 43.988 77.184 42.703 1.00111.34 C
+ATOM 1148 N3 A A 53 42.958 77.419 41.892 1.00110.90 N
+ATOM 1149 C4 A A 53 42.361 76.266 41.542 1.00110.47 C
+ATOM 1150 P U A 54 40.720 75.399 35.403 1.00107.30 P
+ATOM 1151 OP1 U A 54 40.655 75.985 34.040 1.00107.24 O
+ATOM 1152 OP2 U A 54 39.952 74.165 35.708 1.00107.10 O
+ATOM 1153 O5' U A 54 42.250 75.138 35.772 1.00104.79 O
+ATOM 1154 C5' U A 54 43.228 76.148 35.560 1.00101.43 C
+ATOM 1155 C4' U A 54 44.377 75.983 36.522 1.00 99.06 C
+ATOM 1156 O4' U A 54 43.865 75.376 37.739 1.00 98.18 O
+ATOM 1157 C3' U A 54 45.481 75.031 36.092 1.00 98.11 C
+ATOM 1158 O3' U A 54 46.453 75.676 35.281 1.00 97.57 O
+ATOM 1159 C2' U A 54 46.093 74.631 37.424 1.00 97.54 C
+ATOM 1160 O2' U A 54 46.934 75.633 37.945 1.00 98.55 O
+ATOM 1161 C1' U A 54 44.850 74.523 38.300 1.00 96.75 C
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+ATOM 1163 C2 U A 54 44.996 72.251 39.131 1.00 93.99 C
+ATOM 1164 O2 U A 54 45.921 72.575 39.851 1.00 94.77 O
+ATOM 1165 N3 U A 54 44.524 70.966 39.077 1.00 92.33 N
+ATOM 1166 C4 U A 54 43.489 70.502 38.302 1.00 92.24 C
+ATOM 1167 O4 U A 54 43.181 69.316 38.357 1.00 90.91 O
+ATOM 1168 C5 U A 54 42.859 71.495 37.488 1.00 93.43 C
+ATOM 1169 C6 U A 54 43.298 72.754 37.521 1.00 94.21 C
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+ATOM 1173 O5' G A 55 48.459 74.154 35.595 1.00 93.42 O
+ATOM 1174 C5' G A 55 49.390 74.964 36.297 1.00 88.24 C
+ATOM 1175 C4' G A 55 50.177 74.134 37.278 1.00 84.14 C
+ATOM 1176 O4' G A 55 49.264 73.510 38.217 1.00 83.46 O
+ATOM 1177 C3' G A 55 50.899 72.957 36.664 1.00 82.28 C
+ATOM 1178 O3' G A 55 52.132 73.333 36.107 1.00 79.65 O
+ATOM 1179 C2' G A 55 51.068 72.020 37.846 1.00 82.45 C
+ATOM 1180 O2' G A 55 52.130 72.351 38.713 1.00 84.02 O
+ATOM 1181 C1' G A 55 49.743 72.224 38.567 1.00 82.65 C
+ATOM 1182 N9 G A 55 48.800 71.227 38.088 1.00 81.63 N
+ATOM 1183 C8 G A 55 47.779 71.396 37.188 1.00 81.42 C
+ATOM 1184 N7 G A 55 47.143 70.286 36.929 1.00 81.40 N
+ATOM 1185 C5 G A 55 47.781 69.334 37.714 1.00 79.68 C
+ATOM 1186 C6 G A 55 47.541 67.944 37.855 1.00 79.26 C
+ATOM 1187 O6 G A 55 46.695 67.247 37.288 1.00 77.42 O
+ATOM 1188 N1 G A 55 48.419 67.366 38.763 1.00 79.31 N
+ATOM 1189 C2 G A 55 49.404 68.036 39.442 1.00 79.67 C
+ATOM 1190 N2 G A 55 50.148 67.311 40.283 1.00 79.56 N
+ATOM 1191 N3 G A 55 49.642 69.324 39.310 1.00 79.52 N
+ATOM 1192 C4 G A 55 48.797 69.905 38.440 1.00 80.03 C
+ATOM 1193 P G A 56 52.789 72.392 35.004 1.00 78.55 P
+ATOM 1194 OP1 G A 56 54.080 72.967 34.550 1.00 77.49 O
+ATOM 1195 OP2 G A 56 51.707 72.125 34.021 1.00 80.25 O
+ATOM 1196 O5' G A 56 53.090 71.050 35.801 1.00 75.12 O
+ATOM 1197 C5' G A 56 54.067 71.039 36.829 1.00 69.26 C
+ATOM 1198 C4' G A 56 54.371 69.628 37.263 1.00 65.32 C
+ATOM 1199 O4' G A 56 53.188 69.046 37.881 1.00 62.82 O
+ATOM 1200 C3' G A 56 54.686 68.665 36.136 1.00 63.79 C
+ATOM 1201 O3' G A 56 56.038 68.731 35.713 1.00 65.54 O
+ATOM 1202 C2' G A 56 54.375 67.320 36.769 1.00 62.66 C
+ATOM 1203 O2' G A 56 55.428 66.873 37.601 1.00 62.67 O
+ATOM 1204 C1' G A 56 53.141 67.657 37.609 1.00 60.08 C
+ATOM 1205 N9 G A 56 51.901 67.352 36.905 1.00 55.37 N
+ATOM 1206 C8 G A 56 51.122 68.217 36.174 1.00 55.74 C
+ATOM 1207 N7 G A 56 50.106 67.629 35.599 1.00 52.72 N
+ATOM 1208 C5 G A 56 50.214 66.302 35.990 1.00 50.91 C
+ATOM 1209 C6 G A 56 49.406 65.204 35.675 1.00 49.97 C
+ATOM 1210 O6 G A 56 48.416 65.180 34.958 1.00 50.77 O
+ATOM 1211 N1 G A 56 49.854 64.038 36.284 1.00 48.77 N
+ATOM 1212 C2 G A 56 50.958 63.951 37.093 1.00 50.36 C
+ATOM 1213 N2 G A 56 51.234 62.732 37.591 1.00 48.97 N
+ATOM 1214 N3 G A 56 51.734 64.983 37.392 1.00 51.51 N
+ATOM 1215 C4 G A 56 51.304 66.118 36.809 1.00 51.89 C
+ATOM 1216 P U A 57 56.393 68.380 34.188 1.00 68.18 P
+ATOM 1217 OP1 U A 57 57.633 67.563 34.126 1.00 68.19 O
+ATOM 1218 OP2 U A 57 56.289 69.634 33.385 1.00 68.11 O
+ATOM 1219 O5' U A 57 55.175 67.458 33.751 1.00 66.24 O
+ATOM 1220 C5' U A 57 55.324 66.486 32.736 1.00 62.03 C
+ATOM 1221 C4' U A 57 55.340 65.129 33.360 1.00 59.74 C
+ATOM 1222 O4' U A 57 54.232 65.038 34.289 1.00 57.88 O
+ATOM 1223 C3' U A 57 55.156 63.959 32.420 1.00 58.61 C
+ATOM 1224 O3' U A 57 56.382 63.599 31.803 1.00 58.26 O
+ATOM 1225 C2' U A 57 54.620 62.895 33.370 1.00 58.38 C
+ATOM 1226 O2' U A 57 55.622 62.306 34.173 1.00 58.99 O
+ATOM 1227 C1' U A 57 53.699 63.732 34.261 1.00 56.63 C
+ATOM 1228 N1 U A 57 52.361 63.811 33.672 1.00 55.20 N
+ATOM 1229 C2 U A 57 51.624 62.655 33.644 1.00 55.04 C
+ATOM 1230 O2 U A 57 52.044 61.605 34.100 1.00 55.79 O
+ATOM 1231 N3 U A 57 50.387 62.767 33.057 1.00 53.93 N
+ATOM 1232 C4 U A 57 49.831 63.906 32.503 1.00 53.12 C
+ATOM 1233 O4 U A 57 48.707 63.850 32.010 1.00 53.57 O
+ATOM 1234 C5 U A 57 50.660 65.073 32.575 1.00 52.60 C
+ATOM 1235 C6 U A 57 51.868 64.988 33.148 1.00 54.55 C
+ATOM 1236 P G A 58 56.449 63.448 30.205 1.00 60.26 P
+ATOM 1237 OP1 G A 58 57.754 62.807 29.877 1.00 60.58 O
+ATOM 1238 OP2 G A 58 56.111 64.754 29.597 1.00 58.54 O
+ATOM 1239 O5' G A 58 55.268 62.426 29.875 1.00 57.10 O
+ATOM 1240 C5' G A 58 55.312 61.107 30.387 1.00 55.69 C
+ATOM 1241 C4' G A 58 54.029 60.369 30.093 1.00 55.43 C
+ATOM 1242 O4' G A 58 52.921 61.007 30.791 1.00 55.24 O
+ATOM 1243 C3' G A 58 53.589 60.368 28.636 1.00 54.18 C
+ATOM 1244 O3' G A 58 54.246 59.338 27.923 1.00 53.96 O
+ATOM 1245 C2' G A 58 52.097 60.092 28.757 1.00 54.41 C
+ATOM 1246 O2' G A 58 51.846 58.731 29.012 1.00 57.23 O
+ATOM 1247 C1' G A 58 51.737 60.887 30.012 1.00 53.85 C
+ATOM 1248 N9 G A 58 51.267 62.217 29.656 1.00 53.03 N
+ATOM 1249 C8 G A 58 51.950 63.400 29.767 1.00 52.08 C
+ATOM 1250 N7 G A 58 51.278 64.419 29.308 1.00 51.44 N
+ATOM 1251 C5 G A 58 50.074 63.877 28.879 1.00 50.05 C
+ATOM 1252 C6 G A 58 48.951 64.496 28.292 1.00 50.75 C
+ATOM 1253 O6 G A 58 48.794 65.685 28.008 1.00 53.29 O
+ATOM 1254 N1 G A 58 47.939 63.583 28.022 1.00 50.16 N
+ATOM 1255 C2 G A 58 48.003 62.239 28.270 1.00 51.00 C
+ATOM 1256 N2 G A 58 46.914 61.522 27.924 1.00 50.63 N
+ATOM 1257 N3 G A 58 49.053 61.641 28.814 1.00 52.48 N
+ATOM 1258 C4 G A 58 50.045 62.521 29.095 1.00 51.88 C
+ATOM 1259 P C A 59 54.759 59.607 26.431 1.00 53.17 P
+ATOM 1260 OP1 C A 59 55.673 58.491 26.089 1.00 55.70 O
+ATOM 1261 OP2 C A 59 55.228 61.001 26.296 1.00 53.99 O
+ATOM 1262 O5' C A 59 53.445 59.435 25.560 1.00 54.08 O
+ATOM 1263 C5' C A 59 52.793 58.183 25.522 1.00 52.32 C
+ATOM 1264 C4' C A 59 51.386 58.359 25.064 1.00 52.96 C
+ATOM 1265 O4' C A 59 50.695 59.217 26.007 1.00 53.34 O
+ATOM 1266 C3' C A 59 51.248 59.093 23.746 1.00 54.55 C
+ATOM 1267 O3' C A 59 51.430 58.198 22.670 1.00 56.10 O
+ATOM 1268 C2' C A 59 49.826 59.625 23.841 1.00 54.97 C
+ATOM 1269 O2' C A 59 48.860 58.610 23.649 1.00 56.71 O
+ATOM 1270 C1' C A 59 49.766 60.033 25.310 1.00 55.15 C
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+ATOM 1272 C2 C A 59 49.218 62.407 25.156 1.00 56.55 C
+ATOM 1273 O2 C A 59 48.077 62.055 24.858 1.00 59.12 O
+ATOM 1274 N3 C A 59 49.563 63.702 25.209 1.00 56.90 N
+ATOM 1275 C4 C A 59 50.800 64.045 25.557 1.00 56.99 C
+ATOM 1276 N4 C A 59 51.083 65.348 25.606 1.00 57.32 N
+ATOM 1277 C5 C A 59 51.793 63.071 25.874 1.00 56.89 C
+ATOM 1278 C6 C A 59 51.433 61.787 25.809 1.00 56.91 C
+ATOM 1279 P C A 60 52.117 58.708 21.315 1.00 58.55 P
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+ATOM 1281 OP2 C A 60 53.091 59.805 21.572 1.00 59.59 O
+ATOM 1282 O5' C A 60 50.930 59.382 20.504 1.00 58.02 O
+ATOM 1283 C5' C A 60 49.699 58.712 20.311 1.00 58.31 C
+ATOM 1284 C4' C A 60 48.692 59.668 19.729 1.00 60.59 C
+ATOM 1285 O4' C A 60 48.367 60.687 20.711 1.00 61.17 O
+ATOM 1286 C3' C A 60 49.215 60.451 18.536 1.00 61.75 C
+ATOM 1287 O3' C A 60 48.977 59.710 17.353 1.00 62.05 O
+ATOM 1288 C2' C A 60 48.336 61.689 18.549 1.00 62.65 C
+ATOM 1289 O2' C A 60 47.085 61.451 17.947 1.00 65.68 O
+ATOM 1290 C1' C A 60 48.151 61.920 20.050 1.00 62.43 C
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+ATOM 1300 OP1 A A 61 51.287 59.065 16.739 1.00 62.45 O
+ATOM 1301 OP2 A A 61 50.159 61.053 15.587 1.00 61.91 O
+ATOM 1302 O5' A A 61 49.427 58.698 15.124 1.00 60.51 O
+ATOM 1303 C5' A A 61 49.093 57.375 15.519 1.00 59.15 C
+ATOM 1304 C4' A A 61 48.325 56.663 14.432 1.00 57.25 C
+ATOM 1305 O4' A A 61 49.094 56.675 13.204 1.00 57.46 O
+ATOM 1306 C3' A A 61 48.113 55.187 14.715 1.00 56.35 C
+ATOM 1307 O3' A A 61 46.952 54.985 15.510 1.00 54.37 O
+ATOM 1308 C2' A A 61 47.924 54.610 13.325 1.00 56.77 C
+ATOM 1309 O2' A A 61 46.606 54.782 12.860 1.00 58.82 O
+ATOM 1310 C1' A A 61 48.893 55.462 12.506 1.00 56.45 C
+ATOM 1311 N9 A A 61 50.194 54.840 12.299 1.00 55.64 N
+ATOM 1312 C8 A A 61 51.375 55.127 12.934 1.00 56.06 C
+ATOM 1313 N7 A A 61 52.390 54.419 12.503 1.00 56.16 N
+ATOM 1314 C5 A A 61 51.836 53.608 11.524 1.00 55.20 C
+ATOM 1315 C6 A A 61 52.389 52.642 10.683 1.00 53.69 C
+ATOM 1316 N6 A A 61 53.685 52.311 10.692 1.00 53.61 N
+ATOM 1317 N1 A A 61 51.563 52.015 9.819 1.00 52.98 N
+ATOM 1318 C2 A A 61 50.275 52.347 9.811 1.00 52.85 C
+ATOM 1319 N3 A A 61 49.634 53.243 10.552 1.00 53.34 N
+ATOM 1320 C4 A A 61 50.484 53.847 11.397 1.00 55.08 C
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+ATOM 1322 OP1 A A 62 45.603 53.723 17.227 1.00 56.55 O
+ATOM 1323 OP2 A A 62 48.168 53.615 17.202 1.00 53.63 O
+ATOM 1324 O5' A A 62 46.816 52.489 15.470 1.00 54.86 O
+ATOM 1325 C5' A A 62 45.702 52.292 14.626 1.00 53.89 C
+ATOM 1326 C4' A A 62 45.976 51.126 13.735 1.00 54.46 C
+ATOM 1327 O4' A A 62 47.097 51.468 12.878 1.00 54.59 O
+ATOM 1328 C3' A A 62 46.438 49.885 14.479 1.00 53.52 C
+ATOM 1329 O3' A A 62 45.316 49.126 14.908 1.00 51.33 O
+ATOM 1330 C2' A A 62 47.214 49.158 13.396 1.00 54.74 C
+ATOM 1331 O2' A A 62 46.297 48.519 12.537 1.00 56.57 O
+ATOM 1332 C1' A A 62 47.893 50.323 12.664 1.00 54.85 C
+ATOM 1333 N9 A A 62 49.247 50.628 13.130 1.00 55.09 N
+ATOM 1334 C8 A A 62 49.610 51.419 14.192 1.00 55.06 C
+ATOM 1335 N7 A A 62 50.908 51.497 14.377 1.00 55.94 N
+ATOM 1336 C5 A A 62 51.434 50.706 13.369 1.00 54.99 C
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+ATOM 1338 N6 A A 62 53.812 50.830 13.683 1.00 52.77 N
+ATOM 1339 N1 A A 62 52.928 49.550 11.980 1.00 53.74 N
+ATOM 1340 C2 A A 62 51.858 49.111 11.318 1.00 54.27 C
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+ATOM 1342 C4 A A 62 50.426 50.169 12.589 1.00 55.03 C
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+ATOM 1344 OP1 U A 63 46.808 47.065 15.295 1.00 52.97 O
+ATOM 1345 OP2 U A 63 44.239 46.994 15.593 1.00 51.06 O
+ATOM 1346 O5' U A 63 45.691 48.165 17.223 1.00 51.23 O
+ATOM 1347 C5' U A 63 44.669 48.915 17.849 1.00 53.41 C
+ATOM 1348 C4' U A 63 44.630 48.623 19.322 1.00 54.01 C
+ATOM 1349 O4' U A 63 44.185 47.260 19.517 1.00 55.92 O
+ATOM 1350 C3' U A 63 46.012 48.682 19.940 1.00 54.73 C
+ATOM 1351 O3' U A 63 46.420 49.839 20.679 1.00 51.79 O
+ATOM 1352 C2' U A 63 46.533 47.253 20.033 1.00 54.94 C
+ATOM 1353 O2' U A 63 47.210 46.942 21.223 1.00 56.33 O
+ATOM 1354 C1' U A 63 45.234 46.451 20.007 1.00 57.13 C
+ATOM 1355 N1 U A 63 45.287 45.226 19.207 1.00 60.34 N
+ATOM 1356 C2 U A 63 45.138 44.028 19.869 1.00 61.56 C
+ATOM 1357 O2 U A 63 44.930 43.959 21.059 1.00 61.71 O
+ATOM 1358 N3 U A 63 45.231 42.914 19.079 1.00 64.02 N
+ATOM 1359 C4 U A 63 45.442 42.883 17.712 1.00 64.85 C
+ATOM 1360 O4 U A 63 45.492 41.795 17.125 1.00 65.14 O
+ATOM 1361 C5 U A 63 45.570 44.173 17.102 1.00 64.42 C
+ATOM 1362 C6 U A 63 45.489 45.272 17.855 1.00 62.18 C
+ATOM 1363 P U A 64 46.459 49.804 22.269 1.00 47.09 P
+ATOM 1364 OP1 U A 64 45.474 48.814 22.740 1.00 49.72 O
+ATOM 1365 OP2 U A 64 46.277 51.213 22.644 1.00 53.47 O
+ATOM 1366 O5' U A 64 47.944 49.291 22.621 1.00 48.05 O
+ATOM 1367 C5' U A 64 49.095 50.077 22.297 1.00 47.89 C
+ATOM 1368 C4' U A 64 50.371 49.234 22.232 1.00 47.96 C
+ATOM 1369 O4' U A 64 50.790 48.792 23.553 1.00 49.48 O
+ATOM 1370 C3' U A 64 50.175 47.926 21.478 1.00 49.78 C
+ATOM 1371 O3' U A 64 50.580 48.044 20.115 1.00 52.62 O
+ATOM 1372 C2' U A 64 51.262 47.014 22.015 1.00 48.66 C
+ATOM 1373 O2' U A 64 52.403 47.113 21.200 1.00 52.21 O
+ATOM 1374 C1' U A 64 51.487 47.568 23.418 1.00 47.24 C
+ATOM 1375 N1 U A 64 51.309 46.702 24.587 1.00 44.75 N
+ATOM 1376 C2 U A 64 52.389 45.900 24.918 1.00 43.26 C
+ATOM 1377 O2 U A 64 53.425 45.886 24.269 1.00 39.02 O
+ATOM 1378 N3 U A 64 52.214 45.120 26.034 1.00 42.01 N
+ATOM 1379 C4 U A 64 51.096 45.064 26.839 1.00 44.23 C
+ATOM 1380 O4 U A 64 51.140 44.403 27.873 1.00 46.83 O
+ATOM 1381 C5 U A 64 50.012 45.904 26.423 1.00 44.86 C
+ATOM 1382 C6 U A 64 50.152 46.679 25.333 1.00 46.40 C
+ATOM 1383 P C A 65 51.326 49.377 19.562 1.00 51.71 P
+ATOM 1384 OP1 C A 65 52.793 49.248 19.702 1.00 52.59 O
+ATOM 1385 OP2 C A 65 50.663 50.616 20.021 1.00 54.65 O
+ATOM 1386 O5' C A 65 50.956 49.256 18.023 1.00 51.76 O
+ATOM 1387 C5' C A 65 49.594 49.033 17.666 1.00 51.17 C
+ATOM 1388 C4' C A 65 49.473 47.942 16.630 1.00 50.61 C
+ATOM 1389 O4' C A 65 50.228 48.336 15.457 1.00 51.33 O
+ATOM 1390 C3' C A 65 50.034 46.584 17.008 1.00 50.04 C
+ATOM 1391 O3' C A 65 49.065 45.811 17.703 1.00 50.23 O
+ATOM 1392 C2' C A 65 50.312 45.974 15.645 1.00 50.59 C
+ATOM 1393 O2' C A 65 49.128 45.495 15.051 1.00 52.19 O
+ATOM 1394 C1' C A 65 50.793 47.192 14.856 1.00 50.72 C
+ATOM 1395 N1 C A 65 52.250 47.341 14.829 1.00 49.53 N
+ATOM 1396 C2 C A 65 52.951 46.590 13.916 1.00 49.03 C
+ATOM 1397 O2 C A 65 52.317 45.825 13.179 1.00 48.88 O
+ATOM 1398 N3 C A 65 54.296 46.704 13.849 1.00 49.20 N
+ATOM 1399 C4 C A 65 54.933 47.538 14.661 1.00 49.64 C
+ATOM 1400 N4 C A 65 56.250 47.644 14.526 1.00 48.30 N
+ATOM 1401 C5 C A 65 54.241 48.311 15.632 1.00 50.78 C
+ATOM 1402 C6 C A 65 52.905 48.188 15.676 1.00 49.60 C
+ATOM 1403 P C A 66 49.544 44.611 18.663 1.00 48.93 P
+ATOM 1404 OP1 C A 66 48.423 44.178 19.537 1.00 48.42 O
+ATOM 1405 OP2 C A 66 50.819 45.058 19.272 1.00 50.19 O
+ATOM 1406 O5' C A 66 49.908 43.433 17.666 1.00 49.16 O
+ATOM 1407 C5' C A 66 48.903 42.780 16.909 1.00 49.92 C
+ATOM 1408 C4' C A 66 49.538 41.774 15.989 1.00 50.54 C
+ATOM 1409 O4' C A 66 50.440 42.461 15.091 1.00 50.00 O
+ATOM 1410 C3' C A 66 50.440 40.788 16.695 1.00 51.95 C
+ATOM 1411 O3' C A 66 49.688 39.704 17.173 1.00 55.18 O
+ATOM 1412 C2' C A 66 51.380 40.343 15.597 1.00 51.22 C
+ATOM 1413 O2' C A 66 50.802 39.365 14.770 1.00 54.36 O
+ATOM 1414 C1' C A 66 51.558 41.640 14.822 1.00 49.83 C
+ATOM 1415 N1 C A 66 52.765 42.358 15.216 1.00 49.69 N
+ATOM 1416 C2 C A 66 53.962 41.892 14.740 1.00 49.58 C
+ATOM 1417 O2 C A 66 53.950 40.868 14.055 1.00 52.02 O
+ATOM 1418 N3 C A 66 55.105 42.549 15.034 1.00 48.70 N
+ATOM 1419 C4 C A 66 55.067 43.641 15.795 1.00 49.07 C
+ATOM 1420 N4 C A 66 56.224 44.276 16.032 1.00 50.40 N
+ATOM 1421 C5 C A 66 53.843 44.135 16.335 1.00 50.89 C
+ATOM 1422 C6 C A 66 52.720 43.464 16.021 1.00 49.92 C
+ATOM 1423 P U A 67 50.160 38.971 18.505 1.00 60.57 P
+ATOM 1424 OP1 U A 67 49.141 37.934 18.832 1.00 59.64 O
+ATOM 1425 OP2 U A 67 50.501 40.029 19.500 1.00 60.62 O
+ATOM 1426 O5' U A 67 51.540 38.286 18.096 1.00 58.02 O
+ATOM 1427 C5' U A 67 51.590 37.228 17.156 1.00 57.98 C
+ATOM 1428 C4' U A 67 53.024 36.859 16.894 1.00 60.31 C
+ATOM 1429 O4' U A 67 53.725 38.007 16.350 1.00 60.03 O
+ATOM 1430 C3' U A 67 53.814 36.475 18.130 1.00 62.18 C
+ATOM 1431 O3' U A 67 53.645 35.077 18.330 1.00 67.36 O
+ATOM 1432 C2' U A 67 55.243 36.786 17.716 1.00 60.43 C
+ATOM 1433 O2' U A 67 55.790 35.730 16.969 1.00 60.29 O
+ATOM 1434 C1' U A 67 55.052 38.027 16.836 1.00 59.24 C
+ATOM 1435 N1 U A 67 55.230 39.310 17.518 1.00 58.88 N
+ATOM 1436 C2 U A 67 56.440 39.956 17.379 1.00 58.64 C
+ATOM 1437 O2 U A 67 57.395 39.461 16.803 1.00 60.38 O
+ATOM 1438 N3 U A 67 56.493 41.205 17.945 1.00 57.00 N
+ATOM 1439 C4 U A 67 55.490 41.839 18.634 1.00 56.08 C
+ATOM 1440 O4 U A 67 55.624 43.017 18.919 1.00 57.14 O
+ATOM 1441 C5 U A 67 54.299 41.077 18.794 1.00 56.32 C
+ATOM 1442 C6 U A 67 54.210 39.869 18.243 1.00 58.50 C
+ATOM 1443 P G A 68 54.230 34.371 19.646 1.00 71.64 P
+ATOM 1444 OP1 G A 68 53.897 32.933 19.519 1.00 71.19 O
+ATOM 1445 OP2 G A 68 53.751 35.126 20.834 1.00 71.67 O
+ATOM 1446 O5' G A 68 55.806 34.568 19.513 1.00 71.77 O
+ATOM 1447 C5' G A 68 56.659 33.491 19.142 1.00 75.69 C
+ATOM 1448 C4' G A 68 58.091 33.830 19.491 1.00 79.27 C
+ATOM 1449 O4' G A 68 58.380 35.132 18.918 1.00 79.57 O
+ATOM 1450 C3' G A 68 58.385 34.004 20.980 1.00 81.28 C
+ATOM 1451 O3' G A 68 58.787 32.812 21.679 1.00 83.11 O
+ATOM 1452 C2' G A 68 59.584 34.943 20.956 1.00 82.22 C
+ATOM 1453 O2' G A 68 60.802 34.283 20.671 1.00 84.89 O
+ATOM 1454 C1' G A 68 59.236 35.853 19.782 1.00 81.50 C
+ATOM 1455 N9 G A 68 58.575 37.093 20.173 1.00 81.29 N
+ATOM 1456 C8 G A 68 57.250 37.289 20.478 1.00 81.20 C
+ATOM 1457 N7 G A 68 56.970 38.535 20.755 1.00 80.75 N
+ATOM 1458 C5 G A 68 58.186 39.194 20.627 1.00 80.02 C
+ATOM 1459 C6 G A 68 58.516 40.567 20.783 1.00 80.22 C
+ATOM 1460 O6 G A 68 57.767 41.520 21.044 1.00 80.59 O
+ATOM 1461 N1 G A 68 59.875 40.791 20.584 1.00 80.75 N
+ATOM 1462 C2 G A 68 60.798 39.828 20.258 1.00 80.78 C
+ATOM 1463 N2 G A 68 62.075 40.236 20.108 1.00 79.89 N
+ATOM 1464 N3 G A 68 60.496 38.555 20.089 1.00 80.70 N
+ATOM 1465 C4 G A 68 59.185 38.312 20.288 1.00 80.39 C
+ATOM 1466 P C A 69 59.229 31.475 20.876 1.00 84.26 P
+ATOM 1467 OP1 C A 69 60.580 31.681 20.282 1.00 80.96 O
+ATOM 1468 OP2 C A 69 58.112 30.992 20.017 1.00 83.67 O
+ATOM 1469 O5' C A 69 59.373 30.393 22.036 1.00 81.95 O
+ATOM 1470 C5' C A 69 60.304 30.567 23.099 1.00 78.18 C
+ATOM 1471 C4' C A 69 59.612 30.374 24.428 1.00 76.05 C
+ATOM 1472 O4' C A 69 58.981 31.619 24.844 1.00 74.44 O
+ATOM 1473 C3' C A 69 58.468 29.372 24.406 1.00 75.69 C
+ATOM 1474 O3' C A 69 58.908 28.028 24.532 1.00 76.59 O
+ATOM 1475 C2' C A 69 57.624 29.805 25.597 1.00 74.75 C
+ATOM 1476 O2' C A 69 58.123 29.297 26.823 1.00 74.80 O
+ATOM 1477 C1' C A 69 57.768 31.329 25.529 1.00 73.22 C
+ATOM 1478 N1 C A 69 56.654 31.993 24.829 1.00 70.35 N
+ATOM 1479 C2 C A 69 55.423 32.067 25.471 1.00 69.49 C
+ATOM 1480 O2 C A 69 55.308 31.549 26.584 1.00 69.27 O
+ATOM 1481 N3 C A 69 54.392 32.698 24.862 1.00 67.72 N
+ATOM 1482 C4 C A 69 54.563 33.232 23.651 1.00 68.13 C
+ATOM 1483 N4 C A 69 53.526 33.851 23.091 1.00 69.40 N
+ATOM 1484 C5 C A 69 55.807 33.158 22.964 1.00 66.89 C
+ATOM 1485 C6 C A 69 56.816 32.536 23.584 1.00 68.40 C
+ATOM 1486 P A A 70 57.971 26.841 23.990 1.00 76.83 P
+ATOM 1487 OP1 A A 70 58.699 25.566 24.172 1.00 76.97 O
+ATOM 1488 OP2 A A 70 57.496 27.236 22.638 1.00 78.32 O
+ATOM 1489 O5' A A 70 56.735 26.838 24.986 1.00 73.56 O
+ATOM 1490 C5' A A 70 56.921 26.420 26.317 1.00 71.88 C
+ATOM 1491 C4' A A 70 55.660 26.599 27.107 1.00 70.52 C
+ATOM 1492 O4' A A 70 55.305 28.006 27.120 1.00 70.13 O
+ATOM 1493 C3' A A 70 54.435 25.933 26.512 1.00 70.69 C
+ATOM 1494 O3' A A 70 54.363 24.549 26.820 1.00 72.81 O
+ATOM 1495 C2' A A 70 53.305 26.731 27.143 1.00 69.29 C
+ATOM 1496 O2' A A 70 53.075 26.359 28.482 1.00 69.16 O
+ATOM 1497 C1' A A 70 53.893 28.138 27.128 1.00 68.11 C
+ATOM 1498 N9 A A 70 53.470 28.894 25.952 1.00 64.00 N
+ATOM 1499 C8 A A 70 54.178 29.247 24.834 1.00 62.02 C
+ATOM 1500 N7 A A 70 53.474 29.925 23.959 1.00 60.61 N
+ATOM 1501 C5 A A 70 52.220 30.021 24.544 1.00 60.84 C
+ATOM 1502 C6 A A 70 51.013 30.616 24.123 1.00 60.96 C
+ATOM 1503 N6 A A 70 50.866 31.271 22.968 1.00 61.70 N
+ATOM 1504 N1 A A 70 49.944 30.517 24.947 1.00 58.65 N
+ATOM 1505 C2 A A 70 50.089 29.880 26.111 1.00 58.26 C
+ATOM 1506 N3 A A 70 51.171 29.287 26.616 1.00 60.01 N
+ATOM 1507 C4 A A 70 52.208 29.393 25.770 1.00 61.17 C
+ATOM 1508 P G A 71 53.262 23.639 26.088 1.00 73.21 P
+ATOM 1509 OP1 G A 71 53.410 22.249 26.575 1.00 75.65 O
+ATOM 1510 OP2 G A 71 53.327 23.913 24.628 1.00 74.68 O
+ATOM 1511 O5' G A 71 51.889 24.194 26.658 1.00 73.13 O
+ATOM 1512 C5' G A 71 51.545 23.948 28.006 1.00 73.66 C
+ATOM 1513 C4' G A 71 50.085 24.200 28.222 1.00 74.68 C
+ATOM 1514 O4' G A 71 49.834 25.619 28.061 1.00 74.96 O
+ATOM 1515 C3' G A 71 49.168 23.560 27.196 1.00 74.87 C
+ATOM 1516 O3' G A 71 48.900 22.193 27.431 1.00 77.06 O
+ATOM 1517 C2' G A 71 47.926 24.423 27.302 1.00 74.74 C
+ATOM 1518 O2' G A 71 47.160 24.095 28.450 1.00 73.45 O
+ATOM 1519 C1' G A 71 48.557 25.807 27.466 1.00 74.47 C
+ATOM 1520 N9 G A 71 48.732 26.500 26.190 1.00 73.18 N
+ATOM 1521 C8 G A 71 49.893 26.651 25.465 1.00 72.22 C
+ATOM 1522 N7 G A 71 49.730 27.362 24.379 1.00 71.34 N
+ATOM 1523 C5 G A 71 48.381 27.690 24.382 1.00 70.99 C
+ATOM 1524 C6 G A 71 47.614 28.457 23.459 1.00 70.89 C
+ATOM 1525 O6 G A 71 47.990 29.025 22.425 1.00 70.62 O
+ATOM 1526 N1 G A 71 46.279 28.535 23.845 1.00 70.13 N
+ATOM 1527 C2 G A 71 45.746 27.955 24.973 1.00 71.44 C
+ATOM 1528 N2 G A 71 44.437 28.147 25.177 1.00 71.27 N
+ATOM 1529 N3 G A 71 46.448 27.240 25.840 1.00 70.99 N
+ATOM 1530 C4 G A 71 47.749 27.153 25.486 1.00 71.48 C
+ATOM 1531 P C A 72 48.570 21.242 26.182 1.00 78.06 P
+ATOM 1532 OP1 C A 72 48.427 19.843 26.654 1.00 79.10 O
+ATOM 1533 OP2 C A 72 49.597 21.571 25.154 1.00 77.70 O
+ATOM 1534 O5' C A 72 47.129 21.735 25.716 1.00 76.34 O
+ATOM 1535 C5' C A 72 46.020 21.583 26.588 1.00 74.73 C
+ATOM 1536 C4' C A 72 44.789 22.243 26.020 1.00 74.94 C
+ATOM 1537 O4' C A 72 44.999 23.681 25.940 1.00 74.18 O
+ATOM 1538 C3' C A 72 44.435 21.873 24.594 1.00 74.74 C
+ATOM 1539 O3' C A 72 43.818 20.614 24.463 1.00 77.63 O
+ATOM 1540 C2' C A 72 43.573 23.046 24.163 1.00 72.71 C
+ATOM 1541 O2' C A 72 42.275 23.012 24.727 1.00 72.93 O
+ATOM 1542 C1' C A 72 44.345 24.199 24.789 1.00 70.56 C
+ATOM 1543 N1 C A 72 45.366 24.656 23.839 1.00 65.60 N
+ATOM 1544 C2 C A 72 44.983 25.549 22.825 1.00 62.36 C
+ATOM 1545 O2 C A 72 43.796 25.935 22.781 1.00 60.28 O
+ATOM 1546 N3 C A 72 45.908 25.962 21.926 1.00 58.47 N
+ATOM 1547 C4 C A 72 47.160 25.518 22.012 1.00 58.31 C
+ATOM 1548 N4 C A 72 48.035 25.941 21.095 1.00 57.64 N
+ATOM 1549 C5 C A 72 47.575 24.616 23.042 1.00 58.81 C
+ATOM 1550 C6 C A 72 46.656 24.215 23.923 1.00 61.58 C
+ATOM 1551 P G A 73 44.246 19.681 23.238 1.00 79.51 P
+ATOM 1552 OP1 G A 73 43.644 18.340 23.446 1.00 79.13 O
+ATOM 1553 OP2 G A 73 45.725 19.817 23.084 1.00 78.76 O
+ATOM 1554 O5' G A 73 43.539 20.372 21.992 1.00 77.35 O
+ATOM 1555 C5' G A 73 42.142 20.629 22.020 1.00 74.33 C
+ATOM 1556 C4' G A 73 41.738 21.509 20.863 1.00 72.37 C
+ATOM 1557 O4' G A 73 42.458 22.769 20.932 1.00 70.30 O
+ATOM 1558 C3' G A 73 42.087 21.020 19.470 1.00 72.08 C
+ATOM 1559 O3' G A 73 41.194 20.013 19.012 1.00 72.84 O
+ATOM 1560 C2' G A 73 41.929 22.305 18.670 1.00 70.65 C
+ATOM 1561 O2' G A 73 40.567 22.611 18.440 1.00 71.39 O
+ATOM 1562 C1' G A 73 42.536 23.329 19.632 1.00 67.90 C
+ATOM 1563 N9 G A 73 43.929 23.628 19.311 1.00 64.50 N
+ATOM 1564 C8 G A 73 45.070 23.161 19.922 1.00 62.79 C
+ATOM 1565 N7 G A 73 46.169 23.599 19.359 1.00 61.48 N
+ATOM 1566 C5 G A 73 45.722 24.411 18.322 1.00 61.69 C
+ATOM 1567 C6 G A 73 46.448 25.169 17.342 1.00 59.71 C
+ATOM 1568 O6 G A 73 47.679 25.276 17.188 1.00 57.76 O
+ATOM 1569 N1 G A 73 45.588 25.842 16.485 1.00 59.01 N
+ATOM 1570 C2 G A 73 44.216 25.798 16.549 1.00 61.75 C
+ATOM 1571 N2 G A 73 43.552 26.506 15.635 1.00 62.68 N
+ATOM 1572 N3 G A 73 43.537 25.106 17.443 1.00 62.36 N
+ATOM 1573 C4 G A 73 44.344 24.442 18.288 1.00 62.76 C
+ATOM 1574 P G A 74 41.787 18.637 18.416 1.00 74.17 P
+ATOM 1575 OP1 G A 74 40.716 17.600 18.506 1.00 74.30 O
+ATOM 1576 OP2 G A 74 43.117 18.392 19.042 1.00 71.62 O
+ATOM 1577 O5' G A 74 42.045 18.934 16.875 1.00 72.80 O
+ATOM 1578 C5' G A 74 42.905 19.983 16.477 1.00 71.35 C
+ATOM 1579 C4' G A 74 42.600 20.383 15.067 1.00 68.80 C
+ATOM 1580 O4' G A 74 43.028 21.760 14.917 1.00 69.15 O
+ATOM 1581 C3' G A 74 43.339 19.614 13.992 1.00 68.58 C
+ATOM 1582 O3' G A 74 42.846 18.468 13.299 1.00 71.01 O
+ATOM 1583 C2' G A 74 44.522 20.455 13.553 1.00 67.98 C
+ATOM 1584 O2' G A 74 44.576 20.558 12.143 1.00 68.13 O
+ATOM 1585 C1' G A 74 44.203 21.839 14.136 1.00 66.63 C
+ATOM 1586 N9 G A 74 45.323 22.134 15.022 1.00 63.24 N
+ATOM 1587 C8 G A 74 45.492 21.692 16.311 1.00 60.66 C
+ATOM 1588 N7 G A 74 46.701 21.882 16.760 1.00 60.19 N
+ATOM 1589 C5 G A 74 47.349 22.547 15.729 1.00 60.81 C
+ATOM 1590 C6 G A 74 48.677 23.004 15.635 1.00 61.76 C
+ATOM 1591 O6 G A 74 49.584 22.902 16.473 1.00 65.71 O
+ATOM 1592 N1 G A 74 48.918 23.642 14.418 1.00 60.45 N
+ATOM 1593 C2 G A 74 47.989 23.822 13.425 1.00 58.92 C
+ATOM 1594 N2 G A 74 48.406 24.479 12.330 1.00 58.54 N
+ATOM 1595 N3 G A 74 46.741 23.391 13.503 1.00 58.36 N
+ATOM 1596 C4 G A 74 46.494 22.764 14.674 1.00 60.52 C
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+ATOM 1598 OP1 A A 75 43.102 16.200 12.276 1.00 73.52 O
+ATOM 1599 OP2 A A 75 43.955 16.648 14.649 1.00 72.26 O
+ATOM 1600 O5' A A 75 45.151 17.547 12.672 1.00 68.58 O
+ATOM 1601 C5' A A 75 46.255 16.653 12.710 1.00 65.94 C
+ATOM 1602 C4' A A 75 47.133 16.874 11.504 1.00 65.49 C
+ATOM 1603 O4' A A 75 46.434 16.429 10.319 1.00 66.68 O
+ATOM 1604 C3' A A 75 47.472 18.333 11.260 1.00 65.46 C
+ATOM 1605 O3' A A 75 48.720 18.628 11.864 1.00 64.21 O
+ATOM 1606 C2' A A 75 47.592 18.420 9.750 1.00 64.16 C
+ATOM 1607 O2' A A 75 48.875 18.031 9.336 1.00 65.40 O
+ATOM 1608 C1' A A 75 46.555 17.396 9.295 1.00 64.67 C
+ATOM 1609 N9 A A 75 45.227 17.950 9.094 1.00 64.06 N
+ATOM 1610 C8 A A 75 44.138 17.744 9.898 1.00 64.00 C
+ATOM 1611 N7 A A 75 43.056 18.349 9.486 1.00 66.17 N
+ATOM 1612 C5 A A 75 43.463 19.001 8.332 1.00 65.71 C
+ATOM 1613 C6 A A 75 42.781 19.821 7.424 1.00 65.96 C
+ATOM 1614 N6 A A 75 41.490 20.141 7.546 1.00 67.52 N
+ATOM 1615 N1 A A 75 43.476 20.311 6.375 1.00 66.21 N
+ATOM 1616 C2 A A 75 44.770 19.991 6.260 1.00 66.15 C
+ATOM 1617 N3 A A 75 45.520 19.231 7.050 1.00 66.38 N
+ATOM 1618 C4 A A 75 44.799 18.763 8.080 1.00 64.69 C
+ATOM 1619 P A A 76 48.870 19.950 12.740 1.00 62.82 P
+ATOM 1620 OP1 A A 76 50.069 19.832 13.600 1.00 63.15 O
+ATOM 1621 OP2 A A 76 47.539 20.165 13.362 1.00 59.79 O
+ATOM 1622 O5' A A 76 49.159 21.073 11.650 1.00 60.99 O
+ATOM 1623 C5' A A 76 50.435 21.172 11.023 1.00 58.74 C
+ATOM 1624 C4' A A 76 50.317 21.995 9.775 1.00 57.81 C
+ATOM 1625 O4' A A 76 49.237 21.437 8.991 1.00 57.97 O
+ATOM 1626 C3' A A 76 49.940 23.455 9.967 1.00 56.91 C
+ATOM 1627 O3' A A 76 51.121 24.238 10.118 1.00 57.19 O
+ATOM 1628 C2' A A 76 49.263 23.779 8.643 1.00 56.44 C
+ATOM 1629 O2' A A 76 50.201 24.001 7.608 1.00 54.76 O
+ATOM 1630 C1' A A 76 48.515 22.475 8.363 1.00 55.29 C
+ATOM 1631 N9 A A 76 47.162 22.417 8.897 1.00 53.64 N
+ATOM 1632 C8 A A 76 46.775 21.938 10.128 1.00 53.02 C
+ATOM 1633 N7 A A 76 45.476 21.937 10.309 1.00 53.29 N
+ATOM 1634 C5 A A 76 44.974 22.466 9.127 1.00 53.22 C
+ATOM 1635 C6 A A 76 43.668 22.715 8.684 1.00 53.02 C
+ATOM 1636 N6 A A 76 42.582 22.451 9.400 1.00 52.94 N
+ATOM 1637 N1 A A 76 43.513 23.251 7.456 1.00 54.02 N
+ATOM 1638 C2 A A 76 44.606 23.509 6.723 1.00 53.06 C
+ATOM 1639 N3 A A 76 45.885 23.312 7.024 1.00 53.73 N
+ATOM 1640 C4 A A 76 46.004 22.782 8.255 1.00 54.00 C
+ATOM 1641 P A A 77 51.041 25.690 10.808 1.00 57.22 P
+ATOM 1642 OP1 A A 77 52.362 26.338 10.668 1.00 56.31 O
+ATOM 1643 OP2 A A 77 50.451 25.502 12.167 1.00 57.57 O
+ATOM 1644 O5' A A 77 50.023 26.495 9.880 1.00 57.05 O
+ATOM 1645 C5' A A 77 50.484 27.150 8.697 1.00 55.43 C
+ATOM 1646 C4' A A 77 49.318 27.660 7.869 1.00 55.21 C
+ATOM 1647 O4' A A 77 48.395 26.566 7.621 1.00 55.90 O
+ATOM 1648 C3' A A 77 48.457 28.764 8.470 1.00 54.93 C
+ATOM 1649 O3' A A 77 48.994 30.044 8.166 1.00 55.04 O
+ATOM 1650 C2' A A 77 47.149 28.572 7.719 1.00 55.16 C
+ATOM 1651 O2' A A 77 47.237 29.094 6.409 1.00 54.30 O
+ATOM 1652 C1' A A 77 47.068 27.048 7.639 1.00 54.33 C
+ATOM 1653 N9 A A 77 46.406 26.464 8.801 1.00 53.13 N
+ATOM 1654 C8 A A 77 46.987 26.001 9.955 1.00 52.87 C
+ATOM 1655 N7 A A 77 46.127 25.506 10.817 1.00 53.79 N
+ATOM 1656 C5 A A 77 44.899 25.658 10.187 1.00 52.32 C
+ATOM 1657 C6 A A 77 43.586 25.329 10.578 1.00 52.60 C
+ATOM 1658 N6 A A 77 43.286 24.748 11.739 1.00 55.40 N
+ATOM 1659 N1 A A 77 42.580 25.618 9.722 1.00 52.52 N
+ATOM 1660 C2 A A 77 42.887 26.202 8.552 1.00 52.91 C
+ATOM 1661 N3 A A 77 44.085 26.561 8.072 1.00 52.18 N
+ATOM 1662 C4 A A 77 45.056 26.256 8.949 1.00 52.16 C
+ATOM 1663 P C A 78 49.484 31.004 9.354 1.00 55.69 P
+ATOM 1664 OP1 C A 78 49.843 32.325 8.764 1.00 54.67 O
+ATOM 1665 OP2 C A 78 50.489 30.262 10.161 1.00 56.60 O
+ATOM 1666 O5' C A 78 48.186 31.175 10.259 1.00 54.42 O
+ATOM 1667 C5' C A 78 47.035 31.822 9.746 1.00 53.71 C
+ATOM 1668 C4' C A 78 45.790 31.247 10.370 1.00 53.69 C
+ATOM 1669 O4' C A 78 45.943 29.803 10.457 1.00 54.25 O
+ATOM 1670 C3' C A 78 45.529 31.646 11.808 1.00 53.72 C
+ATOM 1671 O3' C A 78 44.893 32.906 11.911 1.00 53.94 O
+ATOM 1672 C2' C A 78 44.636 30.518 12.292 1.00 53.88 C
+ATOM 1673 O2' C A 78 43.308 30.647 11.805 1.00 54.27 O
+ATOM 1674 C1' C A 78 45.305 29.325 11.623 1.00 52.32 C
+ATOM 1675 N1 C A 78 46.318 28.721 12.494 1.00 50.20 N
+ATOM 1676 C2 C A 78 45.883 27.995 13.596 1.00 48.56 C
+ATOM 1677 O2 C A 78 44.666 27.900 13.787 1.00 47.16 O
+ATOM 1678 N3 C A 78 46.789 27.419 14.418 1.00 48.57 N
+ATOM 1679 C4 C A 78 48.092 27.546 14.162 1.00 50.34 C
+ATOM 1680 N4 C A 78 48.958 26.946 14.992 1.00 49.92 N
+ATOM 1681 C5 C A 78 48.571 28.290 13.040 1.00 51.43 C
+ATOM 1682 C6 C A 78 47.654 28.859 12.238 1.00 49.99 C
+ATOM 1683 P G A 79 45.068 33.757 13.257 1.00 52.92 P
+ATOM 1684 OP1 G A 79 44.602 35.126 12.971 1.00 55.12 O
+ATOM 1685 OP2 G A 79 46.464 33.538 13.738 1.00 54.61 O
+ATOM 1686 O5' G A 79 44.053 33.066 14.268 1.00 52.03 O
+ATOM 1687 C5' G A 79 42.681 32.970 13.939 1.00 52.92 C
+ATOM 1688 C4' G A 79 41.965 32.101 14.936 1.00 53.20 C
+ATOM 1689 O4' G A 79 42.600 30.794 14.948 1.00 54.24 O
+ATOM 1690 C3' G A 79 42.120 32.560 16.371 1.00 54.77 C
+ATOM 1691 O3' G A 79 41.208 33.586 16.721 1.00 56.81 O
+ATOM 1692 C2' G A 79 41.863 31.284 17.147 1.00 54.49 C
+ATOM 1693 O2' G A 79 40.484 31.015 17.176 1.00 56.96 O
+ATOM 1694 C1' G A 79 42.546 30.252 16.255 1.00 53.50 C
+ATOM 1695 N9 G A 79 43.889 29.889 16.704 1.00 51.11 N
+ATOM 1696 C8 G A 79 45.106 30.274 16.195 1.00 50.11 C
+ATOM 1697 N7 G A 79 46.120 29.761 16.851 1.00 48.60 N
+ATOM 1698 C5 G A 79 45.529 28.995 17.849 1.00 47.30 C
+ATOM 1699 C6 G A 79 46.111 28.202 18.879 1.00 46.07 C
+ATOM 1700 O6 G A 79 47.321 28.008 19.130 1.00 45.96 O
+ATOM 1701 N1 G A 79 45.139 27.600 19.665 1.00 43.73 N
+ATOM 1702 C2 G A 79 43.785 27.738 19.492 1.00 48.40 C
+ATOM 1703 N2 G A 79 42.983 27.078 20.352 1.00 51.24 N
+ATOM 1704 N3 G A 79 43.236 28.469 18.544 1.00 49.81 N
+ATOM 1705 C4 G A 79 44.158 29.064 17.767 1.00 49.45 C
+ATOM 1706 P U A 80 41.696 34.744 17.718 1.00 57.91 P
+ATOM 1707 OP1 U A 80 40.668 35.811 17.699 1.00 58.33 O
+ATOM 1708 OP2 U A 80 43.105 35.066 17.387 1.00 55.86 O
+ATOM 1709 O5' U A 80 41.666 34.031 19.139 1.00 59.76 O
+ATOM 1710 C5' U A 80 40.441 33.510 19.646 1.00 60.84 C
+ATOM 1711 C4' U A 80 40.693 32.611 20.834 1.00 61.61 C
+ATOM 1712 O4' U A 80 41.480 31.465 20.405 1.00 61.05 O
+ATOM 1713 C3' U A 80 41.535 33.217 21.943 1.00 62.84 C
+ATOM 1714 O3' U A 80 40.767 34.025 22.818 1.00 67.34 O
+ATOM 1715 C2' U A 80 42.082 31.983 22.640 1.00 61.11 C
+ATOM 1716 O2' U A 80 41.107 31.381 23.464 1.00 61.83 O
+ATOM 1717 C1' U A 80 42.354 31.067 21.450 1.00 58.89 C
+ATOM 1718 N1 U A 80 43.737 31.189 20.978 1.00 55.50 N
+ATOM 1719 C2 U A 80 44.688 30.431 21.622 1.00 53.56 C
+ATOM 1720 O2 U A 80 44.415 29.688 22.539 1.00 54.05 O
+ATOM 1721 N3 U A 80 45.971 30.581 21.159 1.00 50.66 N
+ATOM 1722 C4 U A 80 46.386 31.399 20.140 1.00 50.72 C
+ATOM 1723 O4 U A 80 47.579 31.424 19.832 1.00 49.30 O
+ATOM 1724 C5 U A 80 45.339 32.157 19.520 1.00 52.21 C
+ATOM 1725 C6 U A 80 44.078 32.027 19.950 1.00 54.00 C
+ATOM 1726 P U A 81 41.512 35.096 23.759 1.00 69.99 P
+ATOM 1727 OP1 U A 81 40.440 35.890 24.422 1.00 70.01 O
+ATOM 1728 OP2 U A 81 42.570 35.792 22.973 1.00 68.74 O
+ATOM 1729 O5' U A 81 42.243 34.197 24.853 1.00 69.66 O
+ATOM 1730 C5' U A 81 41.492 33.546 25.869 1.00 69.69 C
+ATOM 1731 C4' U A 81 42.411 32.874 26.858 1.00 70.12 C
+ATOM 1732 O4' U A 81 43.154 31.827 26.185 1.00 70.30 O
+ATOM 1733 C3' U A 81 43.492 33.765 27.442 1.00 71.48 C
+ATOM 1734 O3' U A 81 43.008 34.521 28.543 1.00 73.23 O
+ATOM 1735 C2' U A 81 44.548 32.755 27.868 1.00 71.16 C
+ATOM 1736 O2' U A 81 44.243 32.119 29.088 1.00 72.71 O
+ATOM 1737 C1' U A 81 44.455 31.733 26.740 1.00 69.65 C
+ATOM 1738 N1 U A 81 45.445 32.005 25.694 1.00 67.60 N
+ATOM 1739 C2 U A 81 46.694 31.456 25.857 1.00 67.36 C
+ATOM 1740 O2 U A 81 46.984 30.751 26.806 1.00 69.28 O
+ATOM 1741 N3 U A 81 47.595 31.762 24.873 1.00 65.88 N
+ATOM 1742 C4 U A 81 47.377 32.543 23.770 1.00 64.36 C
+ATOM 1743 O4 U A 81 48.298 32.741 22.977 1.00 63.94 O
+ATOM 1744 C5 U A 81 46.053 33.070 23.668 1.00 66.08 C
+ATOM 1745 C6 U A 81 45.152 32.786 24.610 1.00 67.30 C
+ATOM 1746 P G A 82 43.833 35.803 29.047 1.00 74.81 P
+ATOM 1747 OP1 G A 82 43.043 36.432 30.132 1.00 76.99 O
+ATOM 1748 OP2 G A 82 44.213 36.612 27.861 1.00 76.87 O
+ATOM 1749 O5' G A 82 45.157 35.176 29.671 1.00 72.53 O
+ATOM 1750 C5' G A 82 45.067 34.297 30.782 1.00 72.61 C
+ATOM 1751 C4' G A 82 46.398 33.635 31.056 1.00 73.05 C
+ATOM 1752 O4' G A 82 46.808 32.836 29.908 1.00 72.32 O
+ATOM 1753 C3' G A 82 47.550 34.606 31.244 1.00 73.03 C
+ATOM 1754 O3' G A 82 47.600 35.046 32.591 1.00 73.81 O
+ATOM 1755 C2' G A 82 48.762 33.750 30.917 1.00 71.15 C
+ATOM 1756 O2' G A 82 49.183 32.982 32.016 1.00 71.55 O
+ATOM 1757 C1' G A 82 48.219 32.851 29.809 1.00 70.45 C
+ATOM 1758 N9 G A 82 48.606 33.304 28.483 1.00 69.22 N
+ATOM 1759 C8 G A 82 47.862 34.024 27.586 1.00 68.93 C
+ATOM 1760 N7 G A 82 48.523 34.307 26.494 1.00 68.74 N
+ATOM 1761 C5 G A 82 49.772 33.732 26.686 1.00 66.17 C
+ATOM 1762 C6 G A 82 50.914 33.717 25.853 1.00 65.71 C
+ATOM 1763 O6 G A 82 51.064 34.234 24.737 1.00 67.39 O
+ATOM 1764 N1 G A 82 51.960 33.015 26.437 1.00 65.06 N
+ATOM 1765 C2 G A 82 51.910 32.409 27.667 1.00 65.49 C
+ATOM 1766 N2 G A 82 53.019 31.776 28.066 1.00 66.07 N
+ATOM 1767 N3 G A 82 50.854 32.422 28.450 1.00 65.40 N
+ATOM 1768 C4 G A 82 49.832 33.098 27.902 1.00 67.06 C
+ATOM 1769 P A A 83 48.714 36.110 33.037 1.00 75.74 P
+ATOM 1770 OP1 A A 83 48.454 36.457 34.461 1.00 76.19 O
+ATOM 1771 OP2 A A 83 48.787 37.192 32.017 1.00 75.92 O
+ATOM 1772 O5' A A 83 50.084 35.306 32.950 1.00 73.07 O
+ATOM 1773 C5' A A 83 51.311 35.996 32.798 1.00 71.48 C
+ATOM 1774 C4' A A 83 52.389 35.042 32.352 1.00 72.32 C
+ATOM 1775 O4' A A 83 52.006 34.431 31.092 1.00 71.90 O
+ATOM 1776 C3' A A 83 53.717 35.706 32.044 1.00 72.39 C
+ATOM 1777 O3' A A 83 54.479 35.854 33.223 1.00 73.75 O
+ATOM 1778 C2' A A 83 54.367 34.722 31.088 1.00 71.88 C
+ATOM 1779 O2' A A 83 55.011 33.652 31.742 1.00 73.47 O
+ATOM 1780 C1' A A 83 53.158 34.234 30.289 1.00 70.66 C
+ATOM 1781 N9 A A 83 52.993 34.981 29.046 1.00 68.56 N
+ATOM 1782 C8 A A 83 51.908 35.688 28.594 1.00 67.12 C
+ATOM 1783 N7 A A 83 52.100 36.253 27.425 1.00 66.12 N
+ATOM 1784 C5 A A 83 53.397 35.888 27.088 1.00 66.03 C
+ATOM 1785 C6 A A 83 54.198 36.164 25.971 1.00 66.42 C
+ATOM 1786 N6 A A 83 53.795 36.897 24.937 1.00 66.62 N
+ATOM 1787 N1 A A 83 55.448 35.651 25.951 1.00 66.47 N
+ATOM 1788 C2 A A 83 55.854 34.913 26.993 1.00 65.81 C
+ATOM 1789 N3 A A 83 55.194 34.582 28.094 1.00 66.02 N
+ATOM 1790 C4 A A 83 53.956 35.106 28.078 1.00 66.63 C
+ATOM 1791 P A A 84 55.352 37.173 33.429 1.00 74.69 P
+ATOM 1792 OP1 A A 84 56.069 37.043 34.725 1.00 74.75 O
+ATOM 1793 OP2 A A 84 54.440 38.322 33.207 1.00 72.53 O
+ATOM 1794 O5' A A 84 56.405 37.108 32.237 1.00 72.08 O
+ATOM 1795 C5' A A 84 57.422 36.109 32.201 1.00 70.69 C
+ATOM 1796 C4' A A 84 58.311 36.343 31.007 1.00 69.31 C
+ATOM 1797 O4' A A 84 57.606 35.966 29.799 1.00 68.54 O
+ATOM 1798 C3' A A 84 58.703 37.790 30.786 1.00 69.05 C
+ATOM 1799 O3' A A 84 59.818 38.159 31.581 1.00 71.70 O
+ATOM 1800 C2' A A 84 58.992 37.827 29.289 1.00 67.78 C
+ATOM 1801 O2' A A 84 60.283 37.385 28.923 1.00 68.74 O
+ATOM 1802 C1' A A 84 57.912 36.881 28.759 1.00 66.10 C
+ATOM 1803 N9 A A 84 56.685 37.615 28.467 1.00 62.63 N
+ATOM 1804 C8 A A 84 55.570 37.709 29.260 1.00 60.97 C
+ATOM 1805 N7 A A 84 54.624 38.454 28.752 1.00 60.47 N
+ATOM 1806 C5 A A 84 55.149 38.877 27.539 1.00 58.77 C
+ATOM 1807 C6 A A 84 54.633 39.693 26.524 1.00 57.48 C
+ATOM 1808 N6 A A 84 53.422 40.254 26.573 1.00 58.08 N
+ATOM 1809 N1 A A 84 55.411 39.919 25.444 1.00 57.00 N
+ATOM 1810 C2 A A 84 56.628 39.354 25.400 1.00 57.46 C
+ATOM 1811 N3 A A 84 57.223 38.568 26.295 1.00 58.36 N
+ATOM 1812 C4 A A 84 56.419 38.367 27.352 1.00 59.63 C
+ATOM 1813 P A A 85 60.045 39.705 31.960 1.00 72.98 P
+ATOM 1814 OP1 A A 85 61.385 39.797 32.591 1.00 74.48 O
+ATOM 1815 OP2 A A 85 58.855 40.226 32.685 1.00 72.40 O
+ATOM 1816 O5' A A 85 60.110 40.435 30.548 1.00 70.44 O
+ATOM 1817 C5' A A 85 61.253 40.307 29.714 1.00 66.23 C
+ATOM 1818 C4' A A 85 61.044 41.084 28.441 1.00 64.90 C
+ATOM 1819 O4' A A 85 59.882 40.545 27.748 1.00 62.64 O
+ATOM 1820 C3' A A 85 60.699 42.549 28.626 1.00 62.94 C
+ATOM 1821 O3' A A 85 61.844 43.363 28.835 1.00 63.23 O
+ATOM 1822 C2' A A 85 59.984 42.868 27.322 1.00 61.52 C
+ATOM 1823 O2' A A 85 60.881 43.020 26.246 1.00 61.55 O
+ATOM 1824 C1' A A 85 59.174 41.592 27.113 1.00 58.58 C
+ATOM 1825 N9 A A 85 57.869 41.712 27.755 1.00 55.06 N
+ATOM 1826 C8 A A 85 57.468 41.210 28.962 1.00 53.46 C
+ATOM 1827 N7 A A 85 56.235 41.526 29.280 1.00 53.24 N
+ATOM 1828 C5 A A 85 55.794 42.281 28.202 1.00 51.20 C
+ATOM 1829 C6 A A 85 54.571 42.927 27.926 1.00 51.15 C
+ATOM 1830 N6 A A 85 53.514 42.908 28.743 1.00 50.33 N
+ATOM 1831 N1 A A 85 54.469 43.605 26.763 1.00 51.08 N
+ATOM 1832 C2 A A 85 55.521 43.623 25.939 1.00 49.66 C
+ATOM 1833 N3 A A 85 56.712 43.057 26.085 1.00 51.02 N
+ATOM 1834 C4 A A 85 56.787 42.396 27.253 1.00 52.63 C
+ATOM 1835 P G A 86 61.717 44.687 29.747 1.00 63.01 P
+ATOM 1836 OP1 G A 86 63.080 45.233 29.962 1.00 63.49 O
+ATOM 1837 OP2 G A 86 60.860 44.331 30.912 1.00 62.23 O
+ATOM 1838 O5' G A 86 60.926 45.717 28.830 1.00 60.62 O
+ATOM 1839 C5' G A 86 61.397 46.003 27.524 1.00 57.16 C
+ATOM 1840 C4' G A 86 60.338 46.713 26.717 1.00 54.53 C
+ATOM 1841 O4' G A 86 59.166 45.857 26.587 1.00 53.07 O
+ATOM 1842 C3' G A 86 59.774 47.960 27.371 1.00 53.14 C
+ATOM 1843 O3' G A 86 60.618 49.084 27.216 1.00 51.63 O
+ATOM 1844 C2' G A 86 58.432 48.112 26.672 1.00 52.73 C
+ATOM 1845 O2' G A 86 58.570 48.629 25.368 1.00 50.58 O
+ATOM 1846 C1' G A 86 57.994 46.657 26.559 1.00 51.72 C
+ATOM 1847 N9 G A 86 57.100 46.230 27.628 1.00 50.07 N
+ATOM 1848 C8 G A 86 57.353 45.289 28.594 1.00 50.13 C
+ATOM 1849 N7 G A 86 56.333 45.083 29.386 1.00 49.23 N
+ATOM 1850 C5 G A 86 55.355 45.948 28.923 1.00 48.44 C
+ATOM 1851 C6 G A 86 54.036 46.158 29.377 1.00 50.00 C
+ATOM 1852 O6 G A 86 53.447 45.603 30.304 1.00 52.45 O
+ATOM 1853 N1 G A 86 53.379 47.127 28.628 1.00 49.28 N
+ATOM 1854 C2 G A 86 53.924 47.806 27.575 1.00 48.05 C
+ATOM 1855 N2 G A 86 53.121 48.698 27.001 1.00 46.91 N
+ATOM 1856 N3 G A 86 55.161 47.618 27.128 1.00 47.93 N
+ATOM 1857 C4 G A 86 55.814 46.677 27.847 1.00 48.84 C
+ATOM 1858 P A A 87 60.528 50.278 28.276 1.00 48.22 P
+ATOM 1859 OP1 A A 87 61.493 51.324 27.903 1.00 50.47 O
+ATOM 1860 OP2 A A 87 60.599 49.663 29.612 1.00 48.71 O
+ATOM 1861 O5' A A 87 59.072 50.870 28.036 1.00 47.96 O
+ATOM 1862 C5' A A 87 58.810 51.665 26.888 1.00 45.52 C
+ATOM 1863 C4' A A 87 57.420 52.245 26.944 1.00 45.17 C
+ATOM 1864 O4' A A 87 56.474 51.163 27.023 1.00 44.86 O
+ATOM 1865 C3' A A 87 57.104 53.065 28.183 1.00 47.55 C
+ATOM 1866 O3' A A 87 57.553 54.398 28.043 1.00 48.74 O
+ATOM 1867 C2' A A 87 55.590 52.985 28.257 1.00 45.69 C
+ATOM 1868 O2' A A 87 54.966 53.829 27.315 1.00 46.31 O
+ATOM 1869 C1' A A 87 55.363 51.547 27.819 1.00 43.13 C
+ATOM 1870 N9 A A 87 55.242 50.601 28.918 1.00 40.51 N
+ATOM 1871 C8 A A 87 56.174 49.711 29.374 1.00 40.58 C
+ATOM 1872 N7 A A 87 55.738 48.948 30.344 1.00 41.86 N
+ATOM 1873 C5 A A 87 54.439 49.376 30.546 1.00 38.70 C
+ATOM 1874 C6 A A 87 53.436 48.953 31.422 1.00 38.67 C
+ATOM 1875 N6 A A 87 53.591 47.957 32.293 1.00 38.56 N
+ATOM 1876 N1 A A 87 52.246 49.589 31.368 1.00 40.88 N
+ATOM 1877 C2 A A 87 52.088 50.575 30.477 1.00 41.68 C
+ATOM 1878 N3 A A 87 52.958 51.054 29.589 1.00 40.58 N
+ATOM 1879 C4 A A 87 54.126 50.402 29.681 1.00 39.79 C
+ATOM 1880 P U A 88 58.198 55.136 29.302 1.00 48.29 P
+ATOM 1881 OP1 U A 88 58.993 56.266 28.738 1.00 47.03 O
+ATOM 1882 OP2 U A 88 58.870 54.083 30.122 1.00 47.21 O
+ATOM 1883 O5' U A 88 56.917 55.689 30.075 1.00 47.92 O
+ATOM 1884 C5' U A 88 56.127 56.707 29.482 1.00 47.38 C
+ATOM 1885 C4' U A 88 54.808 56.850 30.197 1.00 47.01 C
+ATOM 1886 O4' U A 88 54.078 55.598 30.095 1.00 47.37 O
+ATOM 1887 C3' U A 88 54.903 57.067 31.692 1.00 47.34 C
+ATOM 1888 O3' U A 88 55.161 58.407 32.052 1.00 47.14 O
+ATOM 1889 C2' U A 88 53.536 56.615 32.152 1.00 46.01 C
+ATOM 1890 O2' U A 88 52.617 57.604 31.753 1.00 46.16 O
+ATOM 1891 C1' U A 88 53.334 55.384 31.278 1.00 44.84 C
+ATOM 1892 N1 U A 88 53.835 54.171 31.938 1.00 43.85 N
+ATOM 1893 C2 U A 88 53.089 53.677 32.974 1.00 44.35 C
+ATOM 1894 O2 U A 88 52.073 54.213 33.349 1.00 47.48 O
+ATOM 1895 N3 U A 88 53.572 52.538 33.563 1.00 42.79 N
+ATOM 1896 C4 U A 88 54.705 51.864 33.226 1.00 43.22 C
+ATOM 1897 O4 U A 88 55.018 50.851 33.858 1.00 44.99 O
+ATOM 1898 C5 U A 88 55.436 52.443 32.140 1.00 43.46 C
+ATOM 1899 C6 U A 88 54.985 53.554 31.549 1.00 43.73 C
+ATOM 1900 P G A 89 56.009 58.702 33.383 1.00 46.16 P
+ATOM 1901 OP1 G A 89 56.494 60.099 33.290 1.00 45.41 O
+ATOM 1902 OP2 G A 89 56.980 57.592 33.512 1.00 42.04 O
+ATOM 1903 O5' G A 89 54.938 58.588 34.557 1.00 45.55 O
+ATOM 1904 C5' G A 89 53.772 59.397 34.546 1.00 45.93 C
+ATOM 1905 C4' G A 89 52.792 58.945 35.610 1.00 47.23 C
+ATOM 1906 O4' G A 89 52.385 57.568 35.369 1.00 48.15 O
+ATOM 1907 C3' G A 89 53.329 58.926 37.034 1.00 47.10 C
+ATOM 1908 O3' G A 89 53.245 60.232 37.593 1.00 48.88 O
+ATOM 1909 C2' G A 89 52.396 57.933 37.723 1.00 46.50 C
+ATOM 1910 O2' G A 89 51.145 58.503 38.102 1.00 44.07 O
+ATOM 1911 C1' G A 89 52.178 56.906 36.608 1.00 45.89 C
+ATOM 1912 N9 G A 89 53.064 55.750 36.658 1.00 43.74 N
+ATOM 1913 C8 G A 89 54.217 55.571 35.944 1.00 43.64 C
+ATOM 1914 N7 G A 89 54.781 54.412 36.166 1.00 43.02 N
+ATOM 1915 C5 G A 89 53.952 53.797 37.091 1.00 41.41 C
+ATOM 1916 C6 G A 89 54.056 52.525 37.720 1.00 41.45 C
+ATOM 1917 O6 G A 89 54.923 51.659 37.572 1.00 42.99 O
+ATOM 1918 N1 G A 89 53.011 52.301 38.601 1.00 40.30 N
+ATOM 1919 C2 G A 89 51.997 53.182 38.846 1.00 43.16 C
+ATOM 1920 N2 G A 89 51.077 52.782 39.723 1.00 44.32 N
+ATOM 1921 N3 G A 89 51.887 54.375 38.271 1.00 43.05 N
+ATOM 1922 C4 G A 89 52.893 54.612 37.411 1.00 41.85 C
+ATOM 1923 P A A 90 54.261 60.673 38.754 1.00 49.33 P
+ATOM 1924 OP1 A A 90 53.796 62.025 39.132 1.00 50.89 O
+ATOM 1925 OP2 A A 90 55.663 60.483 38.318 1.00 50.02 O
+ATOM 1926 O5' A A 90 53.920 59.654 39.935 1.00 48.11 O
+ATOM 1927 C5' A A 90 52.697 59.783 40.661 1.00 46.82 C
+ATOM 1928 C4' A A 90 52.547 58.662 41.657 1.00 46.54 C
+ATOM 1929 O4' A A 90 52.472 57.405 40.938 1.00 46.05 O
+ATOM 1930 C3' A A 90 53.729 58.460 42.584 1.00 48.87 C
+ATOM 1931 O3' A A 90 53.706 59.332 43.695 1.00 53.87 O
+ATOM 1932 C2' A A 90 53.565 57.013 43.002 1.00 47.31 C
+ATOM 1933 O2' A A 90 52.561 56.871 43.985 1.00 50.65 O
+ATOM 1934 C1' A A 90 53.097 56.384 41.694 1.00 43.08 C
+ATOM 1935 N9 A A 90 54.200 55.832 40.911 1.00 39.20 N
+ATOM 1936 C8 A A 90 54.964 56.432 39.942 1.00 37.90 C
+ATOM 1937 N7 A A 90 55.882 55.642 39.432 1.00 35.96 N
+ATOM 1938 C5 A A 90 55.706 54.448 40.111 1.00 34.77 C
+ATOM 1939 C6 A A 90 56.367 53.206 40.038 1.00 37.49 C
+ATOM 1940 N6 A A 90 57.370 52.939 39.203 1.00 40.40 N
+ATOM 1941 N1 A A 90 55.950 52.227 40.865 1.00 37.63 N
+ATOM 1942 C2 A A 90 54.933 52.484 41.695 1.00 37.37 C
+ATOM 1943 N3 A A 90 54.233 53.606 41.850 1.00 35.09 N
+ATOM 1944 C4 A A 90 54.677 54.554 41.023 1.00 35.63 C
+ATOM 1945 P G A 91 55.092 59.795 44.359 1.00 56.70 P
+ATOM 1946 OP1 G A 91 54.771 60.922 45.270 1.00 57.70 O
+ATOM 1947 OP2 G A 91 56.117 59.995 43.298 1.00 55.05 O
+ATOM 1948 O5' G A 91 55.497 58.514 45.213 1.00 54.40 O
+ATOM 1949 C5' G A 91 54.652 58.066 46.257 1.00 55.05 C
+ATOM 1950 C4' G A 91 55.146 56.755 46.819 1.00 57.40 C
+ATOM 1951 O4' G A 91 54.959 55.689 45.845 1.00 57.63 O
+ATOM 1952 C3' G A 91 56.630 56.703 47.121 1.00 58.60 C
+ATOM 1953 O3' G A 91 56.928 57.302 48.366 1.00 62.00 O
+ATOM 1954 C2' G A 91 56.905 55.208 47.110 1.00 57.65 C
+ATOM 1955 O2' G A 91 56.449 54.586 48.296 1.00 61.81 O
+ATOM 1956 C1' G A 91 56.021 54.752 45.950 1.00 56.16 C
+ATOM 1957 N9 G A 91 56.782 54.738 44.704 1.00 51.72 N
+ATOM 1958 C8 G A 91 56.926 55.756 43.791 1.00 49.57 C
+ATOM 1959 N7 G A 91 57.738 55.451 42.813 1.00 47.94 N
+ATOM 1960 C5 G A 91 58.138 54.151 43.090 1.00 47.47 C
+ATOM 1961 C6 G A 91 59.021 53.291 42.388 1.00 48.13 C
+ATOM 1962 O6 G A 91 59.639 53.516 41.342 1.00 49.59 O
+ATOM 1963 N1 G A 91 59.152 52.056 43.022 1.00 46.53 N
+ATOM 1964 C2 G A 91 58.509 51.695 44.184 1.00 45.93 C
+ATOM 1965 N2 G A 91 58.759 50.457 44.657 1.00 43.94 N
+ATOM 1966 N3 G A 91 57.678 52.491 44.842 1.00 46.16 N
+ATOM 1967 C4 G A 91 57.544 53.693 44.244 1.00 48.37 C
+ATOM 1968 P C A 92 58.460 57.535 48.781 1.00 65.24 P
+ATOM 1969 OP1 C A 92 58.483 58.295 50.060 1.00 65.63 O
+ATOM 1970 OP2 C A 92 59.219 58.050 47.604 1.00 65.80 O
+ATOM 1971 O5' C A 92 58.959 56.063 49.081 1.00 61.36 O
+ATOM 1972 C5' C A 92 60.332 55.789 49.189 1.00 58.00 C
+ATOM 1973 C4' C A 92 60.583 54.344 48.883 1.00 54.97 C
+ATOM 1974 O4' C A 92 59.894 53.989 47.667 1.00 54.29 O
+ATOM 1975 C3' C A 92 62.029 54.026 48.617 1.00 55.01 C
+ATOM 1976 O3' C A 92 62.681 53.819 49.854 1.00 55.30 O
+ATOM 1977 C2' C A 92 61.934 52.781 47.754 1.00 53.19 C
+ATOM 1978 O2' C A 92 61.752 51.585 48.477 1.00 54.48 O
+ATOM 1979 C1' C A 92 60.689 53.090 46.926 1.00 52.53 C
+ATOM 1980 N1 C A 92 61.028 53.742 45.664 1.00 49.85 N
+ATOM 1981 C2 C A 92 61.710 53.010 44.726 1.00 49.42 C
+ATOM 1982 O2 C A 92 61.987 51.826 44.989 1.00 51.77 O
+ATOM 1983 N3 C A 92 62.054 53.592 43.561 1.00 49.14 N
+ATOM 1984 C4 C A 92 61.722 54.858 43.328 1.00 49.22 C
+ATOM 1985 N4 C A 92 62.086 55.389 42.166 1.00 49.50 N
+ATOM 1986 C5 C A 92 61.004 55.632 44.276 1.00 49.21 C
+ATOM 1987 C6 C A 92 60.683 55.041 45.421 1.00 49.19 C
+ATOM 1988 P C A 93 64.095 54.516 50.109 1.00 55.71 P
+ATOM 1989 OP1 C A 93 64.369 54.474 51.568 1.00 57.76 O
+ATOM 1990 OP2 C A 93 64.088 55.822 49.397 1.00 55.38 O
+ATOM 1991 O5' C A 93 65.104 53.533 49.376 1.00 55.30 O
+ATOM 1992 C5' C A 93 65.215 52.186 49.814 1.00 55.96 C
+ATOM 1993 C4' C A 93 66.119 51.421 48.893 1.00 57.33 C
+ATOM 1994 O4' C A 93 65.506 51.340 47.586 1.00 56.23 O
+ATOM 1995 C3' C A 93 67.453 52.093 48.646 1.00 58.35 C
+ATOM 1996 O3' C A 93 68.358 51.720 49.676 1.00 60.91 O
+ATOM 1997 C2' C A 93 67.859 51.519 47.295 1.00 56.28 C
+ATOM 1998 O2' C A 93 68.444 50.245 47.419 1.00 56.69 O
+ATOM 1999 C1' C A 93 66.505 51.408 46.587 1.00 53.87 C
+ATOM 2000 N1 C A 93 66.164 52.519 45.689 1.00 50.29 N
+ATOM 2001 C2 C A 93 66.553 52.449 44.357 1.00 48.90 C
+ATOM 2002 O2 C A 93 67.196 51.459 43.974 1.00 49.47 O
+ATOM 2003 N3 C A 93 66.219 53.459 43.516 1.00 47.11 N
+ATOM 2004 C4 C A 93 65.528 54.508 43.973 1.00 45.79 C
+ATOM 2005 N4 C A 93 65.205 55.474 43.112 1.00 47.26 N
+ATOM 2006 C5 C A 93 65.134 54.610 45.330 1.00 45.95 C
+ATOM 2007 C6 C A 93 65.467 53.599 46.149 1.00 48.81 C
+ATOM 2008 P A A 94 69.700 52.565 49.893 1.00 63.26 P
+ATOM 2009 OP1 A A 94 70.472 51.929 51.000 1.00 63.03 O
+ATOM 2010 OP2 A A 94 69.311 54.001 49.989 1.00 63.37 O
+ATOM 2011 O5' A A 94 70.490 52.381 48.519 1.00 61.77 O
+ATOM 2012 C5' A A 94 71.326 51.253 48.283 1.00 61.29 C
+ATOM 2013 C4' A A 94 72.146 51.475 47.027 1.00 62.44 C
+ATOM 2014 O4' A A 94 71.241 51.538 45.895 1.00 61.92 O
+ATOM 2015 C3' A A 94 72.937 52.778 46.954 1.00 63.29 C
+ATOM 2016 O3' A A 94 74.230 52.643 47.539 1.00 63.03 O
+ATOM 2017 C2' A A 94 73.070 52.992 45.454 1.00 63.82 C
+ATOM 2018 O2' A A 94 74.136 52.237 44.902 1.00 65.97 O
+ATOM 2019 C1' A A 94 71.721 52.471 44.948 1.00 62.06 C
+ATOM 2020 N9 A A 94 70.717 53.521 44.818 1.00 60.30 N
+ATOM 2021 C8 A A 94 69.962 54.073 45.821 1.00 60.55 C
+ATOM 2022 N7 A A 94 69.162 55.030 45.415 1.00 59.61 N
+ATOM 2023 C5 A A 94 69.401 55.106 44.053 1.00 59.00 C
+ATOM 2024 C6 A A 94 68.872 55.924 43.063 1.00 58.81 C
+ATOM 2025 N6 A A 94 67.974 56.874 43.310 1.00 59.79 N
+ATOM 2026 N1 A A 94 69.307 55.745 41.796 1.00 58.99 N
+ATOM 2027 C2 A A 94 70.230 54.798 41.564 1.00 59.88 C
+ATOM 2028 N3 A A 94 70.812 53.965 42.421 1.00 59.48 N
+ATOM 2029 C4 A A 94 70.348 54.174 43.666 1.00 59.71 C
+TER 2030 A A 94
+HETATM 2031 MG MG A 205 44.673 52.089 21.066 1.00 52.79 MG
+HETATM 2032 MG MG A 206 57.959 37.961 33.008 1.00 75.51 MG
+HETATM 2033 IR IRI A 201 53.885 56.740 -0.635 1.00 98.98 IR
+HETATM 2034 N1 IRI A 201 52.485 58.054 -1.822 1.00 97.67 N
+HETATM 2035 N2 IRI A 201 54.266 58.382 0.816 1.00 98.55 N
+HETATM 2036 N3 IRI A 201 55.233 55.348 0.506 1.00 98.59 N
+HETATM 2037 N4 IRI A 201 53.497 55.076 -2.135 1.00 99.01 N
+HETATM 2038 N5 IRI A 201 52.127 56.049 0.598 1.00 98.22 N
+HETATM 2039 N6 IRI A 201 55.669 57.413 -1.820 1.00 99.00 N
+HETATM 2040 IR IRI A 202 53.580 69.128 10.808 1.00 85.21 IR
+HETATM 2041 N1 IRI A 202 51.863 70.294 9.931 1.00 85.46 N
+HETATM 2042 N2 IRI A 202 53.979 70.743 12.294 1.00 85.76 N
+HETATM 2043 N3 IRI A 202 55.263 67.867 11.657 1.00 84.55 N
+HETATM 2044 N4 IRI A 202 53.191 67.483 9.307 1.00 85.84 N
+HETATM 2045 N5 IRI A 202 52.135 68.142 12.244 1.00 85.61 N
+HETATM 2046 N6 IRI A 202 55.040 70.069 9.391 1.00 85.28 N
+HETATM 2047 IR IRI A 203 61.715 45.974 13.576 1.00 89.54 IR
+HETATM 2048 N1 IRI A 203 60.528 47.751 14.317 1.00 90.96 N
+HETATM 2049 N2 IRI A 203 60.570 44.590 14.901 1.00 90.31 N
+HETATM 2050 N3 IRI A 203 62.943 44.257 12.747 1.00 91.15 N
+HETATM 2051 N4 IRI A 203 62.898 47.359 12.224 1.00 90.58 N
+HETATM 2052 N5 IRI A 203 60.217 45.694 11.915 1.00 90.65 N
+HETATM 2053 N6 IRI A 203 63.229 46.280 15.197 1.00 90.26 N
+HETATM 2054 IR IRI A 204 58.679 49.493 35.312 1.00 49.00 IR
+HETATM 2055 N1 IRI A 204 57.796 50.488 33.496 1.00 51.75 N
+HETATM 2056 N2 IRI A 204 56.792 49.834 36.443 1.00 50.76 N
+HETATM 2057 N3 IRI A 204 59.668 48.489 37.085 1.00 53.82 N
+HETATM 2058 N4 IRI A 204 60.576 49.136 34.184 1.00 51.33 N
+HETATM 2059 N5 IRI A 204 57.947 47.503 34.598 1.00 53.62 N
+HETATM 2060 N6 IRI A 204 59.488 51.435 36.079 1.00 53.26 N
+HETATM 2061 N SAM A 301 48.661 58.442 29.234 1.00 71.76 N
+HETATM 2062 CA SAM A 301 48.892 57.767 27.953 1.00 71.83 C
+HETATM 2063 C SAM A 301 47.728 58.043 27.018 1.00 73.09 C
+HETATM 2064 O SAM A 301 47.747 57.608 25.870 1.00 74.98 O
+HETATM 2065 OXT SAM A 301 46.793 58.755 27.385 1.00 73.14 O
+HETATM 2066 CB SAM A 301 49.051 56.247 28.156 1.00 70.42 C
+HETATM 2067 CG SAM A 301 49.924 55.993 29.384 1.00 68.18 C
+HETATM 2068 SD SAM A 301 50.180 54.222 29.811 1.00 68.57 S
+HETATM 2069 CE SAM A 301 49.547 53.321 28.362 1.00 68.16 C
+HETATM 2070 C5' SAM A 301 48.781 54.097 30.945 1.00 63.51 C
+HETATM 2071 C4' SAM A 301 49.142 54.393 32.411 1.00 61.14 C
+HETATM 2072 O4' SAM A 301 49.826 55.679 32.483 1.00 59.00 O
+HETATM 2073 C3' SAM A 301 47.793 54.604 33.049 1.00 59.63 C
+HETATM 2074 O3' SAM A 301 47.357 53.395 33.671 1.00 61.69 O
+HETATM 2075 C2' SAM A 301 48.045 55.680 34.098 1.00 58.07 C
+HETATM 2076 O2' SAM A 301 48.258 55.128 35.392 1.00 60.89 O
+HETATM 2077 C1' SAM A 301 49.315 56.473 33.618 1.00 56.29 C
+HETATM 2078 N9 SAM A 301 49.019 57.807 33.055 1.00 52.35 N
+HETATM 2079 C8 SAM A 301 49.941 58.804 32.897 1.00 49.96 C
+HETATM 2080 N7 SAM A 301 49.391 59.863 32.379 1.00 49.17 N
+HETATM 2081 C5 SAM A 301 48.084 59.618 32.158 1.00 49.87 C
+HETATM 2082 C6 SAM A 301 47.000 60.356 31.619 1.00 49.12 C
+HETATM 2083 N6 SAM A 301 47.179 61.649 31.181 1.00 49.12 N
+HETATM 2084 N1 SAM A 301 45.794 59.770 31.541 1.00 48.62 N
+HETATM 2085 C2 SAM A 301 45.596 58.512 31.950 1.00 48.26 C
+HETATM 2086 N3 SAM A 301 46.578 57.797 32.476 1.00 48.84 N
+HETATM 2087 C4 SAM A 301 47.821 58.293 32.591 1.00 50.12 C
+HETATM 2088 O HOH A 401 57.434 67.701 5.730 1.00 62.83 O
+HETATM 2089 O HOH A 402 66.189 60.895 3.390 1.00102.86 O
+HETATM 2090 O HOH A 403 41.692 28.822 12.775 1.00 79.78 O
+HETATM 2091 O HOH A 404 58.520 32.372 29.001 1.00 87.70 O
+HETATM 2092 O HOH A 405 41.683 78.187 34.648 1.00 90.77 O
+HETATM 2093 O HOH A 406 39.116 52.800 26.854 1.00 47.35 O
+HETATM 2094 O HOH A 407 60.473 27.307 22.789 1.00 55.76 O
+HETATM 2095 O HOH A 408 66.992 61.289 13.604 1.00 74.35 O
+HETATM 2096 O HOH A 409 54.344 44.338 21.904 1.00 44.49 O
+HETATM 2097 O HOH A 410 44.691 72.338 12.049 1.00 50.99 O
+HETATM 2098 O HOH A 411 40.751 63.603 43.590 1.00 89.83 O
+HETATM 2099 O HOH A 412 53.645 41.356 9.844 1.00 90.63 O
+HETATM 2100 O HOH A 413 59.949 37.796 24.955 1.00 70.80 O
+HETATM 2101 O HOH A 415 51.339 54.431 20.373 1.00 76.96 O
+HETATM 2102 O HOH A 416 37.653 77.331 42.105 1.00104.47 O
+HETATM 2103 O HOH A 417 52.864 38.162 12.617 1.00 80.23 O
+HETATM 2104 O HOH A 418 70.042 75.630 9.251 1.00 96.14 O
+HETATM 2105 O HOH A 419 57.849 36.827 16.245 1.00 55.25 O
+HETATM 2106 O HOH A 420 51.199 53.647 16.824 1.00 68.61 O
+HETATM 2107 O HOH A 421 46.270 42.361 39.422 1.00 86.08 O
+HETATM 2108 O HOH A 422 39.748 46.501 33.723 1.00 90.52 O
+HETATM 2109 O HOH A 423 55.402 30.310 22.335 1.00153.77 O
+HETATM 2110 O HOH A 424 62.850 37.633 36.622 1.00 93.90 O
+HETATM 2111 O HOH A 425 52.620 28.934 10.172 1.00 66.53 O
+HETATM 2112 O HOH A 426 46.043 72.059 15.009 1.00 81.11 O
+HETATM 2113 O HOH A 427 44.504 24.559 13.975 1.00 95.67 O
+HETATM 2114 O HOH A 428 64.390 51.541 8.357 1.00 96.89 O
+HETATM 2115 O HOH A 429 62.387 43.098 34.217 1.00 62.96 O
+HETATM 2116 O HOH A 430 40.781 42.498 19.177 1.00 95.04 O
+HETATM 2117 O HOH A 431 51.714 28.135 30.983 1.00 99.10 O
+HETATM 2118 O HOH A 432 56.277 41.684 42.172 1.00 76.07 O
+HETATM 2119 O HOH A 433 71.383 70.114 4.691 1.00115.24 O
+HETATM 2120 O HOH A 434 43.954 36.036 19.243 1.00 60.36 O
+HETATM 2121 O HOH A 435 42.927 80.090 37.718 1.00 93.62 O
+HETATM 2122 O HOH A 436 57.157 36.207 23.849 1.00 66.99 O
+HETATM 2123 O HOH A 437 50.487 54.395 35.797 1.00115.03 O
+HETATM 2124 O HOH A 438 42.557 37.639 16.483 1.00104.97 O
+HETATM 2125 O HOH A 439 52.517 25.349 8.099 1.00 83.24 O
+HETATM 2126 O HOH A 440 43.812 69.893 17.618 1.00 74.07 O
+HETATM 2127 O HOH A 441 42.386 49.215 25.612 1.00 87.62 O
+HETATM 2128 O HOH A 442 43.738 47.793 12.611 1.00 97.20 O
+HETATM 2129 O HOH A 443 56.851 56.881 11.453 1.00 65.45 O
+HETATM 2130 O HOH A 444 41.494 28.883 24.574 1.00 68.68 O
+HETATM 2131 O HOH A 445 66.299 67.845 11.185 1.00119.36 O
+HETATM 2132 O HOH A 446 44.327 43.962 37.114 1.00 59.00 O
+HETATM 2133 O HOH A 447 55.964 29.615 20.081 1.00 95.39 O
+HETATM 2134 O HOH A 448 57.973 59.050 -2.009 1.00109.16 O
+HETATM 2135 O HOH A 449 59.402 59.312 31.449 1.00 68.84 O
+HETATM 2136 O HOH A 450 43.007 16.103 21.017 1.00106.73 O
+HETATM 2137 O HOH A 451 42.422 49.150 15.212 1.00 78.44 O
+HETATM 2138 O HOH A 452 70.835 47.923 38.230 1.00 80.61 O
+HETATM 2139 O HOH A 453 61.705 64.436 22.275 1.00 84.32 O
+HETATM 2140 O HOH A 454 46.943 51.613 25.671 1.00 73.11 O
+HETATM 2141 O HOH A 455 54.648 46.163 19.618 1.00 62.24 O
+HETATM 2142 O HOH A 456 38.484 46.751 20.701 1.00 56.54 O
+HETATM 2143 O HOH A 457 60.794 35.462 31.358 1.00109.99 O
+HETATM 2144 O HOH A 458 44.895 54.912 35.019 1.00 81.53 O
+HETATM 2145 O HOH A 459 60.469 54.509 19.865 1.00 78.35 O
+HETATM 2146 O HOH A 460 40.557 49.152 31.709 1.00 94.98 O
+HETATM 2147 O HOH A 461 49.564 72.961 7.126 1.00127.46 O
+HETATM 2148 O HOH A 462 38.911 32.924 24.206 1.00 94.52 O
+HETATM 2149 O HOH A 463 44.840 67.115 17.805 1.00 64.28 O
+HETATM 2150 O HOH A 464 59.959 60.408 29.152 1.00 87.28 O
+HETATM 2151 O HOH A 465 47.480 63.127 48.379 1.00106.79 O
+HETATM 2152 O HOH A 466 41.379 47.530 27.555 1.00 63.18 O
+HETATM 2153 O HOH A 467 55.256 41.519 33.323 1.00 88.02 O
+HETATM 2154 O HOH A 468 46.278 35.257 34.883 1.00103.21 O
+HETATM 2155 O HOH A 469 50.168 44.685 11.400 1.00 84.54 O
+HETATM 2156 O HOH A 470 55.140 23.817 9.150 1.00 80.25 O
+HETATM 2157 O HOH A 471 59.853 74.716 4.618 1.00 98.69 O
+HETATM 2158 O HOH A 472 50.122 40.345 41.076 1.00 96.48 O
+HETATM 2159 O HOH A 473 65.972 41.974 36.431 1.00117.24 O
+HETATM 2160 O HOH A 474 55.172 63.267 37.006 1.00103.99 O
+HETATM 2161 O HOH A 475 57.260 52.484 35.826 1.00 36.48 O
+HETATM 2162 O HOH A 476 47.778 19.952 7.533 1.00 98.79 O
+HETATM 2163 O HOH A 477 61.467 73.402 3.421 1.00 91.53 O
+HETATM 2164 O HOH A 478 58.411 68.300 -1.259 1.00 79.23 O
+HETATM 2165 O HOH A 479 41.220 45.034 19.654 1.00104.86 O
+HETATM 2166 O HOH A 480 55.599 58.758 22.542 1.00 99.09 O
+HETATM 2167 O HOH A 481 53.744 43.835 45.686 1.00120.41 O
+HETATM 2168 O HOH A 482 59.195 65.528 18.099 1.00 79.51 O
+HETATM 2169 O HOH A 483 61.286 41.409 39.993 1.00 90.87 O
+HETATM 2170 O HOH A 484 49.047 34.291 16.948 1.00101.95 O
+HETATM 2171 O HOH A 485 51.730 71.388 25.674 1.00 52.14 O
+HETATM 2172 O HOH A 486 49.629 29.507 20.165 1.00 58.18 O
+HETATM 2173 O HOH A 487 39.919 50.462 26.232 1.00 67.53 O
+HETATM 2174 O HOH A 488 64.965 67.977 4.650 1.00 80.20 O
+HETATM 2175 O HOH A 489 48.890 37.269 24.529 1.00 49.39 O
+CONECT 194 2031
+CONECT 1351 2031
+CONECT 1365 2031
+CONECT 1792 2032
+CONECT 1794 2032
+CONECT 1799 2032
+CONECT 1815 2032
+CONECT 2031 194 1351 1365
+CONECT 2032 1792 1794 1799 1815
+CONECT 2033 2034 2035 2036 2037
+CONECT 2033 2038 2039
+CONECT 2034 2033
+CONECT 2035 2033
+CONECT 2036 2033
+CONECT 2037 2033
+CONECT 2038 2033
+CONECT 2039 2033
+CONECT 2040 2041 2042 2043 2044
+CONECT 2040 2045 2046
+CONECT 2041 2040
+CONECT 2042 2040
+CONECT 2043 2040
+CONECT 2044 2040
+CONECT 2045 2040
+CONECT 2046 2040
+CONECT 2047 2048 2049 2050 2051
+CONECT 2047 2052 2053
+CONECT 2048 2047
+CONECT 2049 2047
+CONECT 2050 2047
+CONECT 2051 2047
+CONECT 2052 2047
+CONECT 2053 2047
+CONECT 2054 2055 2056 2057 2058
+CONECT 2054 2059 2060
+CONECT 2055 2054
+CONECT 2056 2054
+CONECT 2057 2054
+CONECT 2058 2054
+CONECT 2059 2054
+CONECT 2060 2054
+CONECT 2061 2062
+CONECT 2062 2061 2063 2066
+CONECT 2063 2062 2064 2065
+CONECT 2064 2063
+CONECT 2065 2063
+CONECT 2066 2062 2067
+CONECT 2067 2066 2068
+CONECT 2068 2067 2069 2070
+CONECT 2069 2068
+CONECT 2070 2068 2071
+CONECT 2071 2070 2072 2073
+CONECT 2072 2071 2077
+CONECT 2073 2071 2074 2075
+CONECT 2074 2073
+CONECT 2075 2073 2076 2077
+CONECT 2076 2075
+CONECT 2077 2072 2075 2078
+CONECT 2078 2077 2079 2087
+CONECT 2079 2078 2080
+CONECT 2080 2079 2081
+CONECT 2081 2080 2082 2087
+CONECT 2082 2081 2083 2084
+CONECT 2083 2082
+CONECT 2084 2082 2085
+CONECT 2085 2084 2086
+CONECT 2086 2085 2087
+CONECT 2087 2078 2081 2086
+MASTER 373 0 7 0 0 0 13 6 2174 1 68 8
+END
import java.awt.event.*;
import javax.swing.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.gui.*;
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap, String protocol)
-
{
this.pdbentry = pdbentry;
this.seq = seq;
import java.awt.*;
+import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
import jalview.io.FileParse;
+import jalview.ws.jws1.Annotate3D;
public class PDBfile extends jalview.io.AlignFile
{
id = safeName(getDataName());
chains = new Vector();
-
+ ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
+ entry.setProperty(new Hashtable());
+ entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
// maintain reference to
// dataset
seqs.addElement(chainseq);
+ if(isRNA(chainseq)==true)
+ {
+ rna.add(chainseq);
+ } else {
+ prot.add(chainseq);
+ }
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
if (chainannot != null)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
+
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
+ if (rna.size()>0)
+ try {
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
}
}
}
-
+ private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+ {
+ // process prot sequence with Jmol to get annotated alignment.
+ // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
+// System.out.println("this is a PDB format and RNA sequence");
+ Annotate3D an3d = new Annotate3D();
+ // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
+ AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
+ replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ }
+ private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+ {
+ if (al!=null && al.getHeight()>0)
+ {
+ ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+ ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+
+ for (SequenceI sq:ochains)
+ {
+ SequenceI bestm=null;
+ AlignSeq bestaseq=null;
+ int bestscore=0;
+ for (SequenceI msq:al.getSequences())
+ {
+ AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
+ if (bestm==null || aseq.getMaxScore()>bestscore)
+ {
+ bestscore=aseq.getMaxScore();
+ bestaseq= aseq;
+ bestm=msq;
+ }
+ }
+ System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
+ matches.add(bestm);
+ aligns.add(bestaseq);
+ al.deleteSequence(bestm);
+ }
+ for (int p=0,pSize=seqs.size();p<pSize;p++)
+ {
+ SequenceI sq,sp=seqs.get(p);
+ int q;
+ if ((q=ochains.indexOf(sp))>-1)
+ {
+ seqs.set(p, sq=matches.get(q));
+ sq.setName(sp.getName());
+ sq.setDescription(sp.getDescription());
+ sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
+ int inspos=-1;
+ for (int ap=0;ap<annotations.size();)
+ {
+ if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
+ if (inspos==-1)
+ {
+ inspos=ap;
+ }
+ annotations.remove(ap);
+ } else {
+ ap++;
+ }
+ }
+ annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ }
/**
* make a friendly ID string.
*
1.0f / (float) i, .4f, 1.0f));
}
}
+ public boolean isRNA(SequenceI seqs)
+ {
+ for (int i=0;i<seqs.getLength();i++){
+ if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
+ {
+ return false;
+ }
+ }
+
+ return true;
+
+
+ }
}
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.analysis;
-
import java.util.*;
import java.awt.*;
}
/**
- * DOCUMENT ME!
- *
- * @param s1
- * DOCUMENT ME!
- * @param string1
- * - string to align for sequence1
- * @param s2
- * sequence 2
- * @param string2
- * - string to align for sequence2
+ * Construct score matrix for sequences with standard DNA or PEPTIDE matrix
+ * @param s1 - sequence 1
+ * @param string1 - string to use for s1
+ * @param s2 - sequence 2
+ * @param string2 - string to use for s2
* @param type
* DNA or PEPTIDE
*/
SeqInit(string1, string2);
}
+ /**
+ * Construct score matrix for sequences with custom substitution matrix
+ * @param s1 - sequence 1
+ * @param string1 - string to use for s1
+ * @param s2 - sequence 2
+ * @param string2 - string to use for s2
+ * @param scoreMatrix - substitution matrix to use for alignment
+ */
public void SeqInit(SequenceI s1, String string1, SequenceI s2,
String string2, ScoreMatrix scoreMatrix)
{
* construct score matrix for string1 and string2 (after removing any existing
* gaps
*
- * @param string1
+ * @param string1
* @param string2
*/
private void SeqInit(String string1, String string2)
}
/**
+ * Compute a globally optimal needleman and wunsch alignment between two
+ * sequences
+ *
+ * @param s1
+ * @param s2
+ * @param type
+ * AlignSeq.DNA or AlignSeq.PEP
+ */
+ public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
+ String type)
+ {
+ AlignSeq as = new AlignSeq(s1, s2, type);
+
+ as.calcScoreMatrix();
+ as.traceAlignment();
+ return as;
+ }
+
+ /**
+ *
+ * @return mapping from positions in S1 to corresponding positions in S2
+ */
+ public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
+ {
+ ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
+ int pdbpos = s2.getStart() + getSeq2Start() - 2;
+ int alignpos = s1.getStart() + getSeq1Start() - 2;
+ int lp2 = pdbpos - 3, lp1 = alignpos - 3;
+ boolean lastmatch = false;
+ // and now trace the alignment onto the atom set.
+ for (int i = 0; i < astr1.length(); i++)
+ {
+ char c1 = astr1.charAt(i), c2 = astr2.charAt(i);
+ if (c1 != '-')
+ {
+ alignpos++;
+ }
+
+ if (c2 != '-')
+ {
+ pdbpos++;
+ }
+
+ if (allowmismatch || c1 == c2)
+ {
+ lastmatch = true;
+ // extend mapping interval.
+ if (lp1 + 1 != alignpos)
+ {
+ as1.add(Integer.valueOf(alignpos));
+ lp1 = alignpos;
+ }
+
+ if (lp2 + 1 != pdbpos)
+ {
+ as2.add(Integer.valueOf(pdbpos));
+ lp2 = pdbpos;
+ }
+ }
+ else
+ {
+ lastmatch = false;
+ }
+ }
+ // construct range pairs
+ int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
+ .size() + (lastmatch ? 1 : 0)];
+ int i = 0;
+ for (Integer ip : as1)
+ {
+ mapseq1[i++] = ip;
+ }
+ ;
+ i = 0;
+ for (Integer ip : as2)
+ {
+ mapseq2[i++] = ip;
+ }
+ ;
+ if (lastmatch)
+ {
+ mapseq1[mapseq1.length - 1] = alignpos;
+ mapseq2[mapseq2.length - 1] = pdbpos;
+ }
+ MapList map = new MapList(mapseq1, mapseq2, 1, 1);
+
+ jalview.datamodel.Mapping mapping = new Mapping(map);
+ mapping.setTo(s2);
+ return mapping;
+ }
+
+ /**
* compute the PID vector used by the redundancy filter.
*
* @param originalSequences
{
char base = line.charAt(i);
- if ((base == '<') || (base == '(') || (base == '{') || (base == '['))
+ if ((base == '<') || (base == '(') || (base == '{') || (base == '[')|| (base == 'A')|| (base == 'B')|| (base == 'C')|| (base == 'D')|| (base == '1')|| (base == 'F')|| (base == 'G')|| (base == '2')|| (base == 'I')|| (base == 'J')|| (base == 'K')|| (base == 'L')|| (base == 'M')|| (base == 'N')|| (base == 'O')|| (base == 'P')|| (base == 'Q')|| (base == 'R')|| (base == 'S')|| (base == 'T')|| (base == 'U')|| (base == 'V')|| (base == 'W')|| (base == 'X')|| (base == 'Y')|| (base == 'Z'))
{
stack.push(i);
}
- else if ((base == '>') || (base == ')') || (base == '}')
- || (base == ']'))
+ else if ((base == '>') || (base == ')') || (base == '}')|| (base == ']')|| (base == 'a')|| (base == 'b')|| (base == 'c')|| (base == 'd')|| (base == 'e')|| (base == 'f')|| (base == 'g')|| (base == 'h')|| (base == 'i')|| (base == 'j')|| (base == 'k')|| (base == 'l')|| (base == 'm')|| (base == 'n')|| (base == 'o')|| (base == 'p')|| (base == 'q')|| (base == 'r')|| (base == 's')|| (base == 't')|| (base == 'u')|| (base == 'v')|| (base == 'w')|| (base == 'x')|| (base == 'y')|| (base == 'z'))
+
{
if (stack.isEmpty())
}
Object temp = stack.pop();
pairs.addElement(temp);
- pairs.addElement(i);
+ pairs.addElement(i);
}
i++;
*/
public static int findPair(SequenceFeature[] pairs, int indice)
{
+ System.out.print("indice"+indice+" ");
for (int i = 0; i < pairs.length; i++)
{
if (pairs[i].getBegin() == indice)
+
{
+ System.out.println(pairs[i].getEnd());
return pairs[i].getEnd();
+
}
}
return -1;
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
+// System.out.println("longueur="+sequences.length);
+// for(int l=0;l<=(sequences.length-1);l++){
+// System.out.println("sequences "+l+":"+sequences[l].getSequenceAsString());
+// }
+// System.out.println("start="+start);
+ System.out.println("end="+end);
+// System.out.println("result="+result.length);
+//
+// System.out.println("profile="+profile);
+// System.out.println("rnaStruc="+rnaStruc);
Hashtable residueHash;
String maxResidue;
- char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
+ char[] struc = rnaStruc.getRNAStruc().toCharArray();
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
- int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+ int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
int[] values;
int[][] pairs;
float percentage;
+ boolean wooble = true;
for (i = start; i < end; i++) // foreach column
{
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
+ //System.out.println("s="+struc[i]);
if (i < struc.length)
{
s = struc[i];
+
}
else
{
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
}
else
{
+
+
bpEnd = findPair(rna, i);
- if (bpEnd > -1)
+
+ if (bpEnd>-1)
{
- for (j = 0; j < jSize; j++) // foreach row
+ for (j = 0; j < jSize; j++) // foreach row
+ {
+ if (sequences[j] == null)
{
- if (sequences[j] == null)
+ System.err
+ .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ continue;
+ }
+ c = sequences[j].getCharAt(i);
+ //System.out.println("c="+c);
+
+
+ // standard representation for gaps in sequence and structure
+ if (c == '.' || c == ' ')
{
System.err
.println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- c = sequences[j].getCharAt(i);
+ cEnd = sequences[j].getCharAt(bpEnd);
+
+
+ System.out.println("pairs ="+c+","+cEnd);
+ if (checkBpType(c, cEnd)==true)
{
-
- // standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (c == '-')
- {
- values['-']++;
- continue;
- }
- cEnd = sequences[j].getCharAt(bpEnd);
- if (checkBpType(c, cEnd))
- {
- values['(']++; // H means it's a helix (structured)
- }
- pairs[c][cEnd]++;
-
+ values['(']++; // H means it's a helix (structured)
maxResidue = "(";
+ wooble=true;
+ System.out.println("It's a pair wc");
+
}
- }
+ if (checkBpType(c, cEnd)==false)
+ {
+ wooble =false;
+ values['[']++; // H means it's a helix (structured)
+ maxResidue = "[";
+ System.out.println("It's an pair non canonic");
+ System.out.println(sequences[j].getRNA());
+ System.out.println(rnaStruc.getRNAStruc().charAt(i));
+ }
+ pairs[c][cEnd]++;
+
+
+ }
+
}
// nonGap++;
}
residueHash.put(PAIRPROFILE, pairs);
}
-
+ if (wooble==true)
+ {
count = values['('];
-
+ }
+ if (wooble==false)
+ {
+ count = values['['];
+ }
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
}
if (bpEnd > 0)
{
- values[')'] = values['('];
+ values[')'] = values['('];
+ values[']'] = values['['];
values['('] = 0;
-
+ values['['] = 0;
residueHash = new Hashtable();
- maxResidue = ")";
-
+ if (wooble==true){
+ System.out.println(maxResidue+","+wooble);
+ maxResidue = ")";
+ }
+ if(wooble==false){
+ System.out.println(maxResidue+","+wooble);
+ maxResidue = "]";
+ }
if (profile)
{
residueHash.put(PROFILE, new int[][]
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * 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/>.
- */
-package jalview.appletgui;
-
-import jalview.analysis.AlignmentSorter;
-import jalview.analysis.Conservation;
-import jalview.api.SequenceStructureBinding;
-import jalview.bin.JalviewLite;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.OrderCommand;
-import jalview.commands.RemoveGapColCommand;
-import jalview.commands.RemoveGapsCommand;
-import jalview.commands.SlideSequencesCommand;
-import jalview.commands.TrimRegionCommand;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentOrder;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.AnnotationFile;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FeaturesFile;
-import jalview.io.TCoffeeScoreFile;
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
-
-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.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-public class AlignFrame extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
-{
- public AlignmentPanel alignPanel;
-
- public AlignViewport viewport;
-
- int DEFAULT_WIDTH = 700;
-
- int DEFAULT_HEIGHT = 500;
-
- String jalviewServletURL;
-
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
- String title, boolean embedded)
- {
- if (applet != null)
- {
- jalviewServletURL = applet.getParameter("APPLICATION_URL");
- }
-
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- viewport = new AlignViewport(al, applet);
- alignPanel = new AlignmentPanel(this, viewport);
-
- viewport.updateConservation(alignPanel);
- viewport.updateConsensus(alignPanel);
-
- annotationPanelMenuItem.setState(viewport.showAnnotation);
- displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
- followMouseOverFlag.setState(viewport.getFollowHighlight());
- showGroupConsensus.setState(viewport.isShowGroupConsensus());
- showGroupConservation.setState(viewport.isShowGroupConservation());
- showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
- showSequenceLogo.setState(viewport.isShowSequenceLogo());
- normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
-
- seqLimits.setState(viewport.showJVSuffix);
-
- if (applet != null)
- {
- String param = applet.getParameter("sortBy");
- if (param != null)
- {
- if (param.equalsIgnoreCase("Id"))
- {
- sortIDMenuItem_actionPerformed();
- }
- else if (param.equalsIgnoreCase("Pairwise Identity"))
- {
- sortPairwiseMenuItem_actionPerformed();
- }
- else if (param.equalsIgnoreCase("Length"))
- {
- sortLengthMenuItem_actionPerformed();
- }
- }
-
- param = applet.getParameter("wrap");
- if (param != null)
- {
- if (param.equalsIgnoreCase("true"))
- {
- wrapMenuItem.setState(true);
- wrapMenuItem_actionPerformed();
- }
- }
- param = applet.getParameter("centrecolumnlabels");
- if (param != null)
- {
- centreColumnLabelFlag.setState(true);
- centreColumnLabelFlag_stateChanged();
- }
- try
- {
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
- }
- } catch (Exception ex)
- {
- }
-
- }
- if (viewport.getAlignment().isNucleotide())
- {
- viewport.updateStrucConsensus(alignPanel);
- if (viewport.getAlignment().hasRNAStructure())
- {
- RNAHelixColour.setEnabled(true);
- }
- else
- {
- RNAHelixColour.setEnabled(false);
- }
- }
- else
- {
- RNAHelixColour.setEnabled(false);
- purinePyrimidineColour.setEnabled(false);
- }
- // Some JVMS send keyevents to Top frame or lowest panel,
- // Havent worked out why yet. So add to both this frame and seqCanvas for
- // now
- this.addKeyListener(this);
- alignPanel.seqPanel.seqCanvas.addKeyListener(this);
- alignPanel.idPanel.idCanvas.addKeyListener(this);
- alignPanel.scalePanel.addKeyListener(this);
- alignPanel.annotationPanel.addKeyListener(this);
- alignPanel.annotationPanelHolder.addKeyListener(this);
- alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
- alignPanel.alabels.addKeyListener(this);
- createAlignFrameWindow(embedded, title);
-
- validate();
- alignPanel.adjustAnnotationHeight();
- alignPanel.paintAlignment(true);
- }
-
- public AlignViewport getAlignViewport()
- {
- return viewport;
- }
-
- public SeqCanvas getSeqcanvas()
- {
- return alignPanel.seqPanel.seqCanvas;
- }
-
- /**
- * Load a features file onto the alignment
- *
- * @param file
- * file URL, content, or other resolvable path
- * @param type
- * is protocol for accessing data referred to by file
- */
-
- public boolean parseFeaturesFile(String file, String type)
- {
- return parseFeaturesFile(file, type, true);
- }
-
- /**
- * Load a features file onto the alignment
- *
- * @param file
- * file URL, content, or other resolvable path
- * @param type
- * is protocol for accessing data referred to by file
- * @param autoenabledisplay
- * when true, display features flag will be automatically enabled if
- * features are loaded
- * @return true if data parsed as a features file
- */
- public boolean parseFeaturesFile(String file, String type,
- boolean autoenabledisplay)
- {
- // TODO: test if importing a features file onto an alignment which already
- // has features with links overwrites the original links.
-
- Hashtable featureLinks = new Hashtable();
- boolean featuresFile = false;
- try
- {
- featuresFile = new jalview.io.FeaturesFile(file, type)
- .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureColours, featureLinks,
- true, viewport.applet.getDefaultParameter(
- "relaxedidmatch", false));
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- if (featuresFile)
- {
- if (featureLinks.size() > 0)
- {
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
- }
- if (autoenabledisplay)
- {
- viewport.showSequenceFeatures = true;
- sequenceFeatures.setState(true);
- }
- if (viewport.featureSettings != null)
- {
- viewport.featureSettings.refreshTable();
- }
- alignPanel.paintAlignment(true);
- statusBar.setText("Successfully added features to alignment.");
- }
- return featuresFile;
- }
-
- @Override
- public void keyPressed(KeyEvent evt)
- {
- if (viewport.cursorMode
- && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
- .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
- .getKeyCode() <= KeyEvent.VK_NUMPAD9))
- && Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
- switch (evt.getKeyCode())
- {
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed();
-
- alignPanel.alabels.cancelDrag();
- break;
- case KeyEvent.VK_X:
- if (evt.isControlDown() || evt.isMetaDown())
- {
- cut_actionPerformed();
- }
- break;
- case KeyEvent.VK_C:
- if (viewport.cursorMode && !evt.isControlDown())
- {
- alignPanel.seqPanel.setCursorColumn();
- }
- if (evt.isControlDown() || evt.isMetaDown())
- {
- copy_actionPerformed();
- }
- break;
- case KeyEvent.VK_V:
- if (evt.isControlDown())
- {
- paste(evt.isShiftDown());
- }
- break;
- case KeyEvent.VK_A:
- if (evt.isControlDown() || evt.isMetaDown())
- {
- selectAllSequenceMenuItem_actionPerformed();
- }
- break;
- case KeyEvent.VK_DOWN:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, 1);
- }
- else
- {
- moveSelectedSequences(false);
- }
- break;
-
- case KeyEvent.VK_UP:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, -1);
- }
- else
- {
- moveSelectedSequences(true);
- }
- break;
-
- case KeyEvent.VK_LEFT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor(-1, 0);
- break;
-
- case KeyEvent.VK_RIGHT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor(1, 0);
- break;
-
- case KeyEvent.VK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
- }
- break;
-
- case KeyEvent.VK_DELETE:
- case KeyEvent.VK_BACK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
- }
- else
- {
- cut_actionPerformed();
- alignPanel.seqPanel.seqCanvas.repaint();
- }
- break;
-
- case KeyEvent.VK_S:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRow();
- }
- break;
- case KeyEvent.VK_P:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorPosition();
- }
- break;
-
- case KeyEvent.VK_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
-
- case KeyEvent.VK_Q:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
- }
- break;
- case KeyEvent.VK_M:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
- }
- break;
-
- case KeyEvent.VK_F2:
- viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is "
- + (viewport.cursorMode ? "on" : "off"));
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
- }
- break;
-
- case KeyEvent.VK_F:
- if (evt.isControlDown())
- {
- findMenuItem_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_H:
- {
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
- toggleHiddenRegions(toggleSeqs, toggleCols);
- break;
- }
-
- case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(true);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
- }
- break;
-
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(false);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
- }
- break;
-
- case KeyEvent.VK_Z:
- if (evt.isControlDown())
- {
- undoMenuItem_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_Y:
- if (evt.isControlDown())
- {
- redoMenuItem_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_L:
- if (evt.isControlDown())
- {
- trimAlignment(true);
- }
- break;
-
- case KeyEvent.VK_R:
- if (evt.isControlDown())
- {
- trimAlignment(false);
- }
- break;
-
- case KeyEvent.VK_E:
- if (evt.isControlDown())
- {
- if (evt.isShiftDown())
- {
- this.removeAllGapsMenuItem_actionPerformed();
- }
- else
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
- }
- break;
- case KeyEvent.VK_I:
- if (evt.isControlDown())
- {
- if (evt.isAltDown())
- {
- invertColSel_actionPerformed();
- }
- else
- {
- invertSequenceMenuItem_actionPerformed();
- }
- }
- break;
-
- case KeyEvent.VK_U:
- if (evt.isControlDown())
- {
- this.deleteGroups_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_T:
- if (evt.isControlDown())
- {
- newView(null);
- }
- break;
-
- }
- alignPanel.paintAlignment(true);
- }
-
- /**
- * called by key handler and the hide all/show all menu items
- *
- * @param toggleSeqs
- * @param toggleCols
- */
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
- {
- boolean hide = false;
- SequenceGroup sg = viewport.getSelectionGroup();
- if (!toggleSeqs && !toggleCols)
- {
- // Hide everything by the current selection - this is a hack - we do the
- // invert and then hide
- // first check that there will be visible columns after the invert.
- if ((viewport.getColumnSelection() != null
- && viewport.getColumnSelection().getSelected() != null && viewport
- .getColumnSelection().getSelected().size() > 0)
- || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
- .getEndRes()))
- {
- // now invert the sequence set, if required - empty selection implies
- // that no hiding is required.
- if (sg != null)
- {
- invertSequenceMenuItem_actionPerformed();
- sg = viewport.getSelectionGroup();
- toggleSeqs = true;
-
- }
- viewport.expandColSelection(sg, true);
- // finally invert the column selection and get the new sequence
- // selection and indicate it should be hidden.
- invertColSel_actionPerformed();
- toggleCols = true;
- }
- }
-
- if (toggleSeqs)
- {
- if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
- {
- hide = true;
- viewport.hideAllSelectedSeqs();
- }
- else if (!(toggleCols && viewport.getColumnSelection().getSelected()
- .size() > 0))
- {
- viewport.showAllHiddenSeqs();
- }
- }
-
- if (toggleCols)
- {
- if (viewport.getColumnSelection().getSelected().size() > 0)
- {
- viewport.hideSelectedColumns();
- if (!toggleSeqs)
- {
- viewport.setSelectionGroup(sg);
- }
- }
- else if (!hide)
- {
- viewport.showAllHiddenColumns();
- }
- }
- }
-
- @Override
- public void keyReleased(KeyEvent evt)
- {
- }
-
- @Override
- public void keyTyped(KeyEvent evt)
- {
- }
-
- @Override
- public void itemStateChanged(ItemEvent evt)
- {
- if (evt.getSource() == displayNonconservedMenuItem)
- {
- displayNonconservedMenuItem_actionPerformed();
- }
- else if (evt.getSource() == colourTextMenuItem)
- {
- colourTextMenuItem_actionPerformed();
- }
- else if (evt.getSource() == wrapMenuItem)
- {
- wrapMenuItem_actionPerformed();
- }
- else if (evt.getSource() == scaleAbove)
- {
- viewport.setScaleAboveWrapped(scaleAbove.getState());
- }
- else if (evt.getSource() == scaleLeft)
- {
- viewport.setScaleLeftWrapped(scaleLeft.getState());
- }
- else if (evt.getSource() == scaleRight)
- {
- viewport.setScaleRightWrapped(scaleRight.getState());
- }
- else if (evt.getSource() == seqLimits)
- {
- seqLimits_itemStateChanged();
- }
- else if (evt.getSource() == viewBoxesMenuItem)
- {
- viewport.setShowBoxes(viewBoxesMenuItem.getState());
- }
- else if (evt.getSource() == viewTextMenuItem)
- {
- viewport.setShowText(viewTextMenuItem.getState());
- }
- else if (evt.getSource() == renderGapsMenuItem)
- {
- viewport.setRenderGaps(renderGapsMenuItem.getState());
- }
- else if (evt.getSource() == annotationPanelMenuItem)
- {
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
- }
- else if (evt.getSource() == sequenceFeatures)
- {
- viewport.showSequenceFeatures(sequenceFeatures.getState());
- alignPanel.seqPanel.seqCanvas.repaint();
- }
- else if (evt.getSource() == conservationMenuItem)
- {
- conservationMenuItem_actionPerformed();
- }
- else if (evt.getSource() == abovePIDThreshold)
- {
- abovePIDThreshold_actionPerformed();
- }
- else if (evt.getSource() == applyToAllGroups)
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
- }
- else if (evt.getSource() == autoCalculate)
- {
- viewport.autoCalculateConsensus = autoCalculate.getState();
- }
- else if (evt.getSource() == sortByTree)
- {
- viewport.sortByTree = sortByTree.getState();
- }
- else if (evt.getSource() == this.centreColumnLabelFlag)
- {
- centreColumnLabelFlag_stateChanged();
- }
- else if (evt.getSource() == this.followMouseOverFlag)
- {
- mouseOverFlag_stateChanged();
- }
- else if (evt.getSource() == showGroupConsensus)
- {
- showGroupConsensus_actionPerformed();
- }
- else if (evt.getSource() == showGroupConservation)
- {
- showGroupConservation_actionPerformed();
- }
- else if (evt.getSource() == showSequenceLogo)
- {
- showSequenceLogo_actionPerformed();
- }
- else if (evt.getSource() == normSequenceLogo)
- {
- normSequenceLogo_actionPerformed();
- }
- else if (evt.getSource() == showConsensusHistogram)
- {
- showConsensusHistogram_actionPerformed();
- }
- else if (evt.getSource() == applyAutoAnnotationSettings)
- {
- applyAutoAnnotationSettings_actionPerformed();
- }
- alignPanel.paintAlignment(true);
- }
-
- private void mouseOverFlag_stateChanged()
- {
- viewport.followHighlight = followMouseOverFlag.getState();
- // TODO: could kick the scrollTo mechanism to reset view for current
- // searchresults.
- }
-
- private void centreColumnLabelFlag_stateChanged()
- {
- viewport.centreColumnLabels = centreColumnLabelFlag.getState();
- this.alignPanel.annotationPanel.repaint();
- }
-
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- Object source = evt.getSource();
-
- if (source == inputText)
- {
- inputText_actionPerformed();
- }
- else if (source == loadTree)
- {
- loadTree_actionPerformed();
- }
- else if (source == loadApplication)
- {
- launchFullApplication();
- }
- else if (source == loadAnnotations)
- {
- loadAnnotations();
- }
- else if (source == outputAnnotations)
- {
- outputAnnotations(true);
- }
- else if (source == outputFeatures)
- {
- outputFeatures(true, "Jalview");
- }
- else if (source == closeMenuItem)
- {
- closeMenuItem_actionPerformed();
- }
- else if (source == copy)
- {
- copy_actionPerformed();
- }
- else if (source == undoMenuItem)
- {
- undoMenuItem_actionPerformed();
- }
- else if (source == redoMenuItem)
- {
- redoMenuItem_actionPerformed();
- }
- else if (source == inputText)
- {
- inputText_actionPerformed();
- }
- else if (source == closeMenuItem)
- {
- closeMenuItem_actionPerformed();
- }
- else if (source == undoMenuItem)
- {
- undoMenuItem_actionPerformed();
- }
- else if (source == redoMenuItem)
- {
- redoMenuItem_actionPerformed();
- }
- else if (source == copy)
- {
- copy_actionPerformed();
- }
- else if (source == pasteNew)
- {
- pasteNew_actionPerformed();
- }
- else if (source == pasteThis)
- {
- pasteThis_actionPerformed();
- }
- else if (source == cut)
- {
- cut_actionPerformed();
- }
- else if (source == delete)
- {
- delete_actionPerformed();
- }
- else if (source == grpsFromSelection)
- {
- makeGrpsFromSelection_actionPerformed();
- }
- else if (source == deleteGroups)
- {
- deleteGroups_actionPerformed();
- }
- else if (source == selectAllSequenceMenuItem)
- {
- selectAllSequenceMenuItem_actionPerformed();
- }
- else if (source == deselectAllSequenceMenuItem)
- {
- deselectAllSequenceMenuItem_actionPerformed();
- }
- else if (source == invertSequenceMenuItem)
- {
- invertSequenceMenuItem_actionPerformed();
- }
- else if (source == invertColSel)
- {
- viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
- }
- else if (source == remove2LeftMenuItem)
- {
- trimAlignment(true);
- }
- else if (source == remove2RightMenuItem)
- {
- trimAlignment(false);
- }
- else if (source == removeGappedColumnMenuItem)
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
- else if (source == removeAllGapsMenuItem)
- {
- removeAllGapsMenuItem_actionPerformed();
- }
- else if (source == findMenuItem)
- {
- findMenuItem_actionPerformed();
- }
- else if (source == font)
- {
- new FontChooser(alignPanel);
- }
- else if (source == newView)
- {
- newView(null);
- }
- else if (source == showColumns)
- {
- viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
- }
- else if (source == showSeqs)
- {
- viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
- }
- else if (source == hideColumns)
- {
- viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
- }
- else if (source == hideSequences
- && viewport.getSelectionGroup() != null)
- {
- viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
- }
- else if (source == hideAllButSelection)
- {
- toggleHiddenRegions(false, false);
- alignPanel.paintAlignment(true);
- }
- else if (source == hideAllSelection)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- viewport.expandColSelection(sg, false);
- viewport.hideAllSelectedSeqs();
- viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
- }
- else if (source == showAllHidden)
- {
- viewport.showAllHiddenColumns();
- viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
- }
- else if (source == showGroupConsensus)
- {
- showGroupConsensus_actionPerformed();
- }
- else if (source == showGroupConservation)
- {
- showGroupConservation_actionPerformed();
- }
- else if (source == showSequenceLogo)
- {
- showSequenceLogo_actionPerformed();
- }
- else if (source == normSequenceLogo)
- {
- normSequenceLogo_actionPerformed();
- }
- else if (source == showConsensusHistogram)
- {
- showConsensusHistogram_actionPerformed();
- }
- else if (source == applyAutoAnnotationSettings)
- {
- applyAutoAnnotationSettings_actionPerformed();
- }
- else if (source == featureSettings)
- {
- new FeatureSettings(alignPanel);
- }
- else if (source == alProperties)
- {
- StringBuffer contents = new jalview.io.AlignmentProperties(
- viewport.getAlignment()).formatAsString();
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
- cap.setText(contents.toString());
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
- + getTitle(), 400, 250);
- }
- else if (source == overviewMenuItem)
- {
- overviewMenuItem_actionPerformed();
- }
- else if (source == noColourmenuItem)
- {
- changeColour(null);
- }
- else if (source == clustalColour)
- {
- abovePIDThreshold.setState(false);
- changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
- }
- else if (source == zappoColour)
- {
- changeColour(new ZappoColourScheme());
- }
- else if (source == taylorColour)
- {
- changeColour(new TaylorColourScheme());
- }
- else if (source == hydrophobicityColour)
- {
- changeColour(new HydrophobicColourScheme());
- }
- else if (source == helixColour)
- {
- changeColour(new HelixColourScheme());
- }
- else if (source == strandColour)
- {
- changeColour(new StrandColourScheme());
- }
- else if (source == turnColour)
- {
- changeColour(new TurnColourScheme());
- }
- else if (source == buriedColour)
- {
- changeColour(new BuriedColourScheme());
- }
- else if (source == nucleotideColour)
- {
- changeColour(new NucleotideColourScheme());
- }
- else if (source == purinePyrimidineColour)
- {
- changeColour(new PurinePyrimidineColourScheme());
- }
- else if (source == RNAHelixColour)
- {
- new RNAHelicesColourChooser(viewport, alignPanel);
- }
- else if (source == modifyPID)
- {
- modifyPID_actionPerformed();
- }
- else if (source == modifyConservation)
- {
- modifyConservation_actionPerformed();
- }
- else if (source == userDefinedColour)
- {
- new UserDefinedColours(alignPanel, null);
- }
- else if (source == PIDColour)
- {
- changeColour(new PIDColourScheme());
- }
- else if (source == BLOSUM62Colour)
- {
- changeColour(new Blosum62ColourScheme());
- }
- else if (source == tcoffeeColour)
- {
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
- }
- else if (source == annotationColour)
- {
- new AnnotationColourChooser(viewport, alignPanel);
- }
- else if (source == sortPairwiseMenuItem)
- {
- sortPairwiseMenuItem_actionPerformed();
- }
- else if (source == sortIDMenuItem)
- {
- sortIDMenuItem_actionPerformed();
- }
- else if (source == sortLengthMenuItem)
- {
- sortLengthMenuItem_actionPerformed();
- }
- else if (source == sortGroupMenuItem)
- {
- sortGroupMenuItem_actionPerformed();
- }
- else if (source == removeRedundancyMenuItem)
- {
- removeRedundancyMenuItem_actionPerformed();
- }
- else if (source == pairwiseAlignmentMenuItem)
- {
- pairwiseAlignmentMenuItem_actionPerformed();
- }
- else if (source == PCAMenuItem)
- {
- PCAMenuItem_actionPerformed();
- }
- else if (source == averageDistanceTreeMenuItem)
- {
- averageDistanceTreeMenuItem_actionPerformed();
- }
- else if (source == neighbourTreeMenuItem)
- {
- neighbourTreeMenuItem_actionPerformed();
- }
- else if (source == njTreeBlosumMenuItem)
- {
- njTreeBlosumMenuItem_actionPerformed();
- }
- else if (source == avDistanceTreeBlosumMenuItem)
- {
- avTreeBlosumMenuItem_actionPerformed();
- }
- else if (source == documentation)
- {
- documentation_actionPerformed();
- }
- else if (source == about)
- {
- about_actionPerformed();
- }
-
- }
-
- public void inputText_actionPerformed()
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
- }
-
- protected void outputText_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- "Alignment output - " + e.getActionCommand(), 600, 500);
- cap.setText(new AppletFormatAdapter().formatSequences(
- e.getActionCommand(), viewport.getAlignment(),
- viewport.showJVSuffix));
- }
-
- public void loadAnnotations()
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your features / annotations / T-coffee score file here.");
- cap.setAnnotationImport();
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
-
- }
-
- public String outputAnnotations(boolean displayTextbox)
- {
- String annotation = new AnnotationFile().printAnnotations(
- viewport.showAnnotation ? viewport.getAlignment()
- .getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), ((Alignment) viewport
- .getAlignment()).alignmentProperties);
-
- if (displayTextbox)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
- cap.setText(annotation);
- }
-
- return annotation;
- }
-
- private Hashtable getDisplayedFeatureCols()
- {
- if (alignPanel.getFeatureRenderer() != null
- && viewport.featuresDisplayed != null)
- {
- FeatureRenderer fr = alignPanel.getFeatureRenderer();
- Hashtable fcols = new Hashtable();
- Enumeration en = viewport.featuresDisplayed.keys();
- while (en.hasMoreElements())
- {
- Object col = en.nextElement();
- fcols.put(col, fr.featureColours.get(col));
- }
- return fcols;
- }
- return null;
- }
-
- public String outputFeatures(boolean displayTextbox, String format)
- {
- String features;
- if (format.equalsIgnoreCase("Jalview"))
- {
- features = new FeaturesFile().printJalviewFormat(viewport
- .getAlignment().getSequencesArray(),
- getDisplayedFeatureCols());
- }
- else
- {
- features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
- }
-
- if (displayTextbox)
- {
- boolean frimport = false;
- if (features == null || features.equals("No Features Visible"))
- {
- features = "# No features visible - paste some and import them here.";
- frimport = true;
- }
-
- CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
- if (frimport)
- {
- cap.setAnnotationImport();
- }
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
- cap.setText(features);
- }
- else
- {
- if (features == null)
- features = "";
- }
-
- return features;
- }
-
- void launchFullApplication()
- {
- StringBuffer url = new StringBuffer(jalviewServletURL);
-
- url.append("?open="
- + appendProtocol(viewport.applet.getParameter("file")));
-
- if (viewport.applet.getParameter("features") != null)
- {
- url.append("&features=");
- url.append(appendProtocol(viewport.applet.getParameter("features")));
- }
-
- if (viewport.applet.getParameter("annotations") != null)
- {
- url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("annotations")));
- }
-
- if (viewport.applet.getParameter("jnetfile") != null)
- {
- url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
- }
-
- if (viewport.applet.getParameter("defaultColour") != null)
- {
- url.append("&colour="
- + removeWhiteSpace(viewport.applet
- .getParameter("defaultColour")));
- }
-
- if (viewport.applet.getParameter("userDefinedColour") != null)
- {
- url.append("&colour="
- + removeWhiteSpace(viewport.applet
- .getParameter("userDefinedColour")));
- }
- if (viewport.applet.getParameter("tree") != null)
- {
- url.append("&tree="
- + appendProtocol(viewport.applet.getParameter("tree")));
- }
- if (viewport.applet.getParameter("treeFile") != null)
- {
- url.append("&tree="
- + appendProtocol(viewport.applet.getParameter("treeFile")));
- }
-
- showURL(url.toString(), "FULL_APP");
- }
-
- String removeWhiteSpace(String colour)
- {
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < colour.length(); i++)
- {
- if (Character.isWhitespace(colour.charAt(i)))
- {
- sb.append("%20");
- }
- else
- {
- sb.append(colour.charAt(i));
- }
- }
-
- return sb.toString();
- }
-
- String appendProtocol(String url)
- {
- try
- {
- new URL(url);
- url = URLEncoder.encode(url);
- }
- /*
- * When we finally deprecate 1.1 compatibility, we can start to use
- * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
- * (UnsupportedEncodingException ex) { System.err.println("WARNING -
- * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
- * ex.printStackTrace(); }
- */
- catch (java.net.MalformedURLException ex)
- {
- url = viewport.applet.getCodeBase() + url;
- }
- return url;
- }
-
- public void closeMenuItem_actionPerformed()
- {
- PaintRefresher.RemoveComponent(alignPanel);
- if (alignPanel.seqPanel != null
- && alignPanel.seqPanel.seqCanvas != null)
- {
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
- }
- if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
- {
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
- }
-
- if (PaintRefresher.components.size() == 0 && viewport.applet == null)
- {
- System.exit(0);
- }
- else
- {
- }
- viewport = null;
- alignPanel = null;
- this.dispose();
- }
-
- /**
- * TODO: JAL-1104
- */
- void updateEditMenuBar()
- {
-
- if (viewport.historyList.size() > 0)
- {
- undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setLabel("Undo " + command.getDescription());
- }
- else
- {
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- }
-
- if (viewport.redoList.size() > 0)
- {
- redoMenuItem.setEnabled(true);
-
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setLabel("Redo " + command.getDescription());
- }
- else
- {
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- }
- }
-
- /**
- * TODO: JAL-1104
- */
- public void addHistoryItem(CommandI command)
- {
- if (command.getSize() > 0)
- {
- viewport.historyList.push(command);
- viewport.redoList.removeAllElements();
- updateEditMenuBar();
- viewport.updateHiddenColumns();
- }
- }
-
- /**
- * TODO: JAL-1104 DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void undoMenuItem_actionPerformed()
- {
- if (viewport.historyList.size() < 1)
- {
- return;
- }
-
- CommandI command = (CommandI) viewport.historyList.pop();
- viewport.redoList.push(command);
- command.undoCommand(null);
-
- AlignViewport originalSource = getOriginatingSource(command);
- // JBPNote Test
- if (originalSource != viewport)
- {
- System.err
- .println("Warning: Viewport object mismatch whilst undoing");
- }
- originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
- // viewport.getColumnSelection().getHiddenColumns()
- // != null;
- updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null, originalSource
- .getAlignment().getSequences());
- }
-
- /**
- * TODO: JAL-1104 DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void redoMenuItem_actionPerformed()
- {
- if (viewport.redoList.size() < 1)
- {
- return;
- }
-
- CommandI command = (CommandI) viewport.redoList.pop();
- viewport.historyList.push(command);
- command.doCommand(null);
-
- AlignViewport originalSource = getOriginatingSource(command);
- // JBPNote Test
- if (originalSource != viewport)
- {
- System.err
- .println("Warning: Viewport object mismatch whilst re-doing");
- }
- originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
- // viewport.getColumnSelection().getHiddenColumns()
- // != null;
-
- updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null, originalSource
- .getAlignment().getSequences());
- }
-
- AlignViewport getOriginatingSource(CommandI command)
- {
- AlignViewport originalSource = null;
- // For sequence removal and addition, we need to fire
- // the property change event FROM the viewport where the
- // original alignment was altered
- AlignmentI al = null;
- if (command instanceof EditCommand)
- {
- EditCommand editCommand = (EditCommand) command;
- al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
- for (int i = 0; i < comps.size(); i++)
- {
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
- {
- originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
- break;
- }
- }
- }
- }
-
- if (originalSource == null)
- {
- // The original view is closed, we must validate
- // the current view against the closed view first
- if (al != null)
- {
- PaintRefresher.validateSequences(al, viewport.getAlignment());
- }
-
- originalSource = viewport;
- }
-
- return originalSource;
- }
-
- public void moveSelectedSequences(boolean up)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
- {
- return;
- }
- viewport.getAlignment().moveSelectedSequencesByOne(sg,
- up ? null : viewport.getHiddenRepSequences(), up);
- alignPanel.paintAlignment(true);
- }
-
- synchronized void slideSequences(boolean right, int size)
- {
- List<SequenceI> sg = new Vector<SequenceI>();
- if (viewport.cursorMode)
- {
- sg.add(viewport.getAlignment().getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
- }
- else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport
- .getAlignment().getHeight())
- {
- sg = viewport.getSelectionGroup().getSequences(
- viewport.getHiddenRepSequences());
- }
-
- if (sg.size() < 1)
- {
- return;
- }
-
- Vector<SequenceI> invertGroup = new Vector();
-
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
- {
- if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
- invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
- }
-
- SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
-
- SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
- .size()]);
- for (int i = 0; i < invertGroup.size(); i++)
- seqs2[i] = invertGroup.elementAt(i);
-
- SlideSequencesCommand ssc;
- if (right)
- ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
- size, viewport.getGapCharacter());
- else
- ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
- size, viewport.getGapCharacter());
-
- int groupAdjustment = 0;
- if (ssc.getGapsInsertedBegin() && right)
- {
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(size, 0);
- else
- groupAdjustment = size;
- }
- else if (!ssc.getGapsInsertedBegin() && !right)
- {
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(-size, 0);
- else
- groupAdjustment = -size;
- }
-
- if (groupAdjustment != 0)
- {
- viewport.getSelectionGroup().setStartRes(
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);
- viewport.getSelectionGroup().setEndRes(
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);
- }
-
- boolean appendHistoryItem = false;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
- {
- appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
- .peek());
- }
-
- if (!appendHistoryItem)
- addHistoryItem(ssc);
-
- repaint();
- }
-
- static StringBuffer copiedSequences;
-
- static Vector copiedHiddenColumns;
-
- protected void copy_actionPerformed()
- {
- if (viewport.getSelectionGroup() == null)
- {
- return;
- }
-
- SequenceGroup sg = viewport.getSelectionGroup();
- copiedSequences = new StringBuffer();
- Hashtable orderedSeqs = new Hashtable();
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.getAlignment().findIndex(seq);
- orderedSeqs.put(index + "", seq);
- }
-
- int index = 0, startRes, endRes;
- char ch;
-
- if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
- {
- copiedHiddenColumns = new Vector();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
- .size(); i++)
- {
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
-
- copiedHiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
- }
- }
- else
- {
- copiedHiddenColumns = null;
- }
-
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI seq = null;
-
- while (seq == null)
- {
- if (orderedSeqs.containsKey(index + ""))
- {
- seq = (SequenceI) orderedSeqs.get(index + "");
- index++;
-
- break;
- }
- else
- {
- index++;
- }
- }
-
- // FIND START RES
- // Returns residue following index if gap
- startRes = seq.findPosition(sg.getStartRes());
-
- // FIND END RES
- // Need to find the residue preceeding index if gap
- endRes = 0;
-
- for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
- {
- ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap((ch)))
- {
- endRes++;
- }
- }
-
- if (endRes > 0)
- {
- endRes += seq.getStart() - 1;
- }
-
- copiedSequences.append(seq.getName()
- + "\t"
- + startRes
- + "\t"
- + endRes
- + "\t"
- + seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1) + "\n");
- }
-
- }
-
- protected void pasteNew_actionPerformed()
- {
- paste(true);
- }
-
- protected void pasteThis_actionPerformed()
- {
- paste(false);
- }
-
- void paste(boolean newAlignment)
- {
- try
- {
-
- if (copiedSequences == null)
- {
- return;
- }
-
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());
- Vector seqs = new Vector();
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- int start = Integer.parseInt(st.nextToken());
- int end = Integer.parseInt(st.nextToken());
- seqs.addElement(new Sequence(name, st.nextToken(), start, end));
- }
- SequenceI[] newSeqs = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- newSeqs[i] = (SequenceI) seqs.elementAt(i);
- }
-
- if (newAlignment)
- {
- String newtitle = new String("Copied sequences");
- if (getTitle().startsWith("Copied sequences"))
- {
- newtitle = getTitle();
- }
- else
- {
- newtitle = newtitle.concat("- from " + getTitle());
- }
- AlignFrame af = new AlignFrame(new Alignment(newSeqs),
- viewport.applet, newtitle, false);
- if (copiedHiddenColumns != null)
- {
- for (int i = 0; i < copiedHiddenColumns.size(); i++)
- {
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
-
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- }
- else
- {
- addSequences(newSeqs);
- }
-
- } catch (Exception ex)
- {
- } // could be anything being pasted in here
-
- }
-
- void addSequences(SequenceI[] seqs)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- viewport.getAlignment().addSequence(seqs[i]);
- }
-
- // !newAlignment
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
- seqs, 0, viewport.getAlignment().getWidth(),
- viewport.getAlignment()));
-
- viewport.setEndSeq(viewport.getAlignment().getHeight());
- viewport.getAlignment().getWidth();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- }
-
- protected void cut_actionPerformed()
- {
- copy_actionPerformed();
- delete_actionPerformed();
- }
-
- protected void delete_actionPerformed()
- {
-
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
- {
- return;
- }
-
- Vector seqs = new Vector();
- SequenceI seq;
- for (int i = 0; i < sg.getSize(); i++)
- {
- seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
- }
-
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.getAlignment().getHeight())
- {
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
-
- SequenceI[] cut = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- cut[i] = (SequenceI) seqs.elementAt(i);
- }
-
- /*
- * //ADD HISTORY ITEM
- */
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- if (viewport.getAlignment().getHeight() < 1)
- {
- this.setVisible(false);
- }
- viewport.sendSelection();
- }
-
- /**
- * group consensus toggled
- *
- */
- protected void showGroupConsensus_actionPerformed()
- {
- viewport.setShowGroupConsensus(showGroupConsensus.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-
- }
-
- /**
- * group conservation toggled.
- */
- protected void showGroupConservation_actionPerformed()
- {
- viewport.setShowGroupConservation(showGroupConservation.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
- * .event.ActionEvent)
- */
- protected void showConsensusHistogram_actionPerformed()
- {
- viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
- * .event.ActionEvent)
- */
- protected void showSequenceLogo_actionPerformed()
- {
- viewport.setShowSequenceLogo(showSequenceLogo.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- protected void normSequenceLogo_actionPerformed()
- {
- showSequenceLogo.setState(true);
- viewport.setShowSequenceLogo(true);
- viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- protected void applyAutoAnnotationSettings_actionPerformed()
- {
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- protected void makeGrpsFromSelection_actionPerformed()
- {
- if (viewport.getSelectionGroup() != null)
- {
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- // set view properties for each group
- for (int g = 0; g < gps.length; g++)
- {
- // gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
- viewport.setSequenceColour(sq, col);
- }
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
- }
- }
-
- protected void deleteGroups_actionPerformed()
- {
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
-
- alignPanel.paintAlignment(true);
- }
-
- public void selectAllSequenceMenuItem_actionPerformed()
- {
- SequenceGroup sg = new SequenceGroup();
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
- sg.setEndRes(viewport.getAlignment().getWidth() - 1);
- viewport.setSelectionGroup(sg);
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- public void deselectAllSequenceMenuItem_actionPerformed()
- {
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.keyboardNo1 = null;
- alignPanel.seqPanel.keyboardNo2 = null;
- }
- viewport.setSelectionGroup(null);
- viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
- alignPanel.idPanel.idCanvas.searchResults = null;
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- public void invertSequenceMenuItem_actionPerformed()
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
- }
-
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- public void invertColSel_actionPerformed()
- {
- viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- void trimAlignment(boolean trimLeft)
- {
- ColumnSelection colSel = viewport.getColumnSelection();
- int column;
-
- if (colSel.size() > 0)
- {
- if (trimLeft)
- {
- column = colSel.getMin();
- }
- else
- {
- column = colSel.getMax();
- }
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
- }
- else
- {
- seqs = viewport.getAlignment().getSequencesArray();
- }
-
- TrimRegionCommand trimRegion;
- if (trimLeft)
- {
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
- viewport.setStartRes(0);
- }
- else
- {
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
- }
-
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
-
- addHistoryItem(trimRegion);
-
- for (SequenceGroup sg : viewport.getAlignment().getGroups())
- {
- if ((trimLeft && !sg.adjustForRemoveLeft(column))
- || (!trimLeft && !sg.adjustForRemoveRight(column)))
- {
- viewport.getAlignment().deleteGroup(sg);
- }
- }
-
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
- }
- }
-
- public void removeGappedColumnMenuItem_actionPerformed()
- {
- int start = 0, end = viewport.getAlignment().getWidth() - 1;
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
- start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes();
- }
- else
- {
- seqs = viewport.getAlignment().getSequencesArray();
- }
-
- RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
- "Remove Gapped Columns", seqs, start, end,
- viewport.getAlignment());
-
- addHistoryItem(removeGapCols);
-
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
-
- // This is to maintain viewport position on first residue
- // of first sequence
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
- // ShiftList shifts;
- // viewport.getAlignment().removeGaps(shifts=new ShiftList());
- // edit.alColumnChanges=shifts.getInverse();
- // if (viewport.hasHiddenColumns)
- // viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- }
-
- public void removeAllGapsMenuItem_actionPerformed()
- {
- int start = 0, end = viewport.getAlignment().getWidth() - 1;
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
- start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes();
- }
- else
- {
- seqs = viewport.getAlignment().getSequencesArray();
- }
-
- // This is to maintain viewport position on first residue
- // of first sequence
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
-
- addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- viewport.getAlignment()));
-
- viewport.setStartRes(seq.findIndex(startRes) - 1);
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- }
-
- public void findMenuItem_actionPerformed()
- {
- new Finder(alignPanel);
- }
-
- /**
- * create a new view derived from the current view
- *
- * @param viewtitle
- * @return frame for the new view
- */
- public AlignFrame newView(String viewtitle)
- {
- AlignmentI newal;
- if (viewport.hasHiddenRows())
- {
- newal = new Alignment(viewport.getAlignment().getHiddenSequences()
- .getFullAlignment().getSequencesArray());
- }
- else
- {
- newal = new Alignment(viewport.getAlignment().getSequencesArray());
- }
-
- if (viewport.getAlignment().getAlignmentAnnotation() != null)
- {
- for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
- {
- if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
- {
- newal.addAnnotation(viewport.getAlignment()
- .getAlignmentAnnotation()[i]);
- }
- }
- }
-
- AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
-
- newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
- PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
- PaintRefresher.Register(newaf.alignPanel,
- newaf.alignPanel.av.getSequenceSetId());
-
- PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
- newaf.alignPanel.av.getSequenceSetId());
- PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
- newaf.alignPanel.av.getSequenceSetId());
-
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
- int viewSize = -1;
- for (int i = 0; i < comps.size(); i++)
- {
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- viewSize++;
- }
- }
-
- String title = new String(this.getTitle());
- if (viewtitle != null)
- {
- title = viewtitle + " ( " + title + ")";
- }
- else
- {
- if (title.indexOf("(View") > -1)
- {
- title = title.substring(0, title.indexOf("(View"));
- }
- title += "(View " + viewSize + ")";
- }
-
- newaf.setTitle(title.toString());
-
- newaf.viewport.historyList = viewport.historyList;
- newaf.viewport.redoList = viewport.redoList;
- return newaf;
- }
-
- /**
- *
- * @return list of feature groups on the view
- */
- public String[] getFeatureGroups()
- {
- FeatureRenderer fr = null;
- if (alignPanel != null
- && (fr = alignPanel.getFeatureRenderer()) != null)
- {
- return fr.getGroups();
- }
- return null;
- }
-
- /**
- * get sequence feature groups that are hidden or shown
- *
- * @param visible
- * true is visible
- * @return list
- */
- public String[] getFeatureGroupsOfState(boolean visible)
- {
- FeatureRenderer fr = null;
- if (alignPanel != null
- && (fr = alignPanel.getFeatureRenderer()) != null)
- {
- return fr.getGroups(visible);
- }
- return null;
- }
-
- /**
- * Change the display state for the given feature groups
- *
- * @param groups
- * list of group strings
- * @param state
- * visible or invisible
- */
- public void setFeatureGroupState(String[] groups, boolean state)
- {
- FeatureRenderer fr = null;
- this.sequenceFeatures.setState(true);
- viewport.showSequenceFeatures(true);
- if (alignPanel != null
- && (fr = alignPanel.getFeatureRenderer()) != null)
- {
- fr.setGroupState(groups, state);
- alignPanel.seqPanel.seqCanvas.repaint();
- if (alignPanel.overviewPanel != null)
- {
- alignPanel.overviewPanel.updateOverviewImage();
- }
- }
- }
-
- public void seqLimits_itemStateChanged()
- {
- viewport.setShowJVSuffix(seqLimits.getState());
- alignPanel.fontChanged();
- alignPanel.paintAlignment(true);
- }
-
- protected void colourTextMenuItem_actionPerformed()
- {
- viewport.setColourText(colourTextMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- protected void displayNonconservedMenuItem_actionPerformed()
- {
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- protected void wrapMenuItem_actionPerformed()
- {
- viewport.setWrapAlignment(wrapMenuItem.getState());
- alignPanel.setWrapAlignment(wrapMenuItem.getState());
- scaleAbove.setEnabled(wrapMenuItem.getState());
- scaleLeft.setEnabled(wrapMenuItem.getState());
- scaleRight.setEnabled(wrapMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- public void overviewMenuItem_actionPerformed()
- {
- if (alignPanel.overviewPanel != null)
- {
- return;
- }
-
- Frame frame = new Frame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
- frame.add(overview);
- // +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
- overview.getPreferredSize().width,
- overview.getPreferredSize().height + 50);
-
- frame.pack();
- final AlignmentPanel ap = alignPanel;
- frame.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent e)
- {
- if (ap != null)
- {
- ap.setOverviewPanel(null);
- }
- };
- });
-
- alignPanel.setOverviewPanel(overview);
-
- }
-
- void changeColour(ColourSchemeI cs)
- {
- int threshold = 0;
-
- if (cs != null)
- {
- if (viewport.getAbovePIDThreshold())
- {
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
-
- Alignment al = (Alignment) viewport.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
-
- }
- else
- {
- cs.setConservation(null);
- }
-
- cs.setConsensus(viewport.getSequenceConsensusHash());
-
- }
- viewport.setGlobalColourScheme(cs);
-
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
-
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(viewport.applet)
- .sequenceColoursChanged(alignPanel);
-
- alignPanel.paintAlignment(true);
- }
-
- protected void modifyPID_actionPerformed()
- {
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
- }
-
- protected void modifyConservation_actionPerformed()
- {
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showConservationSlider();
- }
- }
-
- protected void conservationMenuItem_actionPerformed()
- {
- viewport.setConservationSelected(conservationMenuItem.getState());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setState(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyConservation_actionPerformed();
- }
-
- public void abovePIDThreshold_actionPerformed()
- {
- viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
- conservationMenuItem.setState(false);
- viewport.setConservationSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed();
- }
-
- public void sortPairwiseMenuItem_actionPerformed()
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
-
- addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- public void sortIDMenuItem_actionPerformed()
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- public void sortLengthMenuItem_actionPerformed()
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByLength(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Length Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- public void sortGroupMenuItem_actionPerformed()
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByGroup(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
-
- }
-
- public void removeRedundancyMenuItem_actionPerformed()
- {
- new RedundancyPanel(alignPanel);
- }
-
- public void pairwiseAlignmentMenuItem_actionPerformed()
- {
- if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() > 1)
- {
- Frame frame = new Frame();
- frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
- 500);
- }
- }
-
- public void PCAMenuItem_actionPerformed()
- {
- // are the sequences aligned?
- if (!viewport.getAlignment().isAligned(false))
- {
- SequenceI current;
- int Width = viewport.getAlignment().getWidth();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- current = viewport.getAlignment().getSequenceAt(i);
-
- if (current.getLength() < Width)
- {
- current.insertCharAt(Width - 1, viewport.getGapCharacter());
- }
- }
- alignPanel.paintAlignment(true);
- }
-
- if ((viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() < 4 && viewport
- .getSelectionGroup().getSize() > 0)
- || viewport.getAlignment().getHeight() < 4)
- {
- return;
- }
-
- try
- {
- new PCAPanel(viewport);
- } catch (java.lang.OutOfMemoryError ex)
- {
- }
-
- }
-
- public void averageDistanceTreeMenuItem_actionPerformed()
- {
- NewTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- public void neighbourTreeMenuItem_actionPerformed()
- {
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
- protected void njTreeBlosumMenuItem_actionPerformed()
- {
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed()
- {
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- void NewTreePanel(String type, String pwType, String title)
- {
- // are the sequences aligned?
- if (!viewport.getAlignment().isAligned(false))
- {
- SequenceI current;
- int Width = viewport.getAlignment().getWidth();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- current = viewport.getAlignment().getSequenceAt(i);
-
- if (current.getLength() < Width)
- {
- current.insertCharAt(Width - 1, viewport.getGapCharacter());
- }
- }
- alignPanel.paintAlignment(true);
-
- }
-
- if ((viewport.getSelectionGroup() != null && viewport
- .getSelectionGroup().getSize() > 1)
- || (viewport.getAlignment().getHeight() > 1))
- {
- final TreePanel tp = new TreePanel(alignPanel, type, pwType);
-
- addTreeMenuItem(tp, title);
-
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
- }
- }
-
- void loadTree_actionPerformed()
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your Newick tree file here.");
- cap.setTreeImport();
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
- }
-
- public void loadTree(jalview.io.NewickFile tree, String treeFile)
- {
- TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
- addTreeMenuItem(tp, treeFile);
- }
-
- /**
- * sort the alignment using the given treePanel
- *
- * @param treePanel
- * tree used to sort view
- * @param title
- * string used for undo event name
- */
- public void sortByTree(TreePanel treePanel, String title)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter
- .sortByTree(viewport.getAlignment(), treePanel.getTree());
- // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- // HistoryItem.SORT));
- addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * Do any automatic reordering of the alignment and add the necessary bits to
- * the menu structure for the new tree
- *
- * @param treePanel
- * @param title
- */
- protected void addTreeMenuItem(final TreePanel treePanel,
- final String title)
- {
- final MenuItem item = new MenuItem(title);
- sortByTreeMenu.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- sortByTree(treePanel, title); // treePanel.getTitle());
- }
- });
-
- treePanel.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowOpened(WindowEvent e)
- {
- if (viewport.sortByTree)
- {
- sortByTree(treePanel, title);
- }
- super.windowOpened(e);
- }
-
- @Override
- public void windowClosing(WindowEvent e)
- {
- sortByTreeMenu.remove(item);
- };
- });
- }
-
- public boolean sortBy(AlignmentOrder alorder, String undoname)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- if (viewport.applet.debug)
- {
- System.err.println("Sorting " + alorder.getOrder().size()
- + " in alignment '" + getTitle() + "'");
- }
- AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
- if (undoname != null)
- {
- addHistoryItem(new OrderCommand(undoname, oldOrder,
- viewport.getAlignment()));
- }
- alignPanel.paintAlignment(true);
- return true;
- }
-
- protected void documentation_actionPerformed()
- {
- alignPanel.av.applet.openJalviewHelpUrl();
- }
-
- protected void about_actionPerformed()
- {
-
- class AboutPanel extends Canvas
- {
- String version;
-
- String builddate;
-
- public AboutPanel(String version, String builddate)
- {
- this.version = version;
- this.builddate = builddate;
- }
-
- @Override
- public void paint(Graphics g)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getSize().width, getSize().height);
- g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- FontMetrics fm = g.getFontMetrics();
- int fh = fm.getHeight();
- int y = 5, x = 7;
- g.setColor(Color.black);
- // TODO: update this text for each release or centrally store it for
- // lite and application
- g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString("JalviewLite - Release " + version, x, y += fh);
- g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString("Build date: " + builddate, x, y += fh);
- g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString(
- "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
- x, y += fh * 1.5);
- g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
- g.drawString(
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
- x, y += fh);
- g.drawString(
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
- x, y += fh);
- g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
- g.drawString(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
- x, y += fh);
- g.drawString(
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
- x, y += fh);
- g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
- x, y += fh);
- }
- }
-
- Frame frame = new Frame();
- frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
- .getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
-
- }
-
- public void showURL(String url, String target)
- {
- if (viewport.applet == null)
- {
- System.out.println("Not running as applet - no browser available.");
- }
- else
- {
- viewport.applet.showURL(url, target);
- }
- }
-
- // ////////////////////////////////////////////////////////////////////////////////
- // JBuilder Graphics here
-
- MenuBar alignFrameMenuBar = new MenuBar();
-
- Menu fileMenu = new Menu("File");
-
- MenuItem loadApplication = new MenuItem("View in Full Application");
-
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");
-
- MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
-
- MenuItem outputFeatures = new MenuItem("Export Features ...");
-
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
-
- MenuItem closeMenuItem = new MenuItem("Close");
-
- Menu editMenu = new Menu("Edit");
-
- Menu viewMenu = new Menu("View");
-
- Menu colourMenu = new Menu("Colour");
-
- Menu calculateMenu = new Menu("Calculate");
-
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
-
- MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
-
- MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
-
- MenuItem remove2LeftMenuItem = new MenuItem();
-
- MenuItem remove2RightMenuItem = new MenuItem();
-
- MenuItem removeGappedColumnMenuItem = new MenuItem();
-
- MenuItem removeAllGapsMenuItem = new MenuItem();
-
- CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
-
- CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
-
- MenuItem sortPairwiseMenuItem = new MenuItem();
-
- MenuItem sortIDMenuItem = new MenuItem();
-
- MenuItem sortLengthMenuItem = new MenuItem();
-
- MenuItem sortGroupMenuItem = new MenuItem();
-
- MenuItem removeRedundancyMenuItem = new MenuItem();
-
- MenuItem pairwiseAlignmentMenuItem = new MenuItem();
-
- MenuItem PCAMenuItem = new MenuItem();
-
- MenuItem averageDistanceTreeMenuItem = new MenuItem();
-
- MenuItem neighbourTreeMenuItem = new MenuItem();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- public Label statusBar = new Label();
-
- Menu outputTextboxMenu = new Menu();
-
- MenuItem clustalColour = new MenuItem();
-
- MenuItem zappoColour = new MenuItem();
-
- MenuItem taylorColour = new MenuItem();
-
- MenuItem hydrophobicityColour = new MenuItem();
-
- MenuItem helixColour = new MenuItem();
-
- MenuItem strandColour = new MenuItem();
-
- MenuItem turnColour = new MenuItem();
-
- MenuItem buriedColour = new MenuItem();
-
- MenuItem purinePyrimidineColour = new MenuItem();
-
- MenuItem RNAHelixColour = new MenuItem();
-
- MenuItem userDefinedColour = new MenuItem();
-
- MenuItem PIDColour = new MenuItem();
-
- MenuItem BLOSUM62Colour = new MenuItem();
-
- MenuItem tcoffeeColour = new MenuItem();
-
- MenuItem njTreeBlosumMenuItem = new MenuItem();
-
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
-
- CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
-
- CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
-
- CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
-
- MenuItem alProperties = new MenuItem("Alignment Properties...");
-
- MenuItem overviewMenuItem = new MenuItem();
-
- MenuItem undoMenuItem = new MenuItem();
-
- MenuItem redoMenuItem = new MenuItem();
-
- CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
-
- MenuItem noColourmenuItem = new MenuItem();
-
- CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
-
- CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
-
- MenuItem findMenuItem = new MenuItem();
-
- CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
-
- MenuItem nucleotideColour = new MenuItem();
-
- MenuItem deleteGroups = new MenuItem();
-
- MenuItem grpsFromSelection = new MenuItem();
-
- MenuItem delete = new MenuItem();
-
- MenuItem copy = new MenuItem();
-
- MenuItem cut = new MenuItem();
-
- Menu pasteMenu = new Menu();
-
- MenuItem pasteNew = new MenuItem();
-
- MenuItem pasteThis = new MenuItem();
-
- CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
-
- MenuItem font = new MenuItem();
-
- CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
-
- CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
-
- CheckboxMenuItem scaleRight = new CheckboxMenuItem();
-
- MenuItem modifyPID = new MenuItem();
-
- MenuItem modifyConservation = new MenuItem();
-
- CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
- "Autocalculate Consensus", true);
-
- 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 seqLimits = new CheckboxMenuItem();
-
- CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-
- CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
-
- Menu autoAnnMenu = new Menu();
-
- CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
-
- CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
-
- CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
-
- CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
-
- CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
-
- CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
-
- private void jbInit() throws Exception
- {
-
- setMenuBar(alignFrameMenuBar);
-
- MenuItem item;
-
- // dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
- {
-
- item = new MenuItem(
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
-
- item.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- outputText_actionPerformed(e);
- }
- });
-
- outputTextboxMenu.add(item);
- }
- 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);
- remove2LeftMenuItem.setLabel("Remove Left");
- remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
- remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
- removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
- removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
- sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel("by Length");
- sortLengthMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel("by Group");
- sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");
- removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
- pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel("Principal Component Analysis");
- PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem
- .setLabel("Average Distance Using % Identity");
- averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
- neighbourTreeMenuItem.addActionListener(this);
- statusBar.setBackground(Color.white);
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText("Status bar");
- outputTextboxMenu.setLabel("Output to Textbox");
- clustalColour.setLabel("Clustalx");
-
- clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
- zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
- taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
- hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
- helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
- strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
- turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
- buriedColour.addActionListener(this);
- purinePyrimidineColour.setLabel("Purine/Pyrimidine");
- purinePyrimidineColour.addActionListener(this);
- RNAHelixColour.setLabel("by RNA Helices");
- RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
- userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62 Score");
- BLOSUM62Colour.addActionListener(this);
- tcoffeeColour.setLabel("T-Coffee Scores");
- tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
- // provided
- tcoffeeColour.addActionListener(this);
- avDistanceTreeBlosumMenuItem
- .setLabel("Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
- njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel("Show Annotations");
- annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel("Colour Text");
- colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel("Show nonconserved");
- displayNonconservedMenuItem.addItemListener(this);
- alProperties.addActionListener(this);
- overviewMenuItem.setLabel("Overview Window");
- overviewMenuItem.addActionListener(this);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
- conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("None");
- noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel("Wrap");
- wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("Find...");
- findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel("Above Identity Threshold");
- abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
- nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
- deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel("Make Groups for selection");
- grpsFromSelection.addActionListener(this);
- copy.setLabel("Copy");
- copy.addActionListener(this);
- cut.setLabel("Cut");
- cut.addActionListener(this);
- delete.setLabel("Delete");
- delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
- pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
- pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
- font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
- scaleAbove.setState(true);
- scaleAbove.setEnabled(false);
- scaleAbove.addItemListener(this);
- scaleLeft.setEnabled(false);
- scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
- scaleLeft.addItemListener(this);
- scaleRight.setEnabled(false);
- scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
- scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
- modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
- modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
- autoCalculate.addItemListener(this);
- sortByTree.addItemListener(this);
- inputText.setLabel("Input from textbox");
- inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel("Centre column labels");
- centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel("Automatic Scrolling");
- followMouseOverFlag.addItemListener(this);
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
- documentation.addActionListener(this);
-
- about.setLabel("About...");
- about.addActionListener(this);
- seqLimits.setState(true);
- seqLimits.setLabel("Show Sequence Limits");
- seqLimits.addItemListener(this);
- featureSettings.setLabel("Feature Settings...");
- featureSettings.addActionListener(this);
- sequenceFeatures.setLabel("Sequence Features");
- sequenceFeatures.addItemListener(this);
- sequenceFeatures.setState(false);
- annotationColour.setLabel("by Annotation...");
- annotationColour.addActionListener(this);
- invertSequenceMenuItem.setLabel("Invert Sequence Selection");
- invertColSel.setLabel("Invert Column Selection");
- menu1.setLabel("Show");
- showColumns.setLabel("All Columns ");
- showSeqs.setLabel("All Sequences");
- menu2.setLabel("Hide");
- hideColumns.setLabel("Selected Columns");
- hideSequences.setLabel("Selected Sequences");
- hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
- hideAllSelection.setLabel("Selected Region");
- showAllHidden.setLabel("All Sequences and Columns");
- showGroupConsensus.setLabel("Group Consensus");
- showGroupConservation.setLabel("Group Conservation");
- showConsensusHistogram.setLabel("Show Consensus Histogram");
- showSequenceLogo.setLabel("Show Consensus Logo");
- normSequenceLogo.setLabel("Normalise Consensus Logo");
- applyAutoAnnotationSettings.setLabel("Apply to all groups");
- applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel("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);
- showGroupConsensus.addItemListener(this);
- showGroupConservation.addItemListener(this);
- showConsensusHistogram.addItemListener(this);
- showSequenceLogo.addItemListener(this);
- normSequenceLogo.addItemListener(this);
-
- applyAutoAnnotationSettings.addItemListener(this);
- formatMenu.setLabel("Format");
- selectMenu.setLabel("Select");
- newView.setLabel("New View");
- newView.addActionListener(this);
- alignFrameMenuBar.add(fileMenu);
- alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(selectMenu);
- alignFrameMenuBar.add(viewMenu);
- alignFrameMenuBar.add(formatMenu);
- alignFrameMenuBar.add(colourMenu);
- alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(helpMenu);
-
- 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);
-
- editMenu.add(undoMenuItem);
- editMenu.add(redoMenuItem);
- editMenu.add(cut);
- editMenu.add(copy);
- editMenu.add(pasteMenu);
- editMenu.add(delete);
- editMenu.addSeparator();
- editMenu.add(remove2LeftMenuItem);
- editMenu.add(remove2RightMenuItem);
- editMenu.add(removeGappedColumnMenuItem);
- editMenu.add(removeAllGapsMenuItem);
- editMenu.add(removeRedundancyMenuItem);
- viewMenu.add(newView);
- viewMenu.addSeparator();
- viewMenu.add(menu1);
- viewMenu.add(menu2);
- 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.addSeparator();
- viewMenu.add(alProperties);
- viewMenu.addSeparator();
- viewMenu.add(overviewMenuItem);
- colourMenu.add(applyToAllGroups);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideColour);
- colourMenu.add(purinePyrimidineColour);
- colourMenu.add(tcoffeeColour);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
- colourMenu.add(RNAHelixColour);
- calculateMenu.add(sort);
- calculateMenu.add(calculate);
- 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);
- 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(grpsFromSelection);
- selectMenu.add(deleteGroups);
-
- }
-
- MenuItem featureSettings = new MenuItem();
-
- CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
-
- MenuItem annotationColour = new MenuItem();
-
- 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 hideAllButSelection = new MenuItem();
-
- MenuItem hideAllSelection = new MenuItem();
-
- MenuItem showAllHidden = new MenuItem();
-
- Menu formatMenu = new Menu();
-
- Menu selectMenu = new Menu();
-
- MenuItem newView = new MenuItem();
-
- /**
- * Attach the alignFrame panels after embedding menus, if necessary. This used
- * to be called setEmbedded, but is now creates the dropdown menus in a
- * platform independent manner to avoid OSX/Mac menu appendage daftness.
- *
- * @param reallyEmbedded
- * 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)
- {
- 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, 10, 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();
- }
- else
- {
- // //////
- // test and embed menu bar if necessary.
- //
- if (embedMenuIfNeeded(alignPanel))
- {
- // adjust for status bar height too
- alignPanel.setSize(getSize().width, getSize().height
- - statusBar.HEIGHT);
- }
- 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,
- DEFAULT_HEIGHT);
- }
- }
-
- /**
- * 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
- * structures in the original jmol window. Note This method doesn't work
- * without an additional javascript library to exchange messages between the
- * distinct applets. See http://issues.jalview.org/browse/JAL-621
- *
- * @param viewer
- * JmolViewer instance
- * @param sequenceIds
- * - sequence Ids to search for associations
- */
- public SequenceStructureBinding addStructureViewInstance(
- Object jmolviewer, String[] sequenceIds)
- {
- org.jmol.api.JmolViewer viewer = null;
- try
- {
- viewer = (org.jmol.api.JmolViewer) jmolviewer;
- } catch (ClassCastException ex)
- {
- System.err.println("Unsupported viewer object :"
- + jmolviewer.getClass());
- }
- if (viewer == null)
- {
- System.err.println("Can't use this object as a structure viewer:"
- + jmolviewer.getClass());
- return null;
- }
- SequenceI[] seqs = null;
- if (sequenceIds == null || sequenceIds.length == 0)
- {
- seqs = viewport.getAlignment().getSequencesArray();
- }
- else
- {
- Vector sqi = new Vector();
- AlignmentI al = viewport.getAlignment();
- for (int sid = 0; sid < sequenceIds.length; sid++)
- {
- SequenceI sq = al.findName(sequenceIds[sid]);
- if (sq != null)
- {
- sqi.addElement(sq);
- }
- }
- if (sqi.size() > 0)
- {
- seqs = new SequenceI[sqi.size()];
- for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
- {
- seqs[sid] = (SequenceI) sqi.elementAt(sid);
- }
- }
- else
- {
- return null;
- }
- }
- ExtJmol jmv = null;
- // TODO: search for a jmv that involves viewer
- if (jmv == null)
- { // create a new viewer/jalview binding.
- jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
- { seqs });
- }
- return jmv;
-
- }
-
- /**
- * bind a pdb file to a sequence in the current view
- *
- * @param sequenceId
- * - sequenceId within the dataset.
- * @param pdbEntryString
- * - the short name for the PDB file
- * @param pdbFile
- * - pdb file - either a URL or a valid PDB file.
- * @return true if binding was as success TODO: consider making an exception
- * structure for indicating when PDB parsing or sequenceId location
- * fails.
- */
- public boolean addPdbFile(String sequenceId, String pdbEntryString,
- String pdbFile)
- {
- SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
- boolean needtoadd = false;
- if (toaddpdb != null)
- {
- Vector pdbe = toaddpdb.getPDBId();
- PDBEntry pdbentry = null;
- if (pdbe != null && pdbe.size() > 0)
- {
- for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
- {
- pdbentry = (PDBEntry) pdbe.elementAt(pe);
- if (!pdbentry.getId().equals(pdbEntryString)
- && !pdbentry.getFile().equals(pdbFile))
- {
- pdbentry = null;
- }
- else
- {
- continue;
- }
- }
- }
- if (pdbentry == null)
- {
- pdbentry = new PDBEntry();
- pdbentry.setId(pdbEntryString);
- pdbentry.setFile(pdbFile);
- needtoadd = true; // add this new entry to sequence.
- }
- // resolve data source
- // TODO: this code should be a refactored to an io package
- String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
- if (protocol == null)
- {
- return false;
- }
- if (needtoadd)
- {
- // make a note of the access mode and add
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable());
- }
- pdbentry.getProperty().put("protocol", protocol);
- toaddpdb.addPDBId(pdbentry);
- }
- }
- return true;
- }
-
- private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
- {
- if (seqs != null)
- {
- Vector sequences = new Vector();
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- sequences.addElement(new Object[]
- { seqs[i], (chains != null) ? chains[i] : null });
- }
- }
- seqs = new SequenceI[sequences.size()];
- chains = new String[sequences.size()];
- for (int i = 0, isize = sequences.size(); i < isize; i++)
- {
- Object[] oj = (Object[]) sequences.elementAt(i);
-
- seqs[i] = (SequenceI) oj[0];
- chains[i] = (String) oj[1];
- }
- }
- return new Object[]
- { seqs, chains };
-
- }
-
- public void newStructureView(JalviewLite applet, PDBEntry pdb,
- SequenceI[] seqs, String[] chains, String protocol)
- {
- // Scrub any null sequences from the array
- Object[] sqch = cleanSeqChainArrays(seqs, chains);
- seqs = (SequenceI[]) sqch[0];
- chains = (String[]) sqch[1];
- if (seqs == null || seqs.length == 0)
- {
- System.err
- .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
- }
- if (protocol == null || protocol.trim().length() == 0
- || protocol.equals("null"))
- {
- protocol = (String) pdb.getProperty().get("protocol");
- if (protocol == null)
- {
- System.err.println("Couldn't work out protocol to open structure: "
- + pdb.getId());
- return;
- }
- }
- if (applet.useXtrnalSviewer)
- {
- // register the association(s) and quit, don't create any windows.
- if (StructureSelectionManager.getStructureSelectionManager(applet)
- .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
- {
- System.err.println("Failed to map " + pdb.getFile() + " ("
- + protocol + ") to any sequences");
- }
- return;
- }
- if (applet.isAlignPdbStructures() && applet.jmolAvailable)
- {
- // can only do alignments with Jmol
- // find the last jmol window assigned to this alignment
- jalview.appletgui.AppletJmol ajm = null, tajm;
- Vector jmols = applet
- .getAppletWindow(jalview.appletgui.AppletJmol.class);
- for (int i = 0, iSize = jmols.size(); i < iSize; i++)
- {
- tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
- if (tajm.ap.alignFrame == this)
- {
- ajm = tajm;
- break;
- }
- }
- if (ajm != null)
- {
- System.err
- .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
- // try and add the pdb structure
- // ajm.addS
- ajm = null;
- }
- }
- // otherwise, create a new window
- if (applet.jmolAvailable)
- {
- new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
- protocol);
- applet.lastFrameX += 40;
- applet.lastFrameY += 40;
- }
- else
- {
- new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
- }
-
- }
-
- public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
- SequenceI[][] seqs, String[][] chains, String[] protocols)
- {
- // TODO Auto-generated method stub
- System.err.println("Aligned Structure View: Not yet implemented.");
- }
-
- /**
- * modify the current selection, providing the user has not made a selection
- * already.
- *
- * @param sel
- * - sequences from this alignment
- * @param csel
- * - columns to be selected on the alignment
- */
- public void select(SequenceGroup sel, ColumnSelection csel)
- {
- alignPanel.seqPanel.selection(sel, csel, null);
- }
-
- public void scrollTo(int row, int column)
- {
- alignPanel.seqPanel.scrollTo(row, column);
- }
-
- public void scrollToRow(int row)
- {
- alignPanel.seqPanel.scrollToRow(row);
- }
-
- public void scrollToColumn(int column)
- {
- alignPanel.seqPanel.scrollToColumn(column);
- }
-
- /**
- * @return the alignments unique ID.
- */
- public String getSequenceSetId()
- {
- return viewport.getSequenceSetId();
- }
-
- /**
- * Load the (T-Coffee) score file from the specified url
- *
- * @param source
- * File/URL/T-COFFEE score file contents
- * @throws IOException
- * @return true if alignment was annotated with data from source
- */
- public boolean loadScoreFile(String source) throws IOException
- {
-
- TCoffeeScoreFile file = new TCoffeeScoreFile(source,
- AppletFormatAdapter.checkProtocol(source));
- if (!file.isValid())
- {
- // TODO: raise dialog for gui
- System.err.println("Problems parsing T-Coffee scores: "
- + file.getWarningMessage());
- System.err.println("Origin was:\n" + source);
- return false;
- }
-
- /*
- * check that the score matrix matches the alignment dimensions
- */
- AlignmentI aln;
- if ((aln = viewport.getAlignment()) != null
- && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
- .getWidth()))
- {
- // TODO: raise a dialog box here rather than bomb out.
- System.err
- .println("The scores matrix does not match the alignment dimensions");
-
- }
-
- // TODO add parameter to indicate if matching should be done
- if (file.annotateAlignment(alignPanel.getAlignment(), false))
- {
- alignPanel.fontChanged();
- tcoffeeColour.setEnabled(true);
- // switch to this color
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
- return true;
- }
- else
- {
- System.err.println("Problems resolving T-Coffee scores:");
- if (file.getWarningMessage() != null)
- {
- System.err.println(file.getWarningMessage());
- }
- }
- return false;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.analysis.AAFrequency;\r
+import jalview.analysis.AlignmentSorter;\r
+import jalview.analysis.Conservation;\r
+import jalview.api.SequenceStructureBinding;\r
+import jalview.bin.JalviewLite;\r
+import jalview.commands.CommandI;\r
+import jalview.commands.EditCommand;\r
+import jalview.commands.OrderCommand;\r
+import jalview.commands.RemoveGapColCommand;\r
+import jalview.commands.RemoveGapsCommand;\r
+import jalview.commands.SlideSequencesCommand;\r
+import jalview.commands.TrimRegionCommand;\r
+import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentOrder;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceCollectionI;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.io.AnnotationFile;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.FeaturesFile;\r
+import jalview.io.TCoffeeScoreFile;\r
+import jalview.schemes.Blosum62ColourScheme;\r
+import jalview.schemes.BuriedColourScheme;\r
+import jalview.schemes.ClustalxColourScheme;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.schemes.HelixColourScheme;\r
+import jalview.schemes.HydrophobicColourScheme;\r
+import jalview.schemes.NucleotideColourScheme;\r
+import jalview.schemes.PIDColourScheme;\r
+import jalview.schemes.PurinePyrimidineColourScheme;\r
+import jalview.schemes.RNAHelicesColourChooser;\r
+import jalview.schemes.RNAInteractionColourScheme;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.schemes.StrandColourScheme;\r
+import jalview.schemes.TCoffeeColourScheme;\r
+import jalview.schemes.TaylorColourScheme;\r
+import jalview.schemes.TurnColourScheme;\r
+import jalview.schemes.ZappoColourScheme;\r
+import jalview.structure.StructureSelectionManager;\r
+\r
+import java.awt.BorderLayout;\r
+import java.awt.Canvas;\r
+import java.awt.CheckboxMenuItem;\r
+import java.awt.Color;\r
+import java.awt.Font;\r
+import java.awt.FontMetrics;\r
+import java.awt.Frame;\r
+import java.awt.Graphics;\r
+import java.awt.Label;\r
+import java.awt.Menu;\r
+import java.awt.MenuBar;\r
+import java.awt.MenuItem;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.FocusEvent;\r
+import java.awt.event.FocusListener;\r
+import java.awt.event.ItemEvent;\r
+import java.awt.event.ItemListener;\r
+import java.awt.event.KeyEvent;\r
+import java.awt.event.KeyListener;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.io.IOException;\r
+import java.net.URL;\r
+import java.net.URLEncoder;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.List;\r
+import java.util.StringTokenizer;\r
+import java.util.Vector;\r
+\r
+\r
+public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
+ ItemListener, KeyListener\r
+{\r
+ public AlignmentPanel alignPanel;\r
+\r
+ public AlignViewport viewport;\r
+\r
+ int DEFAULT_WIDTH = 700;\r
+\r
+ int DEFAULT_HEIGHT = 500;\r
+\r
+ String jalviewServletURL;\r
+\r
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
+ String title, boolean embedded)\r
+ {\r
+ if (applet != null)\r
+ {\r
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+ }\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ viewport = new AlignViewport(al, applet);\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+\r
+ viewport.updateConservation(alignPanel);\r
+ viewport.updateConsensus(alignPanel);\r
+\r
+ annotationPanelMenuItem.setState(viewport.showAnnotation);\r
+ displayNonconservedMenuItem.setState(viewport.getShowUnconserved());\r
+ followMouseOverFlag.setState(viewport.getFollowHighlight());\r
+ showGroupConsensus.setState(viewport.isShowGroupConsensus());\r
+ showGroupConservation.setState(viewport.isShowGroupConservation());\r
+ showConsensusHistogram.setState(viewport.isShowConsensusHistogram());\r
+ showSequenceLogo.setState(viewport.isShowSequenceLogo());\r
+ normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());\r
+\r
+ seqLimits.setState(viewport.showJVSuffix);\r
+\r
+ if (applet != null)\r
+ {\r
+ String param = applet.getParameter("sortBy");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("Id"))\r
+ {\r
+ sortIDMenuItem_actionPerformed();\r
+ }\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ }\r
+ else if (param.equalsIgnoreCase("Length"))\r
+ {\r
+ sortLengthMenuItem_actionPerformed();\r
+ }\r
+ }\r
+\r
+ param = applet.getParameter("wrap");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("true"))\r
+ {\r
+ wrapMenuItem.setState(true);\r
+ wrapMenuItem_actionPerformed();\r
+ }\r
+ }\r
+ param = applet.getParameter("centrecolumnlabels");\r
+ if (param != null)\r
+ {\r
+ centreColumnLabelFlag.setState(true);\r
+ centreColumnLabelFlag_stateChanged();\r
+ }\r
+ try\r
+ {\r
+ param = applet.getParameter("windowWidth");\r
+ if (param != null)\r
+ {\r
+ int width = Integer.parseInt(param);\r
+ DEFAULT_WIDTH = width;\r
+ }\r
+ param = applet.getParameter("windowHeight");\r
+ if (param != null)\r
+ {\r
+ int height = Integer.parseInt(param);\r
+ DEFAULT_HEIGHT = height;\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ }\r
+ if (viewport.getAlignment().isNucleotide())\r
+ {\r
+ viewport.updateStrucConsensus(alignPanel);\r
+ if (viewport.getAlignment().hasRNAStructure())\r
+ {\r
+ RNAHelixColour.setEnabled(true);\r
+ }\r
+ else\r
+ {\r
+ RNAHelixColour.setEnabled(false);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ RNAHelixColour.setEnabled(false);\r
+ purinePyrimidineColour.setEnabled(false);\r
+ }\r
+\r
+ // Some JVMS send keyevents to Top frame or lowest panel,\r
+ // Havent worked out why yet. So add to both this frame and seqCanvas for\r
+ // now\r
+ this.addKeyListener(this);\r
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+ alignPanel.idPanel.idCanvas.addKeyListener(this);\r
+ alignPanel.scalePanel.addKeyListener(this);\r
+ alignPanel.annotationPanel.addKeyListener(this);\r
+ alignPanel.annotationPanelHolder.addKeyListener(this);\r
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);\r
+ alignPanel.alabels.addKeyListener(this);\r
+ createAlignFrameWindow(embedded, title);\r
+\r
+ validate();\r
+ alignPanel.adjustAnnotationHeight();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public AlignViewport getAlignViewport()\r
+ {\r
+ return viewport;\r
+ }\r
+\r
+ public SeqCanvas getSeqcanvas()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas;\r
+ }\r
+\r
+ /**\r
+ * Load a features file onto the alignment\r
+ * \r
+ * @param file\r
+ * file URL, content, or other resolvable path\r
+ * @param type\r
+ * is protocol for accessing data referred to by file\r
+ */\r
+\r
+ public boolean parseFeaturesFile(String file, String type)\r
+ {\r
+ return parseFeaturesFile(file, type, true);\r
+ }\r
+\r
+ /**\r
+ * Load a features file onto the alignment\r
+ * \r
+ * @param file\r
+ * file URL, content, or other resolvable path\r
+ * @param type\r
+ * is protocol for accessing data referred to by file\r
+ * @param autoenabledisplay\r
+ * when true, display features flag will be automatically enabled if\r
+ * features are loaded\r
+ * @return true if data parsed as a features file\r
+ */\r
+ public boolean parseFeaturesFile(String file, String type,\r
+ boolean autoenabledisplay)\r
+ {\r
+ // TODO: test if importing a features file onto an alignment which already\r
+ // has features with links overwrites the original links.\r
+\r
+ Hashtable featureLinks = new Hashtable();\r
+ boolean featuresFile = false;\r
+ try\r
+ {\r
+ featuresFile = new jalview.io.FeaturesFile(file, type)\r
+ .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas\r
+ .getFeatureRenderer().featureColours, featureLinks,\r
+ true, viewport.applet.getDefaultParameter(\r
+ "relaxedidmatch", false));\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if (featuresFile)\r
+ {\r
+ if (featureLinks.size() > 0)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;\r
+ }\r
+ if (autoenabledisplay)\r
+ {\r
+ viewport.showSequenceFeatures = true;\r
+ sequenceFeatures.setState(true);\r
+ }\r
+ if (viewport.featureSettings != null)\r
+ {\r
+ viewport.featureSettings.refreshTable();\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ statusBar.setText("Successfully added features to alignment.");\r
+ }\r
+ return featuresFile;\r
+ }\r
+\r
+ @Override\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ if (viewport.cursorMode\r
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt\r
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt\r
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))\r
+ && Character.isDigit(evt.getKeyChar()))\r
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+\r
+ alignPanel.alabels.cancelDrag();\r
+ break;\r
+ case KeyEvent.VK_X:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (viewport.cursorMode && !evt.isControlDown())\r
+ {\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ if (evt.isControlDown())\r
+ {\r
+ paste(evt.isShiftDown());\r
+ }\r
+ break;\r
+ case KeyEvent.VK_A:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_DOWN:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0, 1);\r
+ }\r
+ else\r
+ {\r
+ moveSelectedSequences(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0, -1);\r
+ }\r
+ else\r
+ {\r
+ moveSelectedSequences(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_LEFT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor(-1, 0);\r
+ break;\r
+\r
+ case KeyEvent.VK_RIGHT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor(1, 0);\r
+ break;\r
+\r
+ case KeyEvent.VK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown() || evt.isAltDown());\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown() || evt.isAltDown());\r
+ }\r
+ else\r
+ {\r
+ cut_actionPerformed();\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_S:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Q:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F2:\r
+ viewport.cursorMode = !viewport.cursorMode;\r
+ statusBar.setText("Keyboard editing mode is "\r
+ + (viewport.cursorMode ? "on" : "off"));\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F:\r
+ if (evt.isControlDown())\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_H:\r
+ {\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
+ toggleHiddenRegions(toggleSeqs, toggleCols);\r
+ break;\r
+ }\r
+\r
+ case KeyEvent.VK_PAGE_UP:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(true);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+ - viewport.endSeq + viewport.startSeq);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_PAGE_DOWN:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(false);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+ + viewport.endSeq - viewport.startSeq);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Z:\r
+ if (evt.isControlDown())\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Y:\r
+ if (evt.isControlDown())\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_L:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_R:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_E:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isShiftDown())\r
+ {\r
+ this.removeAllGapsMenuItem_actionPerformed();\r
+ }\r
+ else\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ }\r
+ break;\r
+ case KeyEvent.VK_I:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown())\r
+ {\r
+ invertColSel_actionPerformed();\r
+ }\r
+ else\r
+ {\r
+ invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_U:\r
+ if (evt.isControlDown())\r
+ {\r
+ this.deleteGroups_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView(null);\r
+ }\r
+ break;\r
+\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * called by key handler and the hide all/show all menu items\r
+ * \r
+ * @param toggleSeqs\r
+ * @param toggleCols\r
+ */\r
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)\r
+ {\r
+ boolean hide = false;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (!toggleSeqs && !toggleCols)\r
+ {\r
+ // Hide everything by the current selection - this is a hack - we do the\r
+ // invert and then hide\r
+ // first check that there will be visible columns after the invert.\r
+ if ((viewport.getColumnSelection() != null\r
+ && viewport.getColumnSelection().getSelected() != null && viewport\r
+ .getColumnSelection().getSelected().size() > 0)\r
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg\r
+ .getEndRes()))\r
+ {\r
+ // now invert the sequence set, if required - empty selection implies\r
+ // that no hiding is required.\r
+ if (sg != null)\r
+ {\r
+ invertSequenceMenuItem_actionPerformed();\r
+ sg = viewport.getSelectionGroup();\r
+ toggleSeqs = true;\r
+\r
+ }\r
+ viewport.expandColSelection(sg, true);\r
+ // finally invert the column selection and get the new sequence\r
+ // selection and indicate it should be hidden.\r
+ invertColSel_actionPerformed();\r
+ toggleCols = true;\r
+ }\r
+ }\r
+\r
+ if (toggleSeqs)\r
+ {\r
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())\r
+ {\r
+ hide = true;\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()\r
+ .size() > 0))\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+ }\r
+\r
+ if (toggleCols)\r
+ {\r
+ if (viewport.getColumnSelection().getSelected().size() > 0)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ if (!toggleSeqs)\r
+ {\r
+ viewport.setSelectionGroup(sg);\r
+ }\r
+ }\r
+ else if (!hide)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ }\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void keyReleased(KeyEvent evt)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void keyTyped(KeyEvent evt)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (evt.getSource() == displayNonconservedMenuItem)\r
+ {\r
+ displayNonconservedMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == colourTextMenuItem)\r
+ {\r
+ colourTextMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == wrapMenuItem)\r
+ {\r
+ wrapMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == scaleAbove)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.getState());\r
+ }\r
+ else if (evt.getSource() == scaleLeft)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.getState());\r
+ }\r
+ else if (evt.getSource() == scaleRight)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.getState());\r
+ }\r
+ else if (evt.getSource() == seqLimits)\r
+ {\r
+ seqLimits_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == viewBoxesMenuItem)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == viewTextMenuItem)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == renderGapsMenuItem)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == annotationPanelMenuItem)\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == sequenceFeatures)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ else if (evt.getSource() == conservationMenuItem)\r
+ {\r
+ conservationMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == abovePIDThreshold)\r
+ {\r
+ abovePIDThreshold_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == applyToAllGroups)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
+ }\r
+ else if (evt.getSource() == autoCalculate)\r
+ {\r
+ viewport.autoCalculateConsensus = autoCalculate.getState();\r
+ }\r
+ else if (evt.getSource() == sortByTree)\r
+ {\r
+ viewport.sortByTree = sortByTree.getState();\r
+ }\r
+ else if (evt.getSource() == this.centreColumnLabelFlag)\r
+ {\r
+ centreColumnLabelFlag_stateChanged();\r
+ }\r
+ else if (evt.getSource() == this.followMouseOverFlag)\r
+ {\r
+ mouseOverFlag_stateChanged();\r
+ }\r
+ else if (evt.getSource() == showGroupConsensus)\r
+ {\r
+ showGroupConsensus_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showGroupConservation)\r
+ {\r
+ showGroupConservation_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showSequenceLogo)\r
+ {\r
+ showSequenceLogo_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == normSequenceLogo)\r
+ {\r
+ normSequenceLogo_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showConsensusHistogram)\r
+ {\r
+ showConsensusHistogram_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == applyAutoAnnotationSettings)\r
+ {\r
+ applyAutoAnnotationSettings_actionPerformed();\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ private void mouseOverFlag_stateChanged()\r
+ {\r
+ viewport.followHighlight = followMouseOverFlag.getState();\r
+ // TODO: could kick the scrollTo mechanism to reset view for current\r
+ // searchresults.\r
+ }\r
+\r
+ private void centreColumnLabelFlag_stateChanged()\r
+ {\r
+ viewport.centreColumnLabels = centreColumnLabelFlag.getState();\r
+ this.alignPanel.annotationPanel.repaint();\r
+ }\r
+\r
+ @Override\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ Object source = evt.getSource();\r
+\r
+ if (source == inputText)\r
+ {\r
+ inputText_actionPerformed();\r
+ }\r
+ else if (source == loadTree)\r
+ {\r
+ loadTree_actionPerformed();\r
+ }\r
+ else if (source == loadApplication)\r
+ {\r
+ launchFullApplication();\r
+ }\r
+ else if (source == loadAnnotations)\r
+ {\r
+ loadAnnotations();\r
+ }\r
+ else if (source == outputAnnotations)\r
+ {\r
+ outputAnnotations(true);\r
+ }\r
+ else if (source == outputFeatures)\r
+ {\r
+ outputFeatures(true, "Jalview");\r
+ }\r
+ else if (source == closeMenuItem)\r
+ {\r
+ closeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ else if (source == undoMenuItem)\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == redoMenuItem)\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == inputText)\r
+ {\r
+ inputText_actionPerformed();\r
+ }\r
+ else if (source == closeMenuItem)\r
+ {\r
+ closeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == undoMenuItem)\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == redoMenuItem)\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ else if (source == pasteNew)\r
+ {\r
+ pasteNew_actionPerformed();\r
+ }\r
+ else if (source == pasteThis)\r
+ {\r
+ pasteThis_actionPerformed();\r
+ }\r
+ else if (source == cut)\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ else if (source == delete)\r
+ {\r
+ delete_actionPerformed();\r
+ }\r
+ else if (source == grpsFromSelection)\r
+ {\r
+ makeGrpsFromSelection_actionPerformed();\r
+ }\r
+ else if (source == deleteGroups)\r
+ {\r
+ deleteGroups_actionPerformed();\r
+ }\r
+ else if (source == selectAllSequenceMenuItem)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == deselectAllSequenceMenuItem)\r
+ {\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == invertSequenceMenuItem)\r
+ {\r
+ invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == invertColSel)\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == remove2LeftMenuItem)\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ else if (source == remove2RightMenuItem)\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ else if (source == removeGappedColumnMenuItem)\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ else if (source == removeAllGapsMenuItem)\r
+ {\r
+ removeAllGapsMenuItem_actionPerformed();\r
+ }\r
+ else if (source == findMenuItem)\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ else if (source == font)\r
+ {\r
+ new FontChooser(alignPanel);\r
+ }\r
+ else if (source == newView)\r
+ {\r
+ newView(null);\r
+ }\r
+ else if (source == showColumns)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showSeqs)\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideColumns)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideSequences\r
+ && viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.hideAllSelectedSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideAllButSelection)\r
+ {\r
+ toggleHiddenRegions(false, false);\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideAllSelection)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ viewport.expandColSelection(sg, false);\r
+ viewport.hideAllSelectedSeqs();\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showAllHidden)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ viewport.showAllHiddenSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showGroupConsensus)\r
+ {\r
+ showGroupConsensus_actionPerformed();\r
+ }\r
+ else if (source == showGroupConservation)\r
+ {\r
+ showGroupConservation_actionPerformed();\r
+ }\r
+ else if (source == showSequenceLogo)\r
+ {\r
+ showSequenceLogo_actionPerformed();\r
+ }\r
+ else if (source == normSequenceLogo)\r
+ {\r
+ normSequenceLogo_actionPerformed();\r
+ }\r
+ else if (source == showConsensusHistogram)\r
+ {\r
+ showConsensusHistogram_actionPerformed();\r
+ }\r
+ else if (source == applyAutoAnnotationSettings)\r
+ {\r
+ applyAutoAnnotationSettings_actionPerformed();\r
+ }\r
+ else if (source == featureSettings)\r
+ {\r
+ new FeatureSettings(alignPanel);\r
+ }\r
+ else if (source == alProperties)\r
+ {\r
+ StringBuffer contents = new jalview.io.AlignmentProperties(\r
+ viewport.getAlignment()).formatAsString();\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ cap.setText(contents.toString());\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "\r
+ + getTitle(), 400, 250);\r
+ }\r
+ else if (source == overviewMenuItem)\r
+ {\r
+ overviewMenuItem_actionPerformed();\r
+ }\r
+ else if (source == noColourmenuItem)\r
+ {\r
+ changeColour(null);\r
+ }\r
+ else if (source == clustalColour)\r
+ {\r
+ abovePIDThreshold.setState(false);\r
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));\r
+ }\r
+ else if (source == zappoColour)\r
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+ else if (source == nucleotideColour)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+ else if (source == purinePyrimidineColour)\r
+ {\r
+ changeColour(new PurinePyrimidineColourScheme());\r
+ }\r
+ else if (source == RNAInteractionColour)\r
+ {\r
+ changeColour(new RNAInteractionColourScheme());\r
+ }\r
+ else if (source == RNAHelixColour)\r
+ {\r
+ new RNAHelicesColourChooser(viewport, alignPanel);\r
+ }\r
+ else if (source == modifyPID)\r
+ {\r
+ modifyPID_actionPerformed();\r
+ }\r
+ else if (source == modifyConservation)\r
+ {\r
+ modifyConservation_actionPerformed();\r
+ }\r
+ else if (source == userDefinedColour)\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else if (source == PIDColour)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+ else if (source == BLOSUM62Colour)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+ else if (source == tcoffeeColour)\r
+ {\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ }\r
+ else if (source == annotationColour)\r
+ {\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ }\r
+ else if (source == sortPairwiseMenuItem)\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortIDMenuItem)\r
+ {\r
+ sortIDMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortLengthMenuItem)\r
+ {\r
+ sortLengthMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortGroupMenuItem)\r
+ {\r
+ sortGroupMenuItem_actionPerformed();\r
+ }\r
+ else if (source == removeRedundancyMenuItem)\r
+ {\r
+ removeRedundancyMenuItem_actionPerformed();\r
+ }\r
+ else if (source == pairwiseAlignmentMenuItem)\r
+ {\r
+ pairwiseAlignmentMenuItem_actionPerformed();\r
+ }\r
+ else if (source == PCAMenuItem)\r
+ {\r
+ PCAMenuItem_actionPerformed();\r
+ }\r
+ else if (source == averageDistanceTreeMenuItem)\r
+ {\r
+ averageDistanceTreeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == neighbourTreeMenuItem)\r
+ {\r
+ neighbourTreeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == njTreeBlosumMenuItem)\r
+ {\r
+ njTreeBlosumMenuItem_actionPerformed();\r
+ }\r
+ else if (source == avDistanceTreeBlosumMenuItem)\r
+ {\r
+ avTreeBlosumMenuItem_actionPerformed();\r
+ }\r
+ else if (source == documentation)\r
+ {\r
+ documentation_actionPerformed();\r
+ }\r
+ else if (source == about)\r
+ {\r
+ about_actionPerformed();\r
+ }\r
+\r
+ }\r
+\r
+ public void inputText_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
+ }\r
+\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Alignment output - " + e.getActionCommand(), 600, 500);\r
+ cap.setText(new AppletFormatAdapter().formatSequences(\r
+ e.getActionCommand(), viewport.getAlignment(),\r
+ viewport.showJVSuffix));\r
+ }\r
+\r
+ public void loadAnnotations()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your features / annotations / T-coffee score file here.");\r
+ cap.setAnnotationImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
+\r
+ }\r
+\r
+ public String outputAnnotations(boolean displayTextbox)\r
+ {\r
+ String annotation = new AnnotationFile().printAnnotations(\r
+ viewport.showAnnotation ? viewport.getAlignment()\r
+ .getAlignmentAnnotation() : null, viewport\r
+ .getAlignment().getGroups(), ((Alignment) viewport\r
+ .getAlignment()).alignmentProperties);\r
+\r
+ if (displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);\r
+ cap.setText(annotation);\r
+ }\r
+\r
+ return annotation;\r
+ }\r
+\r
+ private Hashtable getDisplayedFeatureCols()\r
+ {\r
+ if (alignPanel.getFeatureRenderer() != null\r
+ && viewport.featuresDisplayed != null)\r
+ {\r
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();\r
+ Hashtable fcols = new Hashtable();\r
+ Enumeration en = viewport.featuresDisplayed.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ Object col = en.nextElement();\r
+ fcols.put(col, fr.featureColours.get(col));\r
+ }\r
+ return fcols;\r
+ }\r
+ return null;\r
+ }\r
+\r
+ public String outputFeatures(boolean displayTextbox, String format)\r
+ {\r
+ String features;\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ features = new FeaturesFile().printJalviewFormat(viewport\r
+ .getAlignment().getSequencesArray(),\r
+ getDisplayedFeatureCols());\r
+ }\r
+ else\r
+ {\r
+ features = new FeaturesFile().printGFFFormat(viewport.getAlignment()\r
+ .getSequencesArray(), getDisplayedFeatureCols());\r
+ }\r
+\r
+ if (displayTextbox)\r
+ {\r
+ boolean frimport = false;\r
+ if (features == null || features.equals("No Features Visible"))\r
+ {\r
+ features = "# No features visible - paste some and import them here.";\r
+ frimport = true;\r
+ }\r
+\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);\r
+ if (frimport)\r
+ {\r
+ cap.setAnnotationImport();\r
+ }\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);\r
+ cap.setText(features);\r
+ }\r
+ else\r
+ {\r
+ if (features == null)\r
+ features = "";\r
+ }\r
+\r
+ return features;\r
+ }\r
+\r
+ void launchFullApplication()\r
+ {\r
+ StringBuffer url = new StringBuffer(jalviewServletURL);\r
+\r
+ url.append("?open="\r
+ + appendProtocol(viewport.applet.getParameter("file")));\r
+\r
+ if (viewport.applet.getParameter("features") != null)\r
+ {\r
+ url.append("&features=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("features")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("annotations") != null)\r
+ {\r
+ url.append("&annotations=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("annotations")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("jnetfile") != null)\r
+ {\r
+ url.append("&annotations=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("defaultColour") != null)\r
+ {\r
+ url.append("&colour="\r
+ + removeWhiteSpace(viewport.applet\r
+ .getParameter("defaultColour")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("userDefinedColour") != null)\r
+ {\r
+ url.append("&colour="\r
+ + removeWhiteSpace(viewport.applet\r
+ .getParameter("userDefinedColour")));\r
+ }\r
+ if (viewport.applet.getParameter("tree") != null)\r
+ {\r
+ url.append("&tree="\r
+ + appendProtocol(viewport.applet.getParameter("tree")));\r
+ }\r
+ if (viewport.applet.getParameter("treeFile") != null)\r
+ {\r
+ url.append("&tree="\r
+ + appendProtocol(viewport.applet.getParameter("treeFile")));\r
+ }\r
+\r
+ showURL(url.toString(), "FULL_APP");\r
+ }\r
+\r
+ String removeWhiteSpace(String colour)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ for (int i = 0; i < colour.length(); i++)\r
+ {\r
+ if (Character.isWhitespace(colour.charAt(i)))\r
+ {\r
+ sb.append("%20");\r
+ }\r
+ else\r
+ {\r
+ sb.append(colour.charAt(i));\r
+ }\r
+ }\r
+\r
+ return sb.toString();\r
+ }\r
+\r
+ String appendProtocol(String url)\r
+ {\r
+ try\r
+ {\r
+ new URL(url);\r
+ url = URLEncoder.encode(url);\r
+ }\r
+ /*\r
+ * When we finally deprecate 1.1 compatibility, we can start to use\r
+ * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch\r
+ * (UnsupportedEncodingException ex) { System.err.println("WARNING -\r
+ * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);\r
+ * ex.printStackTrace(); }\r
+ */\r
+ catch (java.net.MalformedURLException ex)\r
+ {\r
+ url = viewport.applet.getCodeBase() + url;\r
+ }\r
+ return url;\r
+ }\r
+\r
+ public void closeMenuItem_actionPerformed()\r
+ {\r
+ PaintRefresher.RemoveComponent(alignPanel);\r
+ if (alignPanel.seqPanel != null\r
+ && alignPanel.seqPanel.seqCanvas != null)\r
+ {\r
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+ }\r
+ if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)\r
+ {\r
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+ }\r
+\r
+ if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
+ {\r
+ System.exit(0);\r
+ }\r
+ else\r
+ {\r
+ }\r
+ viewport = null;\r
+ alignPanel = null;\r
+ this.dispose();\r
+ }\r
+\r
+ /**\r
+ * TODO: JAL-1104\r
+ */\r
+ void updateEditMenuBar()\r
+ {\r
+\r
+ if (viewport.historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ CommandI command = (CommandI) viewport.historyList.peek();\r
+ undoMenuItem.setLabel("Undo " + command.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ }\r
+\r
+ if (viewport.redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ CommandI command = (CommandI) viewport.redoList.peek();\r
+ redoMenuItem.setLabel("Redo " + command.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * TODO: JAL-1104\r
+ */\r
+ public void addHistoryItem(CommandI command)\r
+ {\r
+ if (command.getSize() > 0)\r
+ {\r
+ viewport.historyList.push(command);\r
+ viewport.redoList.removeAllElements();\r
+ updateEditMenuBar();\r
+ viewport.updateHiddenColumns();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * TODO: JAL-1104 DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void undoMenuItem_actionPerformed()\r
+ {\r
+ if (viewport.historyList.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ CommandI command = (CommandI) viewport.historyList.pop();\r
+ viewport.redoList.push(command);\r
+ command.undoCommand(null);\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ // JBPNote Test\r
+ if (originalSource != viewport)\r
+ {\r
+ System.err\r
+ .println("Warning: Viewport object mismatch whilst undoing");\r
+ }\r
+ originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =\r
+ // viewport.getColumnSelection().getHiddenColumns()\r
+ // != null;\r
+ updateEditMenuBar();\r
+ originalSource.firePropertyChange("alignment", null, originalSource\r
+ .getAlignment().getSequences());\r
+ }\r
+\r
+ /**\r
+ * TODO: JAL-1104 DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void redoMenuItem_actionPerformed()\r
+ {\r
+ if (viewport.redoList.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ CommandI command = (CommandI) viewport.redoList.pop();\r
+ viewport.historyList.push(command);\r
+ command.doCommand(null);\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ // JBPNote Test\r
+ if (originalSource != viewport)\r
+ {\r
+ System.err\r
+ .println("Warning: Viewport object mismatch whilst re-doing");\r
+ }\r
+ originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =\r
+ // viewport.getColumnSelection().getHiddenColumns()\r
+ // != null;\r
+\r
+ updateEditMenuBar();\r
+ originalSource.firePropertyChange("alignment", null, originalSource\r
+ .getAlignment().getSequences());\r
+ }\r
+\r
+ AlignViewport getOriginatingSource(CommandI command)\r
+ {\r
+ AlignViewport originalSource = null;\r
+ // For sequence removal and addition, we need to fire\r
+ // the property change event FROM the viewport where the\r
+ // original alignment was altered\r
+ AlignmentI al = null;\r
+ if (command instanceof EditCommand)\r
+ {\r
+ EditCommand editCommand = (EditCommand) command;\r
+ al = editCommand.getAlignment();\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())\r
+ {\r
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (originalSource == null)\r
+ {\r
+ // The original view is closed, we must validate\r
+ // the current view against the closed view first\r
+ if (al != null)\r
+ {\r
+ PaintRefresher.validateSequences(al, viewport.getAlignment());\r
+ }\r
+\r
+ originalSource = viewport;\r
+ }\r
+\r
+ return originalSource;\r
+ }\r
+\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,\r
+ up ? null : viewport.getHiddenRepSequences(), up);\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ synchronized void slideSequences(boolean right, int size)\r
+ {\r
+ List<SequenceI> sg = new Vector<SequenceI>();\r
+ if (viewport.cursorMode)\r
+ {\r
+ sg.add(viewport.getAlignment().getSequenceAt(\r
+ alignPanel.seqPanel.seqCanvas.cursorY));\r
+ }\r
+ else if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() != viewport\r
+ .getAlignment().getHeight())\r
+ {\r
+ sg = viewport.getSelectionGroup().getSequences(\r
+ viewport.getHiddenRepSequences());\r
+ }\r
+\r
+ if (sg.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Vector<SequenceI> invertGroup = new Vector();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
+ {\r
+ if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))\r
+ invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));\r
+ }\r
+\r
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);\r
+\r
+ SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup\r
+ .size()]);\r
+ for (int i = 0; i < invertGroup.size(); i++)\r
+ seqs2[i] = invertGroup.elementAt(i);\r
+\r
+ SlideSequencesCommand ssc;\r
+ if (right)\r
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,\r
+ size, viewport.getGapCharacter());\r
+ else\r
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,\r
+ size, viewport.getGapCharacter());\r
+\r
+ int groupAdjustment = 0;\r
+ if (ssc.getGapsInsertedBegin() && right)\r
+ {\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(size, 0);\r
+ else\r
+ groupAdjustment = size;\r
+ }\r
+ else if (!ssc.getGapsInsertedBegin() && !right)\r
+ {\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(-size, 0);\r
+ else\r
+ groupAdjustment = -size;\r
+ }\r
+\r
+ if (groupAdjustment != 0)\r
+ {\r
+ viewport.getSelectionGroup().setStartRes(\r
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);\r
+ viewport.getSelectionGroup().setEndRes(\r
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);\r
+ }\r
+\r
+ boolean appendHistoryItem = false;\r
+ if (viewport.historyList != null && viewport.historyList.size() > 0\r
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)\r
+ {\r
+ appendHistoryItem = ssc\r
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList\r
+ .peek());\r
+ }\r
+\r
+ if (!appendHistoryItem)\r
+ addHistoryItem(ssc);\r
+\r
+ repaint();\r
+ }\r
+\r
+ static StringBuffer copiedSequences;\r
+\r
+ static Vector copiedHiddenColumns;\r
+\r
+ protected void copy_actionPerformed()\r
+ {\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ copiedSequences = new StringBuffer();\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.getAlignment().findIndex(seq);\r
+ orderedSeqs.put(index + "", seq);\r
+ }\r
+\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
+\r
+ if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)\r
+ {\r
+ copiedHiddenColumns = new Vector();\r
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()\r
+ .size(); i++)\r
+ {\r
+ int[] region = (int[]) viewport.getColumnSelection()\r
+ .getHiddenColumns().elementAt(i);\r
+\r
+ copiedHiddenColumns.addElement(new int[]\r
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });\r
+ }\r
+ }\r
+ else\r
+ {\r
+ copiedHiddenColumns = null;\r
+ }\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
+\r
+ // FIND START RES\r
+ // Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
+\r
+ // FIND END RES\r
+ // Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
+\r
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap((ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
+\r
+ copiedSequences.append(seq.getName()\r
+ + "\t"\r
+ + startRes\r
+ + "\t"\r
+ + endRes\r
+ + "\t"\r
+ + seq.getSequenceAsString(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
+ }\r
+\r
+ }\r
+\r
+ protected void pasteNew_actionPerformed()\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ protected void pasteThis_actionPerformed()\r
+ {\r
+ paste(false);\r
+ }\r
+\r
+ void paste(boolean newAlignment)\r
+ {\r
+ try\r
+ {\r
+\r
+ if (copiedSequences == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
+ Vector seqs = new Vector();\r
+ while (st.hasMoreElements())\r
+ {\r
+ String name = st.nextToken();\r
+ int start = Integer.parseInt(st.nextToken());\r
+ int end = Integer.parseInt(st.nextToken());\r
+ seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
+ }\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+\r
+ if (newAlignment)\r
+ {\r
+ String newtitle = new String("Copied sequences");\r
+ if (getTitle().startsWith("Copied sequences"))\r
+ {\r
+ newtitle = getTitle();\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + getTitle());\r
+ }\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
+ viewport.applet, newtitle, false);\r
+ if (copiedHiddenColumns != null)\r
+ {\r
+ for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
+ {\r
+ int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
+ }\r
+ }\r
+\r
+ jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ addSequences(newSeqs);\r
+ }\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ } // could be anything being pasted in here\r
+\r
+ }\r
+\r
+ void addSequences(SequenceI[] seqs)\r
+ {\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ viewport.getAlignment().addSequence(seqs[i]);\r
+ }\r
+\r
+ // !newAlignment\r
+ addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,\r
+ seqs, 0, viewport.getAlignment().getWidth(),\r
+ viewport.getAlignment()));\r
+\r
+ viewport.setEndSeq(viewport.getAlignment().getHeight());\r
+ viewport.getAlignment().getWidth();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+\r
+ protected void cut_actionPerformed()\r
+ {\r
+ copy_actionPerformed();\r
+ delete_actionPerformed();\r
+ }\r
+\r
+ protected void delete_actionPerformed()\r
+ {\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Vector seqs = new Vector();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ seq = sg.getSequenceAt(i);\r
+ seqs.addElement(seq);\r
+ }\r
+\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (sg.getSize() == viewport.getAlignment().getHeight())\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
+ SequenceI[] cut = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ cut[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+\r
+ /*\r
+ * //ADD HISTORY ITEM\r
+ */\r
+ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,\r
+ sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,\r
+ viewport.getAlignment()));\r
+\r
+ viewport.setSelectionGroup(null);\r
+ viewport.getAlignment().deleteGroup(sg);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ this.setVisible(false);\r
+ }\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ /**\r
+ * group consensus toggled\r
+ * \r
+ */\r
+ protected void showGroupConsensus_actionPerformed()\r
+ {\r
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+\r
+ }\r
+\r
+ /**\r
+ * group conservation toggled.\r
+ */\r
+ protected void showGroupConservation_actionPerformed()\r
+ {\r
+ viewport.setShowGroupConservation(showGroupConservation.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ protected void showConsensusHistogram_actionPerformed()\r
+ {\r
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ protected void showSequenceLogo_actionPerformed()\r
+ {\r
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ protected void normSequenceLogo_actionPerformed()\r
+ {\r
+ showSequenceLogo.setState(true);\r
+ viewport.setShowSequenceLogo(true);\r
+ viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ protected void applyAutoAnnotationSettings_actionPerformed()\r
+ {\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ protected void makeGrpsFromSelection_actionPerformed()\r
+ {\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(\r
+ viewport.getSequenceSelection(),\r
+ viewport.getAlignmentView(true).getSequenceStrings(\r
+ viewport.getGapCharacter()), viewport.getAlignment()\r
+ .getGroups());\r
+ viewport.getAlignment().deleteAllGroups();\r
+ viewport.sequenceColours = null;\r
+ viewport.setSelectionGroup(null);\r
+ // set view properties for each group\r
+ for (int g = 0; g < gps.length; g++)\r
+ {\r
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());\r
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());\r
+ viewport.getAlignment().addGroup(gps[g]);\r
+ Color col = new Color((int) (Math.random() * 255),\r
+ (int) (Math.random() * 255), (int) (Math.random() * 255));\r
+ col = col.brighter();\r
+ for (SequenceI sq : gps[g].getSequences(null))\r
+ viewport.setSequenceColour(sq, col);\r
+ }\r
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
+ alignPanel.updateAnnotation();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ }\r
+\r
+ protected void deleteGroups_actionPerformed()\r
+ {\r
+ viewport.getAlignment().deleteAllGroups();\r
+ viewport.sequenceColours = null;\r
+ viewport.setSelectionGroup(null);\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void selectAllSequenceMenuItem_actionPerformed()\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);\r
+ viewport.setSelectionGroup(sg);\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ public void deselectAllSequenceMenuItem_actionPerformed()\r
+ {\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1 = null;\r
+ alignPanel.seqPanel.keyboardNo2 = null;\r
+ }\r
+ viewport.setSelectionGroup(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ public void invertSequenceMenuItem_actionPerformed()\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ public void invertColSel_actionPerformed()\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ void trimAlignment(boolean trimLeft)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+ int column;\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ if (trimLeft)\r
+ {\r
+ column = colSel.getMin();\r
+ }\r
+ else\r
+ {\r
+ column = colSel.getMax();\r
+ }\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.getHiddenRepSequences());\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
+ }\r
+\r
+ TrimRegionCommand trimRegion;\r
+ if (trimLeft)\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Left",\r
+ TrimRegionCommand.TRIM_LEFT, seqs, column,\r
+ viewport.getAlignment(), viewport.getColumnSelection(),\r
+ viewport.getSelectionGroup());\r
+ viewport.setStartRes(0);\r
+ }\r
+ else\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Right",\r
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,\r
+ viewport.getAlignment(), viewport.getColumnSelection(),\r
+ viewport.getSelectionGroup());\r
+ }\r
+\r
+ statusBar.setText("Removed " + trimRegion.getSize() + " columns.");\r
+\r
+ addHistoryItem(trimRegion);\r
+\r
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())\r
+ {\r
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
+ {\r
+ viewport.getAlignment().deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport\r
+ .getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ public void removeGappedColumnMenuItem_actionPerformed()\r
+ {\r
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.getHiddenRepSequences());\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
+ }\r
+\r
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(\r
+ "Remove Gapped Columns", seqs, start, end,\r
+ viewport.getAlignment());\r
+\r
+ addHistoryItem(removeGapCols);\r
+\r
+ statusBar.setText("Removed " + removeGapCols.getSize()\r
+ + " empty columns.");\r
+\r
+ // This is to maintain viewport position on first residue\r
+ // of first sequence\r
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+ // ShiftList shifts;\r
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
+ // edit.alColumnChanges=shifts.getInverse();\r
+ // if (viewport.hasHiddenColumns)\r
+ // viewport.getColumnSelection().compensateForEdits(shifts);\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+\r
+ public void removeAllGapsMenuItem_actionPerformed()\r
+ {\r
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.getHiddenRepSequences());\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
+ }\r
+\r
+ // This is to maintain viewport position on first residue\r
+ // of first sequence\r
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,\r
+ viewport.getAlignment()));\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+\r
+ public void findMenuItem_actionPerformed()\r
+ {\r
+ new Finder(alignPanel);\r
+ }\r
+\r
+ /**\r
+ * create a new view derived from the current view\r
+ * \r
+ * @param viewtitle\r
+ * @return frame for the new view\r
+ */\r
+ public AlignFrame newView(String viewtitle)\r
+ {\r
+ AlignmentI newal;\r
+ if (viewport.hasHiddenRows())\r
+ {\r
+ newal = new Alignment(viewport.getAlignment().getHiddenSequences()\r
+ .getFullAlignment().getSequencesArray());\r
+ }\r
+ else\r
+ {\r
+ newal = new Alignment(viewport.getAlignment().getSequencesArray());\r
+ }\r
+\r
+ if (viewport.getAlignment().getAlignmentAnnotation() != null)\r
+ {\r
+ for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)\r
+ {\r
+ if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)\r
+ {\r
+ newal.addAnnotation(viewport.getAlignment()\r
+ .getAlignmentAnnotation()[i]);\r
+ }\r
+ }\r
+ }\r
+\r
+ AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);\r
+\r
+ newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
+ int viewSize = -1;\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ viewSize++;\r
+ }\r
+ }\r
+\r
+ String title = new String(this.getTitle());\r
+ if (viewtitle != null)\r
+ {\r
+ title = viewtitle + " ( " + title + ")";\r
+ }\r
+ else\r
+ {\r
+ if (title.indexOf("(View") > -1)\r
+ {\r
+ title = title.substring(0, title.indexOf("(View"));\r
+ }\r
+ title += "(View " + viewSize + ")";\r
+ }\r
+\r
+ newaf.setTitle(title.toString());\r
+\r
+ newaf.viewport.historyList = viewport.historyList;\r
+ newaf.viewport.redoList = viewport.redoList;\r
+ return newaf;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return list of feature groups on the view\r
+ */\r
+ public String[] getFeatureGroups()\r
+ {\r
+ FeatureRenderer fr = null;\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ return fr.getGroups();\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * get sequence feature groups that are hidden or shown\r
+ * \r
+ * @param visible\r
+ * true is visible\r
+ * @return list\r
+ */\r
+ public String[] getFeatureGroupsOfState(boolean visible)\r
+ {\r
+ FeatureRenderer fr = null;\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ return fr.getGroups(visible);\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Change the display state for the given feature groups\r
+ * \r
+ * @param groups\r
+ * list of group strings\r
+ * @param state\r
+ * visible or invisible\r
+ */\r
+ public void setFeatureGroupState(String[] groups, boolean state)\r
+ {\r
+ FeatureRenderer fr = null;\r
+ this.sequenceFeatures.setState(true);\r
+ viewport.showSequenceFeatures(true);\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ fr.setGroupState(groups, state);\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+ }\r
+\r
+ public void seqLimits_itemStateChanged()\r
+ {\r
+ viewport.setShowJVSuffix(seqLimits.getState());\r
+ alignPanel.fontChanged();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ protected void colourTextMenuItem_actionPerformed()\r
+ {\r
+ viewport.setColourText(colourTextMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ protected void displayNonconservedMenuItem_actionPerformed()\r
+ {\r
+ viewport.setShowunconserved(displayNonconservedMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ protected void wrapMenuItem_actionPerformed()\r
+ {\r
+ viewport.setWrapAlignment(wrapMenuItem.getState());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
+ scaleAbove.setEnabled(wrapMenuItem.getState());\r
+ scaleLeft.setEnabled(wrapMenuItem.getState());\r
+ scaleRight.setEnabled(wrapMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void overviewMenuItem_actionPerformed()\r
+ {\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Frame frame = new Frame();\r
+ OverviewPanel overview = new OverviewPanel(alignPanel);\r
+ frame.add(overview);\r
+ // +50 must allow for applet frame window\r
+ jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
+ overview.getPreferredSize().width,\r
+ overview.getPreferredSize().height + 50);\r
+\r
+ frame.pack();\r
+ final AlignmentPanel ap = alignPanel;\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ @Override\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.setOverviewPanel(null);\r
+ }\r
+ };\r
+ });\r
+\r
+ alignPanel.setOverviewPanel(overview);\r
+\r
+ }\r
+\r
+ void changeColour(ColourSchemeI cs)\r
+ {\r
+ int threshold = 0;\r
+\r
+ if (cs != null)\r
+ {\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
+\r
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else\r
+ {\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+\r
+ Alignment al = (Alignment) viewport.getAlignment();\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, viewport.getConsPercGaps());\r
+\r
+ cs.setConservation(c);\r
+\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,\r
+ cs, "Background"));\r
+\r
+ }\r
+ else\r
+ {\r
+ cs.setConservation(null);\r
+ }\r
+\r
+ cs.setConsensus(viewport.getSequenceConsensusHash());\r
+\r
+ }\r
+ viewport.setGlobalColourScheme(cs);\r
+\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+\r
+ jalview.structure.StructureSelectionManager\r
+ .getStructureSelectionManager(viewport.applet)\r
+ .sequenceColoursChanged(alignPanel);\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ protected void modifyPID_actionPerformed()\r
+ {\r
+ if (viewport.getAbovePIDThreshold()\r
+ && viewport.getGlobalColourScheme() != null)\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(), "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ }\r
+\r
+ protected void modifyConservation_actionPerformed()\r
+ {\r
+ if (viewport.getConservationSelected()\r
+ && viewport.getGlobalColourScheme() != null)\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.getGlobalColourScheme(), "Background");\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ }\r
+\r
+ protected void conservationMenuItem_actionPerformed()\r
+ {\r
+ viewport.setConservationSelected(conservationMenuItem.getState());\r
+\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setState(false);\r
+\r
+ changeColour(viewport.getGlobalColourScheme());\r
+\r
+ modifyConservation_actionPerformed();\r
+ }\r
+\r
+ public void abovePIDThreshold_actionPerformed()\r
+ {\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
+\r
+ conservationMenuItem.setState(false);\r
+ viewport.setConservationSelected(false);\r
+\r
+ changeColour(viewport.getGlobalColourScheme());\r
+\r
+ modifyPID_actionPerformed();\r
+ }\r
+\r
+ public void sortPairwiseMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport\r
+ .getAlignment().getSequenceAt(0), null);\r
+\r
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void sortIDMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void sortLengthMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByLength(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void sortGroupMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+\r
+ }\r
+\r
+ public void removeRedundancyMenuItem_actionPerformed()\r
+ {\r
+ new RedundancyPanel(alignPanel);\r
+ }\r
+\r
+ public void pairwiseAlignmentMenuItem_actionPerformed()\r
+ {\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() > 1)\r
+ {\r
+ Frame frame = new Frame();\r
+ frame.add(new PairwiseAlignPanel(alignPanel));\r
+ jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,\r
+ 500);\r
+ }\r
+ }\r
+\r
+ public void PCAMenuItem_actionPerformed()\r
+ {\r
+ // are the sequences aligned?\r
+ if (!viewport.getAlignment().isAligned(false))\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ if ((viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() < 4 && viewport\r
+ .getSelectionGroup().getSize() > 0)\r
+ || viewport.getAlignment().getHeight() < 4)\r
+ {\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ new PCAPanel(viewport);\r
+ } catch (java.lang.OutOfMemoryError ex)\r
+ {\r
+ }\r
+\r
+ }\r
+\r
+ public void averageDistanceTreeMenuItem_actionPerformed()\r
+ {\r
+ NewTreePanel("AV", "PID", "Average distance tree using PID");\r
+ }\r
+\r
+ public void neighbourTreeMenuItem_actionPerformed()\r
+ {\r
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
+ }\r
+\r
+ protected void njTreeBlosumMenuItem_actionPerformed()\r
+ {\r
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
+ }\r
+\r
+ protected void avTreeBlosumMenuItem_actionPerformed()\r
+ {\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+ }\r
+\r
+ void NewTreePanel(String type, String pwType, String title)\r
+ {\r
+ // are the sequences aligned?\r
+ if (!viewport.getAlignment().isAligned(false))\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+\r
+ }\r
+\r
+ if ((viewport.getSelectionGroup() != null && viewport\r
+ .getSelectionGroup().getSize() > 1)\r
+ || (viewport.getAlignment().getHeight() > 1))\r
+ {\r
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);\r
+\r
+ addTreeMenuItem(tp, title);\r
+\r
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+ }\r
+ }\r
+\r
+ void loadTree_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your Newick tree file here.");\r
+ cap.setTreeImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
+ }\r
+\r
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
+ {\r
+ TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
+ }\r
+\r
+ /**\r
+ * sort the alignment using the given treePanel\r
+ * \r
+ * @param treePanel\r
+ * tree used to sort view\r
+ * @param title\r
+ * string used for undo event name\r
+ */\r
+ public void sortByTree(TreePanel treePanel, String title)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter\r
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());\r
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
+ addHistoryItem(new OrderCommand("Order by " + title, oldOrder,\r
+ viewport.getAlignment()));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * Do any automatic reordering of the alignment and add the necessary bits to\r
+ * the menu structure for the new tree\r
+ * \r
+ * @param treePanel\r
+ * @param title\r
+ */\r
+ protected void addTreeMenuItem(final TreePanel treePanel,\r
+ final String title)\r
+ {\r
+ final MenuItem item = new MenuItem(title);\r
+ sortByTreeMenu.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ sortByTree(treePanel, title); // treePanel.getTitle());\r
+ }\r
+ });\r
+\r
+ treePanel.addWindowListener(new WindowAdapter()\r
+ {\r
+ @Override\r
+ public void windowOpened(WindowEvent e)\r
+ {\r
+ if (viewport.sortByTree)\r
+ {\r
+ sortByTree(treePanel, title);\r
+ }\r
+ super.windowOpened(e);\r
+ }\r
+\r
+ @Override\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ sortByTreeMenu.remove(item);\r
+ };\r
+ });\r
+ }\r
+\r
+ public boolean sortBy(AlignmentOrder alorder, String undoname)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ if (viewport.applet.debug)\r
+ {\r
+ System.err.println("Sorting " + alorder.getOrder().size()\r
+ + " in alignment '" + getTitle() + "'");\r
+ }\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
+ if (undoname != null)\r
+ {\r
+ addHistoryItem(new OrderCommand(undoname, oldOrder,\r
+ viewport.getAlignment()));\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ return true;\r
+ }\r
+\r
+ protected void documentation_actionPerformed()\r
+ {\r
+ alignPanel.av.applet.openJalviewHelpUrl();\r
+ }\r
+\r
+ protected void about_actionPerformed()\r
+ {\r
+\r
+ class AboutPanel extends Canvas\r
+ {\r
+ String version;\r
+\r
+ String builddate;\r
+\r
+ public AboutPanel(String version, String builddate)\r
+ {\r
+ this.version = version;\r
+ this.builddate = builddate;\r
+ }\r
+\r
+ @Override\r
+ public void paint(Graphics g)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int fh = fm.getHeight();\r
+ int y = 5, x = 7;\r
+ g.setColor(Color.black);\r
+ // TODO: update this text for each release or centrally store it for\r
+ // lite and application\r
+ g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
+ g.drawString("JalviewLite - Release " + version, x, y += fh);\r
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));\r
+ g.drawString("Build date: " + builddate, x, y += fh);\r
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
+ g.drawString(\r
+ "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",\r
+ x, y += fh * 1.5);\r
+ g.drawString(\r
+ "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",\r
+ x + 50, y += fh + 8);\r
+ g.drawString(\r
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",\r
+ x, y += fh);\r
+ g.drawString("If you use Jalview, please cite:", x, y += fh + 8);\r
+ g.drawString(\r
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",\r
+ x, y += fh);\r
+ g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",\r
+ x, y += fh);\r
+ }\r
+ }\r
+\r
+ Frame frame = new Frame();\r
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite\r
+ .getBuildDate()));\r
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);\r
+\r
+ }\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (viewport.applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ viewport.applet.showURL(url, target);\r
+ }\r
+ }\r
+\r
+ // ////////////////////////////////////////////////////////////////////////////////\r
+ // JBuilder Graphics here\r
+\r
+ MenuBar alignFrameMenuBar = new MenuBar();\r
+\r
+ Menu fileMenu = new Menu("File");\r
+\r
+ MenuItem loadApplication = new MenuItem("View in Full Application");\r
+\r
+ MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+\r
+ MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+\r
+ MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+\r
+ MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+ MenuItem closeMenuItem = new MenuItem("Close");\r
+\r
+ Menu editMenu = new Menu("Edit");\r
+\r
+ Menu viewMenu = new Menu("View");\r
+\r
+ Menu colourMenu = new Menu("Colour");\r
+\r
+ Menu calculateMenu = new Menu("Calculate");\r
+\r
+ MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+\r
+ MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+\r
+ MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+\r
+ MenuItem remove2LeftMenuItem = new MenuItem();\r
+\r
+ MenuItem remove2RightMenuItem = new MenuItem();\r
+\r
+ MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+\r
+ MenuItem removeAllGapsMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem sortPairwiseMenuItem = new MenuItem();\r
+\r
+ MenuItem sortIDMenuItem = new MenuItem();\r
+\r
+ MenuItem sortLengthMenuItem = new MenuItem();\r
+\r
+ MenuItem sortGroupMenuItem = new MenuItem();\r
+\r
+ MenuItem removeRedundancyMenuItem = new MenuItem();\r
+\r
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+\r
+ MenuItem PCAMenuItem = new MenuItem();\r
+\r
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+\r
+ MenuItem neighbourTreeMenuItem = new MenuItem();\r
+\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ public Label statusBar = new Label();\r
+\r
+ Menu outputTextboxMenu = new Menu();\r
+\r
+ MenuItem clustalColour = new MenuItem();\r
+\r
+ MenuItem zappoColour = new MenuItem();\r
+\r
+ MenuItem taylorColour = new MenuItem();\r
+\r
+ MenuItem hydrophobicityColour = new MenuItem();\r
+\r
+ MenuItem helixColour = new MenuItem();\r
+\r
+ MenuItem strandColour = new MenuItem();\r
+\r
+ MenuItem turnColour = new MenuItem();\r
+\r
+ MenuItem buriedColour = new MenuItem();\r
+\r
+ MenuItem purinePyrimidineColour = new MenuItem();\r
+\r
+ MenuItem RNAInteractionColour = new MenuItem();\r
+\r
+ MenuItem RNAHelixColour = new MenuItem();\r
+\r
+ MenuItem userDefinedColour = new MenuItem();\r
+\r
+ MenuItem PIDColour = new MenuItem();\r
+\r
+ MenuItem BLOSUM62Colour = new MenuItem();\r
+\r
+ MenuItem tcoffeeColour = new MenuItem();\r
+\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem alProperties = new MenuItem("Alignment Properties...");\r
+\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+\r
+ MenuItem undoMenuItem = new MenuItem();\r
+\r
+ MenuItem redoMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem findMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+\r
+ MenuItem nucleotideColour = new MenuItem();\r
+\r
+ MenuItem deleteGroups = new MenuItem();\r
+\r
+ MenuItem grpsFromSelection = new MenuItem();\r
+\r
+ MenuItem delete = new MenuItem();\r
+\r
+ MenuItem copy = new MenuItem();\r
+\r
+ MenuItem cut = new MenuItem();\r
+\r
+ Menu pasteMenu = new Menu();\r
+\r
+ MenuItem pasteNew = new MenuItem();\r
+\r
+ MenuItem pasteThis = new MenuItem();\r
+\r
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+\r
+ MenuItem font = new MenuItem();\r
+\r
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+\r
+ MenuItem modifyPID = new MenuItem();\r
+\r
+ MenuItem modifyConservation = new MenuItem();\r
+\r
+ CheckboxMenuItem autoCalculate = new CheckboxMenuItem(\r
+ "Autocalculate Consensus", true);\r
+\r
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(\r
+ "Sort Alignment With New Tree", true);\r
+\r
+ Menu sortByTreeMenu = new Menu();\r
+\r
+ Menu sort = new Menu();\r
+\r
+ Menu calculate = new Menu();\r
+\r
+ MenuItem inputText = new MenuItem();\r
+\r
+ Menu helpMenu = new Menu();\r
+\r
+ MenuItem documentation = new MenuItem();\r
+\r
+ MenuItem about = new MenuItem();\r
+\r
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
+\r
+ Menu autoAnnMenu = new Menu();\r
+\r
+ CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();\r
+\r
+ private void jbInit() throws Exception\r
+ {\r
+\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+\r
+ item = new MenuItem(\r
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ closeMenuItem.addActionListener(this);\r
+ loadApplication.addActionListener(this);\r
+\r
+ loadTree.addActionListener(this);\r
+ loadAnnotations.addActionListener(this);\r
+ outputFeatures.addActionListener(this);\r
+ outputAnnotations.addActionListener(this);\r
+ selectAllSequenceMenuItem.addActionListener(this);\r
+ deselectAllSequenceMenuItem.addActionListener(this);\r
+ invertSequenceMenuItem.addActionListener(this);\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(this);\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(this);\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(this);\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(this);\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(this);\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(this);\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(this);\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(this);\r
+ sortLengthMenuItem.setLabel("by Length");\r
+ sortLengthMenuItem.addActionListener(this);\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(this);\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(this);\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(this);\r
+ PCAMenuItem.setLabel("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(this);\r
+ averageDistanceTreeMenuItem\r
+ .setLabel("Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(this);\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(this);\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(this);\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(this);\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(this);\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(this);\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(this);\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(this);\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(this);\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(this);\r
+ purinePyrimidineColour.setLabel("Purine/Pyrimidine");\r
+ purinePyrimidineColour.addActionListener(this);\r
+ RNAInteractionColour.setLabel("Purine/Pyrimidine");\r
+ RNAInteractionColour.addActionListener(this);\r
+ RNAHelixColour.setLabel("by RNA Helices");\r
+ RNAHelixColour.addActionListener(this);\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(this);\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(this);\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(this);\r
+ tcoffeeColour.setLabel("T-Coffee Scores");\r
+ tcoffeeColour.setEnabled(false); // it will enabled only if a score file is\r
+ // provided\r
+ tcoffeeColour.addActionListener(this);\r
+ avDistanceTreeBlosumMenuItem\r
+ .setLabel("Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(this);\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(this);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(this);\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(this);\r
+ displayNonconservedMenuItem.setLabel("Show nonconserved");\r
+ displayNonconservedMenuItem.addItemListener(this);\r
+ alProperties.addActionListener(this);\r
+ overviewMenuItem.setLabel("Overview Window");\r
+ overviewMenuItem.addActionListener(this);\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(this);\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(this);\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(this);\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(this);\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(this);\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(this);\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(this);\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(this);\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(this);\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(this);\r
+ grpsFromSelection.setLabel("Make Groups for selection");\r
+ grpsFromSelection.addActionListener(this);\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(this);\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(this);\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(this);\r
+ pasteMenu.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(this);\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(this);\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(this);\r
+ font.setLabel("Font...");\r
+ font.addActionListener(this);\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.setEnabled(false);\r
+ scaleAbove.addItemListener(this);\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(this);\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(this);\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(this);\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(this);\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ autoCalculate.addItemListener(this);\r
+ sortByTree.addItemListener(this);\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(this);\r
+ centreColumnLabelFlag.setLabel("Centre column labels");\r
+ centreColumnLabelFlag.addItemListener(this);\r
+ followMouseOverFlag.setLabel("Automatic Scrolling");\r
+ followMouseOverFlag.addItemListener(this);\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(this);\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(this);\r
+ seqLimits.setState(true);\r
+ seqLimits.setLabel("Show Sequence Limits");\r
+ seqLimits.addItemListener(this);\r
+ featureSettings.setLabel("Feature Settings...");\r
+ featureSettings.addActionListener(this);\r
+ sequenceFeatures.setLabel("Sequence Features");\r
+ sequenceFeatures.addItemListener(this);\r
+ sequenceFeatures.setState(false);\r
+ annotationColour.setLabel("by Annotation...");\r
+ annotationColour.addActionListener(this);\r
+ invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
+ invertColSel.setLabel("Invert Column Selection");\r
+ menu1.setLabel("Show");\r
+ showColumns.setLabel("All Columns ");\r
+ showSeqs.setLabel("All Sequences");\r
+ menu2.setLabel("Hide");\r
+ hideColumns.setLabel("Selected Columns");\r
+ hideSequences.setLabel("Selected Sequences");\r
+ hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");\r
+ hideAllSelection.setLabel("Selected Region");\r
+ showAllHidden.setLabel("All Sequences and Columns");\r
+ showGroupConsensus.setLabel("Group Consensus");\r
+ showGroupConservation.setLabel("Group Conservation");\r
+ showConsensusHistogram.setLabel("Show Consensus Histogram");\r
+ showSequenceLogo.setLabel("Show Consensus Logo");\r
+ normSequenceLogo.setLabel("Normalise Consensus Logo");\r
+ applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
+ applyAutoAnnotationSettings.setState(true);\r
+ autoAnnMenu.setLabel("Autocalculated Annotation");\r
+\r
+ invertColSel.addActionListener(this);\r
+ showColumns.addActionListener(this);\r
+ showSeqs.addActionListener(this);\r
+ hideColumns.addActionListener(this);\r
+ hideSequences.addActionListener(this);\r
+ hideAllButSelection.addActionListener(this);\r
+ hideAllSelection.addActionListener(this);\r
+ showAllHidden.addActionListener(this);\r
+ showGroupConsensus.addItemListener(this);\r
+ showGroupConservation.addItemListener(this);\r
+ showConsensusHistogram.addItemListener(this);\r
+ showSequenceLogo.addItemListener(this);\r
+ applyAutoAnnotationSettings.addItemListener(this);\r
+ formatMenu.setLabel("Format");\r
+ selectMenu.setLabel("Select");\r
+ newView.setLabel("New View");\r
+ newView.addActionListener(this);\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(selectMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(formatMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(helpMenu);\r
+\r
+ fileMenu.add(inputText);\r
+ fileMenu.add(loadTree);\r
+ fileMenu.add(loadAnnotations);\r
+\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(outputFeatures);\r
+ fileMenu.add(outputAnnotations);\r
+\r
+ if (jalviewServletURL != null)\r
+ {\r
+ fileMenu.add(loadApplication);\r
+ }\r
+\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(pasteMenu);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ viewMenu.add(newView);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(menu1);\r
+ viewMenu.add(menu2);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(followMouseOverFlag);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ autoAnnMenu.add(applyAutoAnnotationSettings);\r
+ autoAnnMenu.add(showConsensusHistogram);\r
+ autoAnnMenu.add(showSequenceLogo);\r
+ autoAnnMenu.add(normSequenceLogo);\r
+ autoAnnMenu.addSeparator();\r
+ autoAnnMenu.add(showGroupConservation);\r
+ autoAnnMenu.add(showGroupConsensus);\r
+ viewMenu.add(autoAnnMenu);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(alProperties);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(purinePyrimidineColour);\r
+ colourMenu.add(RNAInteractionColour);\r
+ colourMenu.add(tcoffeeColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ colourMenu.add(annotationColour);\r
+ colourMenu.add(RNAHelixColour);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.add(autoCalculate);\r
+ calculateMenu.add(sortByTree);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ pasteMenu.add(pasteNew);\r
+ pasteMenu.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortLengthMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ helpMenu.add(documentation);\r
+ helpMenu.add(about);\r
+ menu1.add(showColumns);\r
+ menu1.add(showSeqs);\r
+ menu1.add(showAllHidden);\r
+ menu2.add(hideColumns);\r
+ menu2.add(hideSequences);\r
+ menu2.add(hideAllSelection);\r
+ menu2.add(hideAllButSelection);\r
+ formatMenu.add(font);\r
+ formatMenu.add(seqLimits);\r
+ formatMenu.add(wrapMenuItem);\r
+ formatMenu.add(scaleAbove);\r
+ formatMenu.add(scaleLeft);\r
+ formatMenu.add(scaleRight);\r
+ formatMenu.add(viewBoxesMenuItem);\r
+ formatMenu.add(viewTextMenuItem);\r
+ formatMenu.add(colourTextMenuItem);\r
+ formatMenu.add(displayNonconservedMenuItem);\r
+ formatMenu.add(renderGapsMenuItem);\r
+ formatMenu.add(centreColumnLabelFlag);\r
+ selectMenu.add(findMenuItem);\r
+ selectMenu.addSeparator();\r
+ selectMenu.add(selectAllSequenceMenuItem);\r
+ selectMenu.add(deselectAllSequenceMenuItem);\r
+ selectMenu.add(invertSequenceMenuItem);\r
+ selectMenu.add(invertColSel);\r
+ selectMenu.add(grpsFromSelection);\r
+ selectMenu.add(deleteGroups);\r
+\r
+ }\r
+\r
+ MenuItem featureSettings = new MenuItem();\r
+\r
+ CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+\r
+ MenuItem annotationColour = new MenuItem();\r
+\r
+ MenuItem invertColSel = new MenuItem();\r
+\r
+ Menu menu1 = new Menu();\r
+\r
+ MenuItem showColumns = new MenuItem();\r
+\r
+ MenuItem showSeqs = new MenuItem();\r
+\r
+ Menu menu2 = new Menu();\r
+\r
+ MenuItem hideColumns = new MenuItem();\r
+\r
+ MenuItem hideSequences = new MenuItem();\r
+\r
+ MenuItem hideAllButSelection = new MenuItem();\r
+\r
+ MenuItem hideAllSelection = new MenuItem();\r
+\r
+ MenuItem showAllHidden = new MenuItem();\r
+\r
+ Menu formatMenu = new Menu();\r
+\r
+ Menu selectMenu = new Menu();\r
+\r
+ MenuItem newView = new MenuItem();\r
+\r
+ /**\r
+ * Attach the alignFrame panels after embedding menus, if necessary. This used\r
+ * to be called setEmbedded, but is now creates the dropdown menus in a\r
+ * platform independent manner to avoid OSX/Mac menu appendage daftness.\r
+ * \r
+ * @param reallyEmbedded\r
+ * true to attach the view to the applet area on the page rather than\r
+ * in a new window\r
+ */\r
+ public void createAlignFrameWindow(boolean reallyEmbedded, String title)\r
+ {\r
+ if (reallyEmbedded)\r
+ {\r
+ // ////\r
+ // Explicly build the embedded menu panel for the on-page applet\r
+ //\r
+ // view cannot be closed if its actually on the page\r
+ fileMenu.remove(closeMenuItem);\r
+ fileMenu.remove(3); // Remove Seperator\r
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",\r
+ Font.PLAIN, 10, false); // use our own fonts.\r
+ // and actually add the components to the applet area\r
+ viewport.applet.setLayout(new BorderLayout());\r
+ viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
+ viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
+ alignPanel.setSize(viewport.applet.getSize().width,\r
+ viewport.applet.getSize().height - embeddedMenu.HEIGHT\r
+ - statusBar.HEIGHT);\r
+ viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
+ final AlignFrame me = this;\r
+ viewport.applet.addFocusListener(new FocusListener()\r
+ {\r
+\r
+ @Override\r
+ public void focusLost(FocusEvent e)\r
+ {\r
+ if (me.viewport.applet.currentAlignFrame == me)\r
+ {\r
+ me.viewport.applet.currentAlignFrame = null;\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void focusGained(FocusEvent e)\r
+ {\r
+ me.viewport.applet.currentAlignFrame = me;\r
+ }\r
+ });\r
+ viewport.applet.validate();\r
+ }\r
+ else\r
+ {\r
+ // //////\r
+ // test and embed menu bar if necessary.\r
+ //\r
+ if (embedMenuIfNeeded(alignPanel))\r
+ {\r
+ // adjust for status bar height too\r
+ alignPanel.setSize(getSize().width, getSize().height\r
+ - statusBar.HEIGHT);\r
+ }\r
+ add(statusBar, BorderLayout.SOUTH);\r
+ add(alignPanel, BorderLayout.CENTER);\r
+ // and register with the applet so it can pass external API calls to us\r
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * create a new binding between structures in an existing jmol viewer instance\r
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,\r
+ * this does not open a new Jmol window, or modify the display of the\r
+ * structures in the original jmol window. Note This method doesn't work\r
+ * without an additional javascript library to exchange messages between the\r
+ * distinct applets. See http://issues.jalview.org/browse/JAL-621\r
+ * \r
+ * @param viewer\r
+ * JmolViewer instance\r
+ * @param sequenceIds\r
+ * - sequence Ids to search for associations\r
+ */\r
+ public SequenceStructureBinding addStructureViewInstance(\r
+ Object jmolviewer, String[] sequenceIds)\r
+ {\r
+ org.jmol.api.JmolViewer viewer = null;\r
+ try\r
+ {\r
+ viewer = (org.jmol.api.JmolViewer) jmolviewer;\r
+ } catch (ClassCastException ex)\r
+ {\r
+ System.err.println("Unsupported viewer object :"\r
+ + jmolviewer.getClass());\r
+ }\r
+ if (viewer == null)\r
+ {\r
+ System.err.println("Can't use this object as a structure viewer:"\r
+ + jmolviewer.getClass());\r
+ return null;\r
+ }\r
+ SequenceI[] seqs = null;\r
+ if (sequenceIds == null || sequenceIds.length == 0)\r
+ {\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ Vector sqi = new Vector();\r
+ AlignmentI al = viewport.getAlignment();\r
+ for (int sid = 0; sid < sequenceIds.length; sid++)\r
+ {\r
+ SequenceI sq = al.findName(sequenceIds[sid]);\r
+ if (sq != null)\r
+ {\r
+ sqi.addElement(sq);\r
+ }\r
+ }\r
+ if (sqi.size() > 0)\r
+ {\r
+ seqs = new SequenceI[sqi.size()];\r
+ for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)\r
+ {\r
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ return null;\r
+ }\r
+ }\r
+ ExtJmol jmv = null;\r
+ // TODO: search for a jmv that involves viewer\r
+ if (jmv == null)\r
+ { // create a new viewer/jalview binding.\r
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]\r
+ { seqs });\r
+ }\r
+ return jmv;\r
+\r
+ }\r
+\r
+ /**\r
+ * bind a pdb file to a sequence in the current view\r
+ * \r
+ * @param sequenceId\r
+ * - sequenceId within the dataset.\r
+ * @param pdbEntryString\r
+ * - the short name for the PDB file\r
+ * @param pdbFile\r
+ * - pdb file - either a URL or a valid PDB file.\r
+ * @return true if binding was as success TODO: consider making an exception\r
+ * structure for indicating when PDB parsing or sequenceId location\r
+ * fails.\r
+ */\r
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,\r
+ String pdbFile)\r
+ {\r
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);\r
+ boolean needtoadd = false;\r
+ if (toaddpdb != null)\r
+ {\r
+ Vector pdbe = toaddpdb.getPDBId();\r
+ PDBEntry pdbentry = null;\r
+ if (pdbe != null && pdbe.size() > 0)\r
+ {\r
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)\r
+ {\r
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);\r
+ if (!pdbentry.getId().equals(pdbEntryString)\r
+ && !pdbentry.getFile().equals(pdbFile))\r
+ {\r
+ pdbentry = null;\r
+ }\r
+ else\r
+ {\r
+ continue;\r
+ }\r
+ }\r
+ }\r
+ if (pdbentry == null)\r
+ {\r
+ pdbentry = new PDBEntry();\r
+ pdbentry.setId(pdbEntryString);\r
+ pdbentry.setFile(pdbFile);\r
+ needtoadd = true; // add this new entry to sequence.\r
+ }\r
+ // resolve data source\r
+ // TODO: this code should be a refactored to an io package\r
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");\r
+ if (protocol == null)\r
+ {\r
+ return false;\r
+ }\r
+ if (needtoadd)\r
+ {\r
+ // make a note of the access mode and add\r
+ if (pdbentry.getProperty() == null)\r
+ {\r
+ pdbentry.setProperty(new Hashtable());\r
+ }\r
+ pdbentry.getProperty().put("protocol", protocol);\r
+ toaddpdb.addPDBId(pdbentry);\r
+ }\r
+ }\r
+ return true;\r
+ }\r
+\r
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)\r
+ {\r
+ if (seqs != null)\r
+ {\r
+ Vector sequences = new Vector();\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i] != null)\r
+ {\r
+ sequences.addElement(new Object[]\r
+ { seqs[i], (chains != null) ? chains[i] : null });\r
+ }\r
+ }\r
+ seqs = new SequenceI[sequences.size()];\r
+ chains = new String[sequences.size()];\r
+ for (int i = 0, isize = sequences.size(); i < isize; i++)\r
+ {\r
+ Object[] oj = (Object[]) sequences.elementAt(i);\r
+\r
+ seqs[i] = (SequenceI) oj[0];\r
+ chains[i] = (String) oj[1];\r
+ }\r
+ }\r
+ return new Object[]\r
+ { seqs, chains };\r
+\r
+ }\r
+\r
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,\r
+ SequenceI[] seqs, String[] chains, String protocol)\r
+ {\r
+ // Scrub any null sequences from the array\r
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);\r
+ seqs = (SequenceI[]) sqch[0];\r
+ chains = (String[]) sqch[1];\r
+ if (seqs == null || seqs.length == 0)\r
+ {\r
+ System.err\r
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");\r
+ }\r
+ if (protocol == null || protocol.trim().length() == 0\r
+ || protocol.equals("null"))\r
+ {\r
+ protocol = (String) pdb.getProperty().get("protocol");\r
+ if (protocol == null)\r
+ {\r
+ System.err.println("Couldn't work out protocol to open structure: "\r
+ + pdb.getId());\r
+ return;\r
+ }\r
+ }\r
+ if (applet.useXtrnalSviewer)\r
+ {\r
+ // register the association(s) and quit, don't create any windows.\r
+ if (StructureSelectionManager.getStructureSelectionManager(applet)\r
+ .setMapping(seqs, chains, pdb.getFile(), protocol) == null)\r
+ {\r
+ System.err.println("Failed to map " + pdb.getFile() + " ("\r
+ + protocol + ") to any sequences");\r
+ }\r
+ return;\r
+ }\r
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)\r
+ {\r
+ // can only do alignments with Jmol\r
+ // find the last jmol window assigned to this alignment\r
+ jalview.appletgui.AppletJmol ajm = null, tajm;\r
+ Vector jmols = applet\r
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);\r
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)\r
+ {\r
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);\r
+ if (tajm.ap.alignFrame == this)\r
+ {\r
+ ajm = tajm;\r
+ break;\r
+ }\r
+ }\r
+ if (ajm != null)\r
+ {\r
+ System.err\r
+ .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");\r
+ // try and add the pdb structure\r
+ // ajm.addS\r
+ ajm = null;\r
+ }\r
+ }\r
+ // otherwise, create a new window\r
+ if (applet.jmolAvailable)\r
+ {\r
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,\r
+ protocol);\r
+ applet.lastFrameX += 40;\r
+ applet.lastFrameY += 40;\r
+ }\r
+ else\r
+ {\r
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);\r
+ }\r
+\r
+ }\r
+\r
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,\r
+ SequenceI[][] seqs, String[][] chains, String[] protocols)\r
+ {\r
+ // TODO Auto-generated method stub\r
+ System.err.println("Aligned Structure View: Not yet implemented.");\r
+ }\r
+\r
+ /**\r
+ * modify the current selection, providing the user has not made a selection\r
+ * already.\r
+ * \r
+ * @param sel\r
+ * - sequences from this alignment\r
+ * @param csel\r
+ * - columns to be selected on the alignment\r
+ */\r
+ public void select(SequenceGroup sel, ColumnSelection csel)\r
+ {\r
+ alignPanel.seqPanel.selection(sel, csel, null);\r
+ }\r
+\r
+ public void scrollTo(int row, int column)\r
+ {\r
+ alignPanel.seqPanel.scrollTo(row, column);\r
+ }\r
+\r
+ public void scrollToRow(int row)\r
+ {\r
+ alignPanel.seqPanel.scrollToRow(row);\r
+ }\r
+\r
+ public void scrollToColumn(int column)\r
+ {\r
+ alignPanel.seqPanel.scrollToColumn(column);\r
+ }\r
+\r
+ /**\r
+ * @return the alignments unique ID.\r
+ */\r
+ public String getSequenceSetId()\r
+ {\r
+ return viewport.getSequenceSetId();\r
+ }\r
+\r
+ /**\r
+ * Load the (T-Coffee) score file from the specified url\r
+ * \r
+ * @param source\r
+ * File/URL/T-COFFEE score file contents\r
+ * @throws IOException\r
+ * @return true if alignment was annotated with data from source\r
+ */\r
+ public boolean loadScoreFile(String source) throws IOException\r
+ {\r
+\r
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source,\r
+ AppletFormatAdapter.checkProtocol(source));\r
+ if (!file.isValid())\r
+ {\r
+ // TODO: raise dialog for gui\r
+ System.err.println("Problems parsing T-Coffee scores: "\r
+ + file.getWarningMessage());\r
+ System.err.println("Origin was:\n" + source);\r
+ return false;\r
+ }\r
+\r
+ /*\r
+ * check that the score matrix matches the alignment dimensions\r
+ */\r
+ AlignmentI aln;\r
+ if ((aln = viewport.getAlignment()) != null\r
+ && (aln.getHeight() != file.getHeight() || aln.getWidth() != file\r
+ .getWidth()))\r
+ {\r
+ // TODO: raise a dialog box here rather than bomb out.\r
+ System.err\r
+ .println("The scores matrix does not match the alignment dimensions");\r
+\r
+ }\r
+\r
+ // TODO add parameter to indicate if matching should be done\r
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
+ {\r
+ alignPanel.fontChanged();\r
+ tcoffeeColour.setEnabled(true);\r
+ // switch to this color\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ System.err.println("Problems resolving T-Coffee scores:");\r
+ if (file.getWarningMessage() != null)\r
+ {\r
+ System.err.println(file.getWarningMessage());\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+}\r
*/
package jalview.bin;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
}
});
}
+ protected static boolean proteine;
/**
* main class for Jalview application
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
+
+ JFrame Typechooser =new JFrame("choose molecule type");
+ FlowLayout fl = new FlowLayout();
+ Typechooser.setLayout(fl);
+ Typechooser.setSize(400,400);
+ Typechooser.setDefaultCloseOperation(Typechooser.DISPOSE_ON_CLOSE);
+ JLabel label = new JLabel("What would you open ? ");
+ JButton rnabutton = new JButton("RNA molecule");
+ JButton pbutton = new JButton("Proteine molecule");
+
+ pbutton.addActionListener(new pbuttonlistener());
+ rnabutton.addActionListener(new rnabuttonlistener());
+ Typechooser.getContentPane().add(label);
+ Typechooser.getContentPane().add(rnabutton);
+ Typechooser.getContentPane().add(pbutton);
+ Typechooser.setVisible(true);
+
+
+
+
if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && proteine == true)
{
file = jalview.bin.Cache.getDefault(
"STARTUP_FILE",
desktop.setInBatchMode(false);
}
}
-
+
+
private static void startUsageStats(final Desktop desktop)
{
/**
* @author Andrew Waterhouse and JBP documented.
*
*/
+
+class rnabuttonlistener implements ActionListener{
+ public void actionPerformed(ActionEvent arg0) {
+ System.out.println("Good idea ! ");
+
+ }
+}
+
+class pbuttonlistener implements ActionListener{
+ public void actionPerformed(ActionEvent arg0) {
+
+
+ }
+}
+
class ArgsParser
{
Vector vargs = null;
{
return queued == 0 && running == 0;
}
+
+
+
};
import jalview.analysis.Rna;
import jalview.analysis.WUSSParseException;
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
/** DOCUMENT ME!! */
public Annotation[] annotations;
+
+
/**
* RNA secondary structure contact positions
else
// Check for RNA secondary structure
{
- if (annotations[i].secondaryStructure == 'S')
+ //System.out.println(annotations[i].secondaryStructure);
+ if (annotations[i].secondaryStructure == '('
+ || annotations[i].secondaryStructure == '['
+ || annotations[i].secondaryStructure == '<'
+ || annotations[i].secondaryStructure == '{'
+ || annotations[i].secondaryStructure == 'A'
+ || annotations[i].secondaryStructure == 'B'
+ || annotations[i].secondaryStructure == 'C'
+ || annotations[i].secondaryStructure == 'D'
+ || annotations[i].secondaryStructure == '1'
+ || annotations[i].secondaryStructure == 'F'
+ || annotations[i].secondaryStructure == 'G'
+ || annotations[i].secondaryStructure == '2'
+ || annotations[i].secondaryStructure == 'I'
+ || annotations[i].secondaryStructure == 'J'
+ || annotations[i].secondaryStructure == 'K'
+ || annotations[i].secondaryStructure == 'L'
+ || annotations[i].secondaryStructure == 'M'
+ || annotations[i].secondaryStructure == 'N'
+ || annotations[i].secondaryStructure == 'O'
+ || annotations[i].secondaryStructure == 'P'
+ || annotations[i].secondaryStructure == 'Q'
+ || annotations[i].secondaryStructure == 'R'
+ || annotations[i].secondaryStructure == 'S'
+ || annotations[i].secondaryStructure == 'T'
+ || annotations[i].secondaryStructure == 'U'
+ || annotations[i].secondaryStructure == 'V'
+ || annotations[i].secondaryStructure == 'W'
+ || annotations[i].secondaryStructure == 'X'
+ || annotations[i].secondaryStructure == 'Y'
+ || annotations[i].secondaryStructure == 'Z')
{
hasIcons |= true;
isrna |= true;
firstChar != ' '
&& firstChar != 'H'
&& firstChar != 'E'
+ && firstChar != '('
+ && firstChar != '['
+ && firstChar != '>'
+ && firstChar != '{'
+ && firstChar != 'A'
+ && firstChar != 'B'
+ && firstChar != 'C'
+ && firstChar != 'D'
+ && firstChar != '1'
+ && firstChar != 'F'
+ && firstChar != 'G'
+ && firstChar != '2'
+ && firstChar != 'I'
+ && firstChar != 'J'
+ && firstChar != 'K'
+ && firstChar != 'L'
+ && firstChar != 'M'
+ && firstChar != 'N'
+ && firstChar != 'O'
+ && firstChar != 'P'
+ && firstChar != 'Q'
+ && firstChar != 'R'
&& firstChar != 'S'
+ && firstChar != 'T'
+ && firstChar != 'U'
+ && firstChar != 'V'
+ && firstChar != 'W'
+ && firstChar != 'X'
+ && firstChar != 'Y'
+ && firstChar != 'Z'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "";
+ annotations[i].displayCharacter = "X";
}
}
}
{
if (annotations[i] == null)
annotations[i] = new Annotation(String.valueOf(gapchar), null,
- ' ', 0f);
+ ' ', 0f,null);
else if (annotations[i].displayCharacter == null
|| annotations[i].displayCharacter.equals(" "))
annotations[i].displayCharacter = String.valueOf(gapchar);
{
this.calcId = calcId;
}
-
}
/** DOCUMENT ME!! */
public float value;
+
+
// add visual cues here
description = desc;
secondaryStructure = ss;
value = val;
+
}
/**
secondaryStructure = that.secondaryStructure;
value = that.value;
colour = that.colour;
+
}
/**
*/
public Annotation(float val)
{
- this(null, null, ' ', val);
+ this(null, null, ' ', val,null);
}
+
+
+
+
}
--- /dev/null
+package jalview.datamodel;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class SecondaryStructureAnnotation extends AlignmentAnnotation
+{
+
+
+ private static RNA _rna = null;
+ public SecondaryStructureAnnotation (RNA rna)
+ {
+ super("Secondary Structure", "Un truc trop cool",getAnnotation(rna));
+
+
+ _rna = rna;
+ }
+
+ public RNA getRNA()
+ {
+ return _rna;
+ }
+ public static Annotation[] getAnnotation(RNA rna)
+ {
+ Annotation[] ann = new Annotation[rna.getSize()];
+ for(int i=0;i<ann.length;i++)
+ {
+ ann[i] = new Annotation(_rna.getStructDBN(true), "", ' ', 0f);;
+ }
+ return ann;
+ }
+}
import java.util.Enumeration;
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
String vamsasId;
DBRefEntry[] dbrefs;
+
+ RNA rna;
/**
* This annotation is displayed below the alignment but the positions are tied
*/
int index = -1;
- /** array of seuqence features - may not be null for a valid sequence object */
+ /** array of sequence features - may not be null for a valid sequence object */
public SequenceFeature[] sequenceFeatures;
/**
{
index = value;
}
+
+ public void setRNA(RNA r){rna=r;}
+
+ public RNA getRNA() { return rna; }
+
}
*/
package jalview.datamodel;
+
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
* @return The index of the sequence in the alignment
*/
public int getIndex();
+
+ /**
+ * @return The RNA of the sequence in the alignment
+ */
+
+ public RNA getRNA();
+
+ /**
+ * @param rna The RNA.
+ */
+ public void setRNA(RNA rna);
+
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.ext.jmol;
+
+import java.io.IOException;
+import java.util.Map;
+
+import org.jmol.api.JmolStatusListener;
+import org.jmol.api.JmolViewer;
+import org.jmol.constant.EnumCallback;
+import org.jmol.modelset.Group;
+import org.jmol.modelset.Model;
+import org.jmol.modelset.ModelSet;
+import org.jmol.modelset.Polymer;
+import org.jmol.modelsetbio.BioPolymer;
+import org.jmol.viewer.Viewer;
+import org.openscience.jmol.app.JmolApp;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
+
+/**
+ * Import and process PDB files with Jmol
+ *
+ * @author jprocter
+ *
+ */
+public class PDBFileWithJmol extends AlignFile implements
+ JmolStatusListener
+{
+
+ JmolApp jmolApp = null;
+
+ Viewer viewer = null;
+
+ public PDBFileWithJmol(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public PDBFileWithJmol()
+ {
+ // TODO Auto-generated constructor stub
+ }
+
+ /**
+ * create a headless jmol instance for dataprocessing
+ *
+ * @return
+ */
+ private Viewer getJmolData()
+ {
+ if (viewer == null)
+ { // note that -o -n -x are all implied
+ jmolApp = new JmolApp();
+ jmolApp.isDataOnly = true;
+ jmolApp.haveConsole = false;
+ jmolApp.haveDisplay = false;
+ jmolApp.exitUponCompletion = true;
+ try
+ {
+ viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
+ null, jmolApp.commandOptions, this);
+ viewer.setScreenDimension(jmolApp.startupWidth,
+ jmolApp.startupHeight);
+ jmolApp.startViewer(viewer, null);
+ } catch (ClassCastException x)
+ {
+ throw new Error(
+ "Jmol version "
+ + JmolViewer.getJmolVersion()
+ + " is not compatible with this version of Jalview. Report this problem at issues.jalview.org",
+ x);
+ }
+ }
+ return viewer;
+ }
+
+ private void waitForScript(Viewer jmd)
+ {
+ while (jmd.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(50);
+
+ } catch (InterruptedException x)
+ {
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ Viewer jmd = getJmolData();
+ jmd.openReader(getDataName(), getDataName(), getReader());
+ waitForScript(jmd);
+ if (jmd.getModelCount() > 0)
+ {
+ ModelSet ms = jmd.getModelSet();
+ String structs = ms.calculateStructures(null, true, false, true);
+ // System.out.println("Structs\n"+structs);
+ for (Model model : ms.getModels())
+ {
+ for (int _bp = 0, _bpc = model.getBioPolymerCount(); _bp < _bpc; _bp++)
+ {
+ Polymer bp = model.getBioPolymer(_bp);
+ if (bp instanceof BioPolymer)
+ {
+ BioPolymer biopoly = (BioPolymer) bp;
+ char _lastChainId = 0;
+ int[] groups = biopoly.getLeadAtomIndices();
+ Group[] bpgrp = biopoly.getGroups();
+ char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
+ int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
+ do
+ {
+ if (groupc >= groups.length
+ || ms.atoms[groups[groupc]].getChainID() != _lastChainId)
+ {
+ if (len > 0)
+ {
+ char newseq[] = new char[len];
+ System.arraycopy(seq, 0, newseq, 0, len);
+ Annotation asecstr[] = new Annotation[len];
+ for (int p = 0; p < len; p++)
+ {
+ if (secstr[p] >= 'A' && secstr[p] <= 'z')
+ {
+ asecstr[p] = new Annotation("" + secstr[p], null,
+ secstrcode[p], Float.NaN);
+ }
+ }
+ SequenceI sq = new Sequence("" + getDataName() + "|"
+ + model.getModelTitle() + "|" + _lastChainId,
+ newseq, firstrnum, lastrnum);
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setFile(getDataName());
+ pdbe.setId(getDataName());
+ sq.addPDBId(pdbe);
+ seqs.add(sq);
+ if (!(biopoly.isDna() || biopoly.isRna()))
+ {
+ AlignmentAnnotation ann = new AlignmentAnnotation(
+ "Secondary Structure",
+ "Secondary Structure from PDB File", asecstr);
+ sq.addAlignmentAnnotation(ann);
+ annotations.add(ann);
+ }
+ }
+ len = 0;
+ firstrnum = 1;
+ lastrnum = 0;
+ }
+ if (groupc < groups.length)
+ {
+ if (len == 0)
+ {
+ firstrnum = bpgrp[groupc].getResno();
+ _lastChainId = bpgrp[groupc].getChainID();
+ }
+ else
+ {
+ lastrnum = bpgrp[groupc].getResno();
+ }
+ seq[len] = bpgrp[groupc].getGroup1();
+ switch (bpgrp[groupc].getProteinStructureSubType())
+ {
+ case HELIX_310:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = '3';
+ }
+ case HELIX_ALPHA:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
+ }
+ case HELIX_PI:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'P';
+ }
+ case HELIX:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
+ }
+ secstrcode[len] = 'H';
+ break;
+ case SHEET:
+ secstr[len] = 'E';
+ secstrcode[len] = 'E';
+ break;
+ default:
+ secstr[len] = 0;
+ secstrcode[len] = 0;
+ }
+ len++;
+ }
+ } while (groupc++ < groups.length);
+
+ }
+ }
+ }
+
+ /*
+ * lastScriptTermination = -9465; String dsspOut =
+ * jmd.evalString("calculate STRUCTURE"); if (dsspOut.equals("pending")) {
+ * while (lastScriptTermination == -9465) { try { Thread.sleep(50); }
+ * catch (Exception x) { } ; } } System.out.println(lastConsoleEcho);
+ */
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#print()
+ */
+ @Override
+ public String print()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setCallbackFunction(String callbackType,
+ String callbackFunction)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /*
+ * @Override public void notifyCallback(EnumCallback type, Object[] data) {
+ * try { switch (type) { case ERROR: case SCRIPT:
+ * notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue());
+ * break; case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) :
+ * (String) data[1]); break; case LOADSTRUCT: notifyFileLoaded((String)
+ * data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer)
+ * data[5]).intValue());
+ *
+ * break; default: // System.err.println("Unhandled callback " + type + " " //
+ * + data[1].toString()); break; } } catch (Exception e) {
+ * System.err.println("Squashed Jmol callback handler error:");
+ * e.printStackTrace(); } }
+ */
+ public void notifyCallback(EnumCallback type, Object[] data)
+ {
+ String strInfo = (data == null || data[1] == null ? null : data[1]
+ .toString());
+ switch (type)
+ {
+ case ECHO:
+ sendConsoleEcho(strInfo);
+ break;
+ case SCRIPT:
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
+ break;
+ case MEASURE:
+ String mystatus = (String) data[3];
+ if (mystatus.indexOf("Picked") >= 0
+ || mystatus.indexOf("Sequence") >= 0) // picking mode
+ sendConsoleMessage(strInfo);
+ else if (mystatus.indexOf("Completed") >= 0)
+ sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
+ strInfo.length() - 1));
+ break;
+ case MESSAGE:
+ sendConsoleMessage(data == null ? null : strInfo);
+ break;
+ case PICK:
+ sendConsoleMessage(strInfo);
+ break;
+ default:
+ break;
+ }
+ }
+
+ private void notifyFileLoaded(String string, String string2,
+ String string3, String string4, int intValue)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ String lastConsoleEcho = "";
+
+ private void sendConsoleEcho(String string)
+ {
+ lastConsoleEcho += string;
+ lastConsoleEcho += "\n";
+ }
+
+ String lastConsoleMessage = "";
+
+ private void sendConsoleMessage(String string)
+ {
+ lastConsoleMessage += string;
+ lastConsoleMessage += "\n";
+ }
+
+ int lastScriptTermination = -1;
+
+ String lastScriptMessage = "";
+
+ private void notifyScriptTermination(String string, int intValue)
+ {
+ lastScriptMessage += string;
+ lastScriptMessage += "\n";
+ lastScriptTermination = intValue;
+ }
+
+ @Override
+ public boolean notifyEnabled(EnumCallback callbackPick)
+ {
+ switch (callbackPick)
+ {
+ case MESSAGE:
+ case SCRIPT:
+ case ECHO:
+ case LOADSTRUCT:
+ case ERROR:
+ return true;
+ case MEASURE:
+ case PICK:
+ case HOVER:
+ case RESIZE:
+ case SYNC:
+ case CLICK:
+ case ANIMFRAME:
+ case MINIMIZATION:
+ }
+ return false;
+ }
+
+ @Override
+ public String eval(String strEval)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public float[][] functionXY(String functionName, int x, int y)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String createImage(String fileName, String type,
+ Object text_or_bytes, int quality)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public Map<String, Object> getRegistryInfo()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void showUrl(String url)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+}
--- /dev/null
+package jalview.ext.paradise;
+
+import jalview.ws.HttpClientUtils;
+
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.http.NameValuePair;
+import org.apache.http.message.BasicNameValuePair;
+
+public class Annotate3D
+{
+
+ public static Reader getRNAMLForPDBFileAsString(String pdbfile)
+ throws Exception
+ {
+ List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ vals.add(new BasicNameValuePair("data", pdbfile));
+ return HttpClientUtils.doHttpUrlPost(
+ "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d",
+ vals);
+ }
+
+ public static Reader getRNAMLForPDBId(String pdbid) throws Exception
+ {
+ List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ vals.add(new BasicNameValuePair("pdbid", pdbid));
+ return HttpClientUtils.doHttpUrlPost(
+ "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d",
+ vals);
+ }
+
+}
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * 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/>.
- */
-package jalview.ext.varna;
-
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
-import java.awt.Color;
-import java.util.ArrayList;
-
-/**
- * Routines for generating Jmol commands for Jalview/Jmol binding another
- * cruisecontrol test.
- *
- * @author JimP
- *
- */
-public class VarnaCommands
-{
-
- /**
- * Jmol utility which constructs the commands to colour chains by the given
- * alignment
- *
- */
- public static String[] getColourBySequenceCommand(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
- {
- ArrayList<String> str = new ArrayList<String>();
- StringBuffer command = new StringBuffer();
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
- int lastPos = -1;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-
- if (fr != null)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
- if (command.length() > newSelcom.length()
- && command.substring(
- command.length() - newSelcom.length())
- .equals(newSelcom))
- {
- command = VarnaCommands.condenseCommand(command, pos);
- continue;
- }
- // TODO: deal with case when buffer is too large for Jmol to parse
- // - execute command and flush
-
- command.append(";");
- if (command.length() > 51200)
- {
- // add another chunk
- str.add(command.toString());
- command.setLength(0);
- }
- command.append("select " + pos);
- command.append(newSelcom);
- }
- break;
- }
- }
- }
- }
- {
- // add final chunk
- str.add(command.toString());
- command.setLength(0);
- }
- return str.toArray(new String[str.size()]);
- }
-
- public static StringBuffer condenseCommand(StringBuffer command, int pos)
- {
-
- // work back to last 'select'
- int p = command.length(), q = p;
- do
- {
- p -= 6;
- if (p < 1)
- {
- p = 0;
- }
- ;
- } while ((q = command.indexOf("select", p)) == -1 && p > 0);
-
- StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
-
- command = command.delete(0, q + 7);
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.ext.varna;\r
+\r
+import jalview.api.FeatureRenderer;\r
+import jalview.api.SequenceRenderer;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.structure.StructureMapping;\r
+import jalview.structure.StructureSelectionManager;\r
+import jalview.util.Comparison;\r
+\r
+import java.awt.Color;\r
+import java.util.ArrayList;\r
+\r
+/**\r
+ * Routines for generating Jmol commands for Jalview/Jmol binding\r
+ * another cruisecontrol test.\r
+ * \r
+ * @author JimP\r
+ *\r
+ */\r
+public class VarnaCommands\r
+{\r
+\r
+ /**\r
+ * Jmol utility which constructs the commands to colour chains by the given alignment\r
+ * \r
+ */\r
+ public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
+ {\r
+ \r
+ ArrayList<String> str = new ArrayList<String>();\r
+ StringBuffer command = new StringBuffer();\r
+ \r
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
+ {\r
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
+ \r
+ if (mapping == null || mapping.length < 1)\r
+ continue;\r
+ \r
+ int lastPos = -1;\r
+ for (int s = 0; s < sequence[pdbfnum].length; s++)\r
+ {\r
+ for (int sp, m = 0; m < mapping.length; m++)\r
+ {\r
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
+ {\r
+ SequenceI asp = alignment.getSequenceAt(sp);\r
+ for (int r = 0; r < asp.getLength(); r++)\r
+ {\r
+ // no mapping to gaps in sequence\r
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
+ {\r
+ continue;\r
+ }\r
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));\r
+ \r
+ if (pos < 1 || pos == lastPos)\r
+ continue;\r
+ \r
+ lastPos = pos;\r
+ \r
+ Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);\r
+ \r
+ if (fr != null)\r
+ col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);\r
+ String newSelcom = (mapping[m].getChain() != " " ? ":"\r
+ + mapping[m].getChain() : "")\r
+ + "/"\r
+ + (pdbfnum + 1)\r
+ + ".1"\r
+ + ";color["\r
+ + col.getRed()\r
+ + ","\r
+ + col.getGreen()\r
+ + ","\r
+ + col.getBlue() + "]";\r
+ if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))\r
+ {\r
+ command = VarnaCommands.condenseCommand(command, pos);\r
+ continue;\r
+ }\r
+ // TODO: deal with case when buffer is too large for Jmol to parse\r
+ // - execute command and flush\r
+ \r
+ command.append(";");\r
+ if (command.length()>51200)\r
+ {\r
+ // add another chunk\r
+ str.add(command.toString());\r
+ command.setLength(0);\r
+ }\r
+ command.append("select " + pos);\r
+ command.append(newSelcom);\r
+ }\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ {\r
+ // add final chunk\r
+ str.add(command.toString());\r
+ command.setLength(0);\r
+ }\r
+ return str.toArray(new String[str.size()]);\r
+ }\r
+\r
+ public static StringBuffer condenseCommand(StringBuffer command, int pos)\r
+ {\r
+ \r
+ // work back to last 'select'\r
+ int p=command.length(),q=p;\r
+ do {\r
+ p-=6;\r
+ if (p<1) { p=0; };\r
+ } while ((q=command.indexOf("select",p))==-1 && p>0);\r
+ \r
+ StringBuffer sb = new StringBuffer(command.substring(0,q+7));\r
+ \r
+ command = command.delete(0,q+7);\r
+ \r
+ String start;\r
+ \r
+ if (command.indexOf("-") > -1)\r
+ {\r
+ start = command.substring(0, command.indexOf("-"));\r
+ }\r
+ else\r
+ {\r
+ start = command.substring(0, command.indexOf(":"));\r
+ }\r
+ \r
+ sb.append(start + "-" + pos + command.substring(command.indexOf(":")));\r
+ \r
+ return sb;\r
+ }\r
+\r
+}\r
*/
package jalview.gui;
-import java.util.*;
+import jalview.bin.Cache;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.ShiftList;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import java.awt.*;
-import javax.swing.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
-import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.util.ShiftList;
import fr.orsay.lri.varna.VARNAPanel;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
public AppVarna(String sname, SequenceI seq, String strucseq,
String struc, String name, AlignmentPanel ap)
{
+ System.out.println("je suis là (AppVarna!!");
+ System.out.println("1:"+sname);
+ System.out.println("2:"+seq);
+ System.out.println("3:"+strucseq);
+ System.out.println("4:"+struc);
+ System.out.println("5:"+name);
+ System.out.println("6:"+ap);
this.ap = ap;
ArrayList<RNA> rnaList = new ArrayList<RNA>();
RNA rna1 = new RNA(name);
try
{
+ System.out.println("ou ici ?");
rna1.setRNA(strucseq, replaceOddGaps(struc));
+ System.out.println("La séquence est :"+rna1.getSeq());
+ System.out.println("La séquence est :"+struc);
+ System.out.println("La séquence est :"+replaceOddGaps(struc).toString());
} catch (ExceptionUnmatchedClosingParentheses e2)
{
e2.printStackTrace();
RNA trim = trimRNA(rna1, "trimmed " + sname);
rnaList.add(trim);
rnaList.add(rna1);
+
rnas.put(seq, rna1);
rnas.put(seq, trim);
rna1.setName(sname + " (with gaps)");
{
seqs.put(trim, seq);
seqs.put(rna1, seq);
-
+
/**
* if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
* shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
// System.out.println("Hallo: "+name);
this.name = sname + " trimmed to " + name;
initVarna();
+
ssm = ap.getStructureSelectionManager();
+ System.out.println(ssm.toString());
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
public void initVarna()
{
+ System.out.println("initialisation VANRA");
// vab.setFinishedInit(false);
varnaPanel = vab.get_varnaPanel();
setBackground(Color.white);
getBounds().width, getBounds().height);
this.pack();
showPanel(true);
+ System.out.println("Sortie initialisation VANRA");
}
public String replaceOddGaps(String oldStr)
public RNA trimRNA(RNA rna, String name)
{
ShiftList offset = new ShiftList();
+
RNA rnaTrim = new RNA(name);
try
{
}
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}
import javax.swing.DefaultListModel;
import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
import javax.swing.JButton;
-import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
import javax.swing.JTextField;
import javax.swing.ListModel;
import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
{
// super("VARNA in Jalview");
initVarna(seq, struc);
+
}
public AppVarnaBinding(ArrayList<RNA> rnaList)
{
+
// super("VARNA in Jalview");
initVarnaEdit(rnaList);
}
private void initVarna(String seq, String str)
{
+
DefaultListModel dlm = new DefaultListModel();
DefaultListSelectionModel m = new DefaultListSelectionModel();
try
{
+
vp = new VARNAPanel("0", ".");
_RNA1.setRNA(seq, str);
_RNA1.drawRNARadiate(vp.getConfig());
private void initVarnaEdit(ArrayList<RNA> rnaInList)
{
+
DefaultListModel dlm = new DefaultListModel();
int marginTools = 40;
FullBackup sel = (FullBackup) _sideList.getSelectedValue();
Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
.getSize(), sel.rna.getSize());
- vp.showRNAInterpolated(sel.rna, sel.config, map);
+ //vp.showRNAInterpolated(sel.rna, sel.config, map);
+ vp.showRNA(sel.rna, sel.config);
// _seq.setText(sel.rna.getSeq());
_str.setText(sel.rna.getStructDBN());
}
try
{
+
vp = new VARNAPanel("0", ".");
for (int i = 0; i < rnaInList.size(); i++)
{
rnaInList.get(i).drawRNARadiate(vp.getConfig());
+
}
} catch (ExceptionNonEqualLength e)
{
public void onUINewStructure(VARNAConfig v, RNA r)
{
- _rnaList.add(v, r, "", true);
+ // patch to fix infinite loop
+ // The problem is that onUINewStructure is called when user clicks
+ // check with Yann about whether Jalview should do anything with this event.
+ // e.g. if user has used VARNA's menu to import a structure .. Jalview may need to be told which structure is displayed.
+
+ // _rnaList.add(v, r, "", true);
}
public void onWarningEmitted(String s)
// TODO Auto-generated method stub
}
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
}
/*
package jalview.gui;
import javax.swing.JOptionPane;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
{
entry.setId(pdbfile.id);
}
+
} catch (java.io.IOException ex)
{
ex.printStackTrace();
sequence.getDatasetSequence().addPDBId(entry);
return entry;
}
-
}
.getSelectedFile().getParent());
String format = null;
- if (chooser.getSelectedFormat().equals("Jalview"))
+ if (chooser.getSelectedFormat()!=null && chooser.getSelectedFormat().equals("Jalview"))
{
format = "Jalview";
}
import java.awt.event.*;
import javax.swing.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.analysis.*;
import jalview.commands.*;
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
+ colours.add(RNAInteractionColour);
// colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
menuItem = new JMenuItem();
menuItem.setText("2D RNA " + structureLine);
menuItem.addActionListener(new java.awt.event.ActionListener()
+
{
public void actionPerformed(ActionEvent e)
{
- new AppVarna(structureLine, seq, seq.getSequenceAsString(),
- rnastruc, seq.getName(), ap);
+ //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");
}
});
viewStructureMenu.add(menuItem);
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
+
new AppVarna(seq.getName() + " structure", seq, seq
.getSequenceAsString(), rnastruc, seq.getName(),
ap);
{
purinePyrimidineColour.setSelected(true);
}
+
+ else if (sg.cs instanceof RNAInteractionColourScheme)
+ {
+ RNAInteractionColour.setSelected(true);
+ }
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
- if (ap.getAlignment().isNucleotide())
- {
- colourMenu.add(purinePyrimidineColour);
+ if (ap.getAlignment().isNucleotide()) {
+ colourMenu.add(RNAInteractionColour);
+ colourMenu.add(purinePyrimidineColour);
}
// colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
purinePyrimidineColour_actionPerformed();
}
});
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed();
+ }
+ });
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
refresh();
}
+ protected void RNAInteractionColour_actionPerformed()
+ {
+ getGroup().cs = new RNAInteractionColourScheme();
+ refresh();
+ }
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
*/
public AlignFile()
{
+ // Shouldn't we init data structures (JBPNote: not sure - initData is for initialising the structures used for reading from a datasource, and the bare constructor hasn't got any datasource)
+ initData();
}
/**
*/
public static final String[] READABLE_FORMATS = new String[]
{ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile" }; // , "SimpleBLAST" };
+ "PDB", "JnetFile" , "RNAML"}; // , "SimpleBLAST" };
/**
* List of valid format strings for use by callers of the formatSequences
* that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+ { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
/**
* List of writable formats by the application. Order must correspond with the
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" }; // ,
+ { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ "sto,stk","xml,rnaml" }; // ,
// ".blast"
// };
*/
public static final String[] READABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm" };// ,
+ "Stockholm","RNAML" };// ,
// "SimpleBLAST"
// };
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(inFile, type);
+ afile = new MCview.PDBfile(inFile, type);
+ // Uncomment to test Jmol data based PDB processing: JAL-1213
+ // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
}
else if (format.equals("STH"))
{
{
afile = new SimpleBlastFile(inFile, type);
}
-
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(inFile, type);
+ }
+
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
*
* @return DOCUMENT ME!
*/
- public Alignment readFromFile(FileParse source, String format)
+ public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
{
afile = new StockholmFile(source);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(source);
+ }
else if (format.equals("SimpleBLAST"))
{
afile = new SimpleBlastFile(source);
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase("RNAML"))
+ {
+ afile = new RnamlFile();
+ }
+
else
{
throw new Exception(
import java.io.*;
+
import jalview.datamodel.*;
/**
*/
package jalview.io;
-import java.util.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
-import javax.swing.*;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
// load
}
loadtime = -System.currentTimeMillis();
- Alignment al = null;
+ AlignmentI al = null;
if (format.equalsIgnoreCase("Jalview"))
{
error = format + "\n" + error;
}
}
-
+
if ((al != null) && (al.getHeight() > 0))
{
if (viewport != null)
break;
}
+
+ if ((data.indexOf("<") > -1))
+ {
+ reply = "RNAML";
+
+ break;
+ }
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
break;
}
+
+
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.io;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+
+public class InputStreamParser extends FileParse
+{
+
+ public InputStreamParser(InputStream is, String dataName)
+ throws IOException
+ {
+ super();
+ setDataName(dataName);
+ dataIn = new BufferedReader(new InputStreamReader(is));
+ error=false;
+ }
+ public InputStreamParser(Reader isreader, String dataName)
+ throws IOException
+ {
+ super();
+ setDataName(dataName);
+ dataIn = new BufferedReader(isreader);
+ error=false;
+ }
+
+
+ @Override
+ protected void finalize() throws Throwable
+ {
+ dataIn = null;
+ super.finalize();
+ }
+
+}
* @param args
* DOCUMENT ME!
*/
- public static void main(String[] args)
+ public static void main(String[] args)
{
try
{
import java.io.*;
import java.util.*;
+
import jalview.datamodel.*;
import jalview.util.*;
*
* @throws IOException
* DOCUMENT ME!
+
*/
public PileUpfile(String inFile, String type) throws IOException
{
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.io;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class RnamlFile extends AlignFile
+{
+ public String id;
+
+ protected ArrayList<RNA> result;
+
+ public RnamlFile()
+ {
+ super();
+
+ }
+
+ public RnamlFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+
+ }
+
+ public RnamlFile(FileParse source) throws IOException
+ {
+ super(source);
+
+ }
+
+ // public RnamlFile(BufferedReader r) throws IOException,
+ // ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException,
+ // ExceptionPermissionDenied, ExceptionLoadingFailed
+ // {
+ // super();
+ // parse(r);
+ // // sets the index of each sequence in the alignment
+ // for( int i=0,c=seqs.size(); i<c; i++ ) {
+ // seqs.get(i).setIndex(i);
+ // }
+ //
+ //
+ // }
+
+ public BufferedReader CreateReader() throws FileNotFoundException
+ {
+ FileReader fr = null;
+ fr = new FileReader(inFile);
+
+ BufferedReader r = new BufferedReader(fr);
+ return r;
+ }
+
+ public void parse() throws IOException
+ {
+ result = null;
+ try
+ {
+ result = RNAFactory.loadSecStrRNAML(getReader());
+
+ } catch (ExceptionPermissionDenied pdx)
+ {
+ errormessage = "Couldn't access datasource (" + pdx.getMessage()
+ + ")";
+ throw new IOException(pdx);
+ } catch (ExceptionLoadingFailed lf)
+ {
+ errormessage = "Couldn't process data as RNAML file ("
+ + lf.getMessage() + ")";
+ throw new IOException(lf);
+ } catch (ExceptionFileFormatOrSyntax iff)
+ {
+ errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
+ throw new IOException(iff);
+ }
+
+ SequenceI[] seqs = new SequenceI[result.size()];
+
+ for (int i = 0; i < result.size(); i++)
+ {
+ // DEBUG System.err.println("RNAML entry "+i);
+ RNA current = result.get(i);
+ String seq = current.getSeq();
+ // DEBUG System.err.println(seq);
+ String rna = current.getStructDBN(true);
+ // DEBUG System.err.println(rna);
+
+ int begin = 1;
+ int end = seq.length(); // TODO: compute non-gapped length for sequence
+
+ id = current.getName();
+ seqs[i] = new Sequence(id, seq, begin, end);
+
+ String[] annot = new String[rna.length()];
+ Annotation[] ann = new Annotation[rna.length()];
+
+ for (int j = 0; j < rna.length(); j++)
+ {
+ annot[j] = rna.substring(j, j + 1);
+
+ }
+
+ for (int k = 0; k < rna.length(); k++)
+ {
+ ann[k] = new Annotation(annot[k], "",
+ jalview.schemes.ResidueProperties.getRNASecStrucState(
+ annot[k]).charAt(0), 0f);
+
+ }
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
+ current.getID(), ann);
+
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+ annotations.addElement(align);
+ }
+ setSeqs(seqs);
+ }
+
+ public static String print(SequenceI[] s)
+ {
+ // TODO: implement RNAML export option
+ return "not yet implemented";
+ }
+
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int b = 0;
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ {
+ dataName = dataName.substring(b + 1).trim();
+
+ }
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;
+ dataName = dataName.substring(1, e).trim();
+ return dataName;
+ }
+}
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * 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/>.
- */
-/*
- * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
- */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import com.stevesoft.pat.*;
-import jalview.datamodel.*;
-
-// import org.apache.log4j.*;
-
-/**
- * This class is supposed to parse a Stockholm format file into Jalview There
- * are TODOs in this class: we do not know what the database source and version
- * is for the file when parsing the #GS= AC tag which associates accessions with
- * sequences. Database references are also not parsed correctly: a separate
- * reference string parser must be added to parse the database reference form
- * into Jalview's local representation.
- *
- * @author bsb at sanger.ac.uk
- * @version 0.3 + jalview mods
- *
- */
-public class StockholmFile extends AlignFile
-{
- // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
-
- public StockholmFile()
- {
- }
-
- public StockholmFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
- public StockholmFile(FileParse source) throws IOException
- {
- super(source);
- }
-
- public void initData()
- {
- super.initData();
- }
-
- /**
- * Parse a file in Stockholm format into Jalview's data model. The file has to
- * be passed at construction time
- *
- * @throws IOException
- * If there is an error with the input file
- */
- public void parse() throws IOException
- {
- StringBuffer treeString = new StringBuffer();
- String treeName = null;
- // --------------- Variable Definitions -------------------
- String line;
- String version;
- // String id;
- Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- Hashtable seqs = new Hashtable();
- Regex p, r, rend, s, x;
-
- // Temporary line for processing RNA annotation
- // String RNAannot = "";
-
- // ------------------ Parsing File ----------------------
- // First, we have to check that this file has STOCKHOLM format, i.e. the
- // first line must match
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");
- if (!r.search(nextLine()))
- {
- throw new IOException(
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
- }
- else
- {
- version = r.stringMatched(1);
- // logger.debug("Stockholm version: " + version);
- }
-
- // We define some Regexes here that will be used regularily later
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
- // id/from/to
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
-
- // Convert all bracket types to parentheses (necessary for passing to VARNA)
- Regex openparen = new Regex("(<|\\[)", "(");
- Regex closeparen = new Regex("(>|\\])", ")");
-
- // Detect if file is RNA by looking for bracket types
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
-
- rend.optimize();
- p.optimize();
- s.optimize();
- r.optimize();
- x.optimize();
- openparen.optimize();
- closeparen.optimize();
-
- while ((line = nextLine()) != null)
- {
- if (line.length() == 0)
- {
- continue;
- }
- if (rend.search(line))
- {
- // End of the alignment, pass stuff back
-
- this.noSeqs = seqs.size();
- // logger.debug("Number of sequences: " + this.noSeqs);
- Enumeration accs = seqs.keys();
- while (accs.hasMoreElements())
- {
- String acc = (String) accs.nextElement();
- // logger.debug("Processing sequence " + acc);
- String seq = (String) seqs.remove(acc);
- if (maxLength < seq.length())
- {
- maxLength = seq.length();
- }
- int start = 1;
- int end = -1;
- String sid = acc;
- /*
- * Retrieve hash of annotations for this accession Associate
- * Annotation with accession
- */
- Hashtable accAnnotations = null;
-
- if (seqAnn != null && seqAnn.containsKey(acc))
- {
- accAnnotations = (Hashtable) seqAnn.remove(acc);
- // TODO: add structures to sequence
- }
-
- // Split accession in id and from/to
- if (p.search(acc))
- {
- sid = p.stringMatched(1);
- start = Integer.parseInt(p.stringMatched(2));
- end = Integer.parseInt(p.stringMatched(3));
- }
- // logger.debug(sid + ", " + start + ", " + end);
-
- Sequence seqO = new Sequence(sid, seq, start, end);
- // Add Description (if any)
- if (accAnnotations != null && accAnnotations.containsKey("DE"))
- {
- String desc = (String) accAnnotations.get("DE");
- seqO.setDescription((desc == null) ? "" : desc);
- }
- // Add DB References (if any)
- if (accAnnotations != null && accAnnotations.containsKey("DR"))
- {
- String dbr = (String) accAnnotations.get("DR");
- if (dbr != null && dbr.indexOf(";") > -1)
- {
- String src = dbr.substring(0, dbr.indexOf(";"));
- String acn = dbr.substring(dbr.indexOf(";") + 1);
- jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
- // seqO.addDBRef(dbref);
- }
- }
- if (accAnnotations != null && accAnnotations.containsKey("SS"))
- {
- Vector v = (Vector) accAnnotations.get("SS");
-
- for (int i = 0; i < v.size(); i++)
- {
- AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);
- seqO.addAlignmentAnnotation(an);
- // annotations.add(an);
- }
- }
-
- Hashtable features = null;
- // We need to adjust the positions of all features to account for gaps
- try
- {
- features = (Hashtable) accAnnotations.remove("features");
- } catch (java.lang.NullPointerException e)
- {
- // loggerwarn("Getting Features for " + acc + ": " +
- // e.getMessage());
- // continue;
- }
- // if we have features
- if (features != null)
- {
- int posmap[] = seqO.findPositionMap();
- Enumeration i = features.keys();
- while (i.hasMoreElements())
- {
- // TODO: parse out secondary structure annotation as annotation
- // row
- // TODO: parse out scores as annotation row
- // TODO: map coding region to core jalview feature types
- String type = i.nextElement().toString();
- Hashtable content = (Hashtable) features.remove(type);
- Enumeration j = content.keys();
- while (j.hasMoreElements())
- {
- String desc = j.nextElement().toString();
- String ns = content.get(desc).toString();
- char[] byChar = ns.toCharArray();
- for (int k = 0; k < byChar.length; k++)
- {
- char c = byChar[k];
- if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
- // uses
- // '.'
- // for
- // feature
- // background
- {
- int new_pos = posmap[k]; // look up nearest seqeunce
- // position to this column
- SequenceFeature feat = new SequenceFeature(type, desc,
- new_pos, new_pos, 0f, null);
-
- seqO.addSequenceFeature(feat);
- }
- }
- }
-
- }
-
- }
- // garbage collect
-
- // logger.debug("Adding seq " + acc + " from " + start + " to " + end
- // + ": " + seq);
- this.seqs.addElement(seqO);
- }
- return; // finished parsing this segment of source
- }
- else if (!r.search(line))
- {
- // System.err.println("Found sequence line: " + line);
-
- // Split sequence in sequence and accession parts
- if (!x.search(line))
- {
- // logger.error("Could not parse sequence line: " + line);
- throw new IOException("Could not parse sequence line: " + line);
- }
- String ns = (String) seqs.get(x.stringMatched(1));
- if (ns == null)
- {
- ns = "";
- }
- ns += x.stringMatched(2);
-
- seqs.put(x.stringMatched(1), ns);
- }
- else
- {
- String annType = r.stringMatched(1);
- String annContent = r.stringMatched(2);
-
- // System.err.println("type:" + annType + " content: " + annContent);
-
- if (annType.equals("GF"))
- {
- /*
- * Generic per-File annotation, free text Magic features: #=GF NH
- * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
- * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
- *
- * Compulsory fields: ------------------
- *
- * AC Accession number: Accession number in form PFxxxxx.version or
- * PBxxxxxx. ID Identification: One word name for family. DE
- * Definition: Short description of family. AU Author: Authors of the
- * entry. SE Source of seed: The source suggesting the seed members
- * belong to one family. GA Gathering method: Search threshold to
- * build the full alignment. TC Trusted Cutoff: Lowest sequence score
- * and domain score of match in the full alignment. NC Noise Cutoff:
- * Highest sequence score and domain score of match not in full
- * alignment. TP Type: Type of family -- presently Family, Domain,
- * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
- * Alignment Method The order ls and fs hits are aligned to the model
- * to build the full align. // End of alignment.
- *
- * Optional fields: ----------------
- *
- * DC Database Comment: Comment about database reference. DR Database
- * Reference: Reference to external database. RC Reference Comment:
- * Comment about literature reference. RN Reference Number: Reference
- * Number. RM Reference Medline: Eight digit medline UI number. RT
- * Reference Title: Reference Title. RA Reference Author: Reference
- * Author RL Reference Location: Journal location. PI Previous
- * identifier: Record of all previous ID lines. KW Keywords: Keywords.
- * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
- * NL Location: Location of nested domains - sequence ID, start and
- * end of insert.
- *
- * Obsolete fields: ----------- AL Alignment method of seed: The
- * method used to align the seed members.
- */
- // Let's save the annotations, maybe we'll be able to do something
- // with them later...
- Regex an = new Regex("(\\w+)\\s*(.*)");
- if (an.search(annContent))
- {
- if (an.stringMatched(1).equals("NH"))
- {
- treeString.append(an.stringMatched(2));
- }
- else if (an.stringMatched(1).equals("TN"))
- {
- if (treeString.length() > 0)
- {
- if (treeName == null)
- {
- treeName = "Tree " + (getTreeCount() + 1);
- }
- addNewickTree(treeName, treeString.toString());
- }
- treeName = an.stringMatched(2);
- treeString = new StringBuffer();
- }
- setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
- }
- }
- else if (annType.equals("GS"))
- {
- // Generic per-Sequence annotation, free text
- /*
- * Pfam uses these features: Feature Description ---------------------
- * ----------- AC <accession> ACcession number DE <freetext>
- * DEscription DR <db>; <accession>; Database Reference OS <organism>
- * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
- * LO <look> Look (Color, etc.)
- */
- if (s.search(annContent))
- {
- String acc = s.stringMatched(1);
- String type = s.stringMatched(2);
- String content = s.stringMatched(3);
- // TODO: store DR in a vector.
- // TODO: store AC according to generic file db annotation.
- Hashtable ann;
- if (seqAnn.containsKey(acc))
- {
- ann = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- ann = new Hashtable();
- }
- ann.put(type, content);
- seqAnn.put(acc, ann);
- }
- else
- {
- throw new IOException("Error parsing " + line);
- }
- }
- else if (annType.equals("GC"))
- {
- // Generic per-Column annotation, exactly 1 char per column
- // always need a label.
- if (x.search(annContent))
- {
- // parse out and create alignment annotation directly.
- parseAnnotationRow(annotations, x.stringMatched(1),
- x.stringMatched(2));
- }
- }
- else if (annType.equals("GR"))
- {
- // Generic per-Sequence AND per-Column markup, exactly 1 char per
- // column
- /*
- * Feature Description Markup letters ------- -----------
- * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
- * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
- * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
- * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
- * or after) [0-2]
- */
- if (s.search(annContent))
- {
- String acc = s.stringMatched(1);
- String type = s.stringMatched(2);
- String seq = new String(s.stringMatched(3));
- String description = null;
- // Check for additional information about the current annotation
- // We use a simple string tokenizer here for speed
- StringTokenizer sep = new StringTokenizer(seq, " \t");
- description = sep.nextToken();
- if (sep.hasMoreTokens())
- {
- seq = sep.nextToken();
- }
- else
- {
- seq = description;
- description = new String();
- }
- // sequence id with from-to fields
-
- Hashtable ann;
- // Get an object with all the annotations for this sequence
- if (seqAnn.containsKey(acc))
- {
- // logger.debug("Found annotations for " + acc);
- ann = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- // logger.debug("Creating new annotations holder for " + acc);
- ann = new Hashtable();
- seqAnn.put(acc, ann);
- }
- // TODO test structure, call parseAnnotationRow with vector from
- // hashtable for specific sequence
- Hashtable features;
- // Get an object with all the content for an annotation
- if (ann.containsKey("features"))
- {
- // logger.debug("Found features for " + acc);
- features = (Hashtable) ann.get("features");
- }
- else
- {
- // logger.debug("Creating new features holder for " + acc);
- features = new Hashtable();
- ann.put("features", features);
- }
-
- Hashtable content;
- if (features.containsKey(this.id2type(type)))
- {
- // logger.debug("Found content for " + this.id2type(type));
- content = (Hashtable) features.get(this.id2type(type));
- }
- else
- {
- // logger.debug("Creating new content holder for " +
- // this.id2type(type));
- content = new Hashtable();
- features.put(this.id2type(type), content);
- }
- String ns = (String) content.get(description);
- if (ns == null)
- {
- ns = "";
- }
- ns += seq;
- content.put(description, ns);
-
- if (type.equals("SS"))
- {
- Hashtable strucAnn;
- if (seqAnn.containsKey(acc))
- {
- strucAnn = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- strucAnn = new Hashtable();
- }
-
- Vector newStruc = new Vector();
- parseAnnotationRow(newStruc, type, ns);
-
- strucAnn.put(type, newStruc);
- seqAnn.put(acc, strucAnn);
- }
- }
- else
- {
- System.err
- .println("Warning - couldn't parse sequence annotation row line:\n"
- + line);
- // throw new IOException("Error parsing " + line);
- }
- }
- else
- {
- throw new IOException("Unknown annotation detected: " + annType
- + " " + annContent);
- }
- }
- }
- if (treeString.length() > 0)
- {
- if (treeName == null)
- {
- treeName = "Tree " + (1 + getTreeCount());
- }
- addNewickTree(treeName, treeString.toString());
- }
- }
-
- protected static AlignmentAnnotation parseAnnotationRow(
- Vector annotation, String label, String annots)
- {
- String convert1, convert2 = null;
-
- // Convert all bracket types to parentheses
- Regex openparen = new Regex("(<|\\[)", "(");
- Regex closeparen = new Regex("(>|\\])", ")");
-
- // Detect if file is RNA by looking for bracket types
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
-
- convert1 = openparen.replaceAll(annots);
- convert2 = closeparen.replaceAll(convert1);
- annots = convert2;
-
- String type = (label.indexOf("_cons") == label.length() - 5) ? label
- .substring(0, label.length() - 5) : label;
- boolean ss = false;
- type = id2type(type);
- if (type.equals("secondary structure"))
- {
- ss = true;
- }
- // decide on secondary structure or not.
- Annotation[] els = new Annotation[annots.length()];
- for (int i = 0; i < annots.length(); i++)
- {
- String pos = annots.substring(i, i + 1);
- Annotation ann;
- ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
- // be written out
- if (ss)
- {
- if (detectbrackets.search(pos))
- {
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getRNASecStrucState(pos).charAt(0);
- }
- else
- {
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getDssp3state(pos).charAt(0);
- }
-
- if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
- {
- ann.displayCharacter = ""; // null; // " ";
- }
- else
- {
- ann.displayCharacter = " " + ann.displayCharacter;
- }
- }
-
- els[i] = ann;
- }
- AlignmentAnnotation annot = null;
- Enumeration e = annotation.elements();
- while (e.hasMoreElements())
- {
- annot = (AlignmentAnnotation) e.nextElement();
- if (annot.label.equals(type))
- break;
- annot = null;
- }
- if (annot == null)
- {
- annot = new AlignmentAnnotation(type, type, els);
- annotation.addElement(annot);
- }
- else
- {
- Annotation[] anns = new Annotation[annot.annotations.length
- + els.length];
- System.arraycopy(annot.annotations, 0, anns, 0,
- annot.annotations.length);
- System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
- annot.annotations = anns;
- // System.out.println("else: ");
- }
- return annot;
- }
-
- public static String print(SequenceI[] s)
- {
- return "not yet implemented";
- }
-
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- private static Hashtable typeIds = null;
- static
- {
- if (typeIds == null)
- {
- typeIds = new Hashtable();
- typeIds.put("SS", "secondary structure");
- typeIds.put("SA", "surface accessibility");
- typeIds.put("TM", "transmembrane");
- typeIds.put("PP", "posterior probability");
- typeIds.put("LI", "ligand binding");
- typeIds.put("AS", "active site");
- typeIds.put("IN", "intron");
- typeIds.put("IR", "interacting residue");
- typeIds.put("AC", "accession");
- typeIds.put("OS", "organism");
- typeIds.put("CL", "class");
- typeIds.put("DE", "description");
- typeIds.put("DR", "reference");
- typeIds.put("LO", "look");
- typeIds.put("RF", "reference positions");
-
- }
- }
-
- protected static String id2type(String id)
- {
- if (typeIds.containsKey(id))
- {
- return (String) typeIds.get(id);
- }
- System.err.println("Warning : Unknown Stockholm annotation type code "
- + id);
- return id;
- }
- /**
- * //ssline is complete secondary structure line private AlignmentAnnotation
- * addHelices(Vector annotation, String label, String ssline) {
- *
- * // decide on secondary structure or not. Annotation[] els = new
- * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {
- * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new
- * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
- *
- * ann.secondaryStructure =
- * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);
- *
- * ann.displayCharacter = "x" + ann.displayCharacter;
- *
- * System.out.println(ann.displayCharacter);
- *
- * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =
- * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =
- * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))
- * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =
- * new AlignmentAnnotation(type, type, els);
- * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new
- * Annotation[helicesAnnot.annotations.length + els.length];
- * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,
- * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,
- * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =
- * anns; }
- *
- * helicesAnnot.features = Rna.GetBasePairs(ssline);
- * Rna.HelixMap(helicesAnnot.features);
- *
- *
- * return helicesAnnot; }
- */
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+/*\r
+ * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk\r
+ */\r
+package jalview.io;\r
+\r
+import jalview.datamodel.AlignmentAnnotation;\r
+import jalview.datamodel.Annotation;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceI;\r
+\r
+import java.io.BufferedReader;\r
+import java.io.FileReader;\r
+import java.io.IOException;\r
+import java.util.ArrayList;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
+\r
+import com.stevesoft.pat.Regex;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+import fr.orsay.lri.varna.factories.RNAFactory;\r
+import fr.orsay.lri.varna.models.rna.RNA;\r
+\r
+// import org.apache.log4j.*;\r
+\r
+/**\r
+ * This class is supposed to parse a Stockholm format file into Jalview There\r
+ * are TODOs in this class: we do not know what the database source and version\r
+ * is for the file when parsing the #GS= AC tag which associates accessions with\r
+ * sequences. Database references are also not parsed correctly: a separate\r
+ * reference string parser must be added to parse the database reference form\r
+ * into Jalview's local representation.\r
+ * \r
+ * @author bsb at sanger.ac.uk\r
+ * @version 0.3 + jalview mods\r
+ * \r
+ */\r
+public class StockholmFile extends AlignFile\r
+{\r
+ // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
+ protected ArrayList<RNA> result;\r
+\r
+ public String id;\r
+\r
+ public StockholmFile()\r
+ {\r
+ }\r
+\r
+ public StockholmFile(String inFile, String type) throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public StockholmFile(FileParse source) throws IOException\r
+ {\r
+ super(source);\r
+ }\r
+\r
+ public void initData()\r
+ {\r
+ super.initData();\r
+ }\r
+\r
+ /**\r
+ * Parse a file in Stockholm format into Jalview's data model. The file has to\r
+ * be passed at construction time\r
+ * \r
+ * @throws IOException\r
+ * If there is an error with the input file\r
+ */\r
+ public void parse() throws IOException\r
+ {\r
+ FileReader fr = null;\r
+ fr = new FileReader(inFile);\r
+\r
+ BufferedReader r = new BufferedReader(fr);\r
+ result = null;\r
+ try\r
+ {\r
+ result = RNAFactory.loadSecStrStockholm(r);\r
+ } catch (ExceptionUnmatchedClosingParentheses umcp)\r
+ {\r
+ errormessage = "Unmatched parentheses in annotation. Aborting ("\r
+ + umcp.getMessage() + ")";\r
+ throw new IOException(umcp);\r
+ }\r
+ // DEBUG System.out.println("this is the secondary scructure:"\r
+ // +result.size());\r
+ SequenceI[] seqs = new SequenceI[result.size()];\r
+ for (int i = 0; i < result.size(); i++)\r
+ {\r
+ // DEBUG System.err.println("Processing i'th sequence in Stockholm file")\r
+ RNA current = result.get(i);\r
+\r
+ String seq = current.getSeq();\r
+ String rna = current.getStructDBN(true);\r
+ // DEBUG System.out.println(seq);\r
+ // DEBUG System.err.println(rna);\r
+ int begin = 0;\r
+ int end = seq.length() - 1;\r
+ id = safeName(getDataName());\r
+ seqs[i] = new Sequence(id, seq, begin, end);\r
+ String[] annot = new String[rna.length()];\r
+ Annotation[] ann = new Annotation[rna.length()];\r
+ for (int j = 0; j < rna.length(); j++)\r
+ {\r
+ annot[j] = rna.substring(j, j + 1);\r
+\r
+ }\r
+\r
+ for (int k = 0; k < rna.length(); k++)\r
+ {\r
+ ann[k] = new Annotation(annot[k], "",\r
+ jalview.schemes.ResidueProperties.getRNASecStrucState(\r
+ annot[k]).charAt(0), 0f);\r
+\r
+ }\r
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",\r
+ current.getID(), ann);\r
+\r
+ seqs[i].addAlignmentAnnotation(align);\r
+ seqs[i].setRNA(result.get(i));\r
+ this.annotations.addElement(align);\r
+ }\r
+ this.setSeqs(seqs);\r
+\r
+ }\r
+\r
+ protected static AlignmentAnnotation parseAnnotationRow(\r
+ Vector annotation, String label, String annots)\r
+ {\r
+ String convert1, convert2 = null;\r
+\r
+ // Convert all bracket types to parentheses\r
+ Regex openparen = new Regex("(<|\\[)", "(");\r
+ Regex closeparen = new Regex("(>|\\])", ")");\r
+\r
+ // Detect if file is RNA by looking for bracket types\r
+ Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
+\r
+ convert1 = openparen.replaceAll(annots);\r
+ convert2 = closeparen.replaceAll(convert1);\r
+ annots = convert2;\r
+\r
+ String type = (label.indexOf("_cons") == label.length() - 5) ? label\r
+ .substring(0, label.length() - 5) : label;\r
+ boolean ss = false;\r
+ type = id2type(type);\r
+ if (type.equals("secondary structure"))\r
+ {\r
+ ss = true;\r
+ }\r
+ // decide on secondary structure or not.\r
+ Annotation[] els = new Annotation[annots.length()];\r
+ for (int i = 0; i < annots.length(); i++)\r
+ {\r
+ String pos = annots.substring(i, i + 1);\r
+ Annotation ann;\r
+ ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
+ // be written out\r
+ if (ss)\r
+ {\r
+ if (detectbrackets.search(pos))\r
+ {\r
+ ann.secondaryStructure = jalview.schemes.ResidueProperties\r
+ .getRNASecStrucState(pos).charAt(0);\r
+ }\r
+ else\r
+ {\r
+ ann.secondaryStructure = jalview.schemes.ResidueProperties\r
+ .getDssp3state(pos).charAt(0);\r
+ }\r
+\r
+ if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')\r
+ {\r
+ ann.displayCharacter = ""; // null; // " ";\r
+ }\r
+ else\r
+ {\r
+ ann.displayCharacter = " " + ann.displayCharacter;\r
+ }\r
+ }\r
+\r
+ els[i] = ann;\r
+ }\r
+ AlignmentAnnotation annot = null;\r
+ Enumeration e = annotation.elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ annot = (AlignmentAnnotation) e.nextElement();\r
+ if (annot.label.equals(type))\r
+ break;\r
+ annot = null;\r
+ }\r
+ if (annot == null)\r
+ {\r
+ annot = new AlignmentAnnotation(type, type, els);\r
+ annotation.addElement(annot);\r
+ }\r
+ else\r
+ {\r
+ Annotation[] anns = new Annotation[annot.annotations.length\r
+ + els.length];\r
+ System.arraycopy(annot.annotations, 0, anns, 0,\r
+ annot.annotations.length);\r
+ System.arraycopy(els, 0, anns, annot.annotations.length, els.length);\r
+ annot.annotations = anns;\r
+ // System.out.println("else: ");\r
+ }\r
+ return annot;\r
+ }\r
+\r
+ public static String print(SequenceI[] s)\r
+ {\r
+ return "not yet implemented";\r
+ }\r
+\r
+ public String print()\r
+ {\r
+ return print(getSeqsAsArray());\r
+ }\r
+\r
+ private static Hashtable typeIds = null;\r
+ static\r
+ {\r
+ if (typeIds == null)\r
+ {\r
+ typeIds = new Hashtable();\r
+ typeIds.put("SS", "secondary structure");\r
+ typeIds.put("SA", "surface accessibility");\r
+ typeIds.put("TM", "transmembrane");\r
+ typeIds.put("PP", "posterior probability");\r
+ typeIds.put("LI", "ligand binding");\r
+ typeIds.put("AS", "active site");\r
+ typeIds.put("IN", "intron");\r
+ typeIds.put("IR", "interacting residue");\r
+ typeIds.put("AC", "accession");\r
+ typeIds.put("OS", "organism");\r
+ typeIds.put("CL", "class");\r
+ typeIds.put("DE", "description");\r
+ typeIds.put("DR", "reference");\r
+ typeIds.put("LO", "look");\r
+ typeIds.put("RF", "reference positions");\r
+\r
+ }\r
+ }\r
+\r
+ protected static String id2type(String id)\r
+ {\r
+ if (typeIds.containsKey(id))\r
+ {\r
+ return (String) typeIds.get(id);\r
+ }\r
+ System.err.println("Warning : Unknown Stockholm annotation type code "\r
+ + id);\r
+ return id;\r
+ }\r
+ /**\r
+ * make a friendly ID string.\r
+ * \r
+ * @param dataName\r
+ * @return truncated dataName to after last '/'\r
+ */\r
+ private String safeName(String dataName)\r
+ {\r
+ int b = 0;\r
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())\r
+ {\r
+ dataName = dataName.substring(b + 1).trim();\r
+\r
+ }\r
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;\r
+ dataName = dataName.substring(1, e).trim();\r
+ return dataName;\r
+ }\r
+}
\ No newline at end of file
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
colours.add(purinePyrimidineColour);
// colours.add(covariationColour);
colours.add(tcoffeeColour);
-
+ colours.add(RNAInteractionColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
purinePyrimidineColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.RNAINTERACTION:
+ RNAInteractionColour.setSelected(true);
+
+ break;
/*
* case ColourSchemeProperty.COVARIATION:
* covariationColour.setSelected(true);
});
purinePyrimidineColour.setText("Purine/Pyrimidine");
- purinePyrimidineColour
- .addActionListener(new java.awt.event.ActionListener()
+ purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
purinePyrimidineColour_actionPerformed(e);
}
});
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
/*
* covariationColour.setText("Covariation");
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(RNAInteractionColour);
// colourMenu.add(covariationColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
{
}
+
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
/*
* protected void covariationColour_actionPerformed(ActionEvent e) { }
*/
private void jbInit() throws Exception
{
+
FileMenu.setText("File");
HelpMenu.setText("Help");
VamsasMenu.setText("Vamsas");
// If a closing base pair half of the stem, display a backward arrow
if (column > 0 && closeparen.search(dc))
{
+
if (diffupstream)
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
}
else
{
+
// display a forward arrow
if (diffdownstream)
{
*/
private int imgWidth;
+
+ public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, Annotation[] row_annotations,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
+ {
+ //System.out.println(nonCanColor);
+
+ g.setColor(nonCanColor);
+ int sCol = (lastSSX / charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * charWidth);
+ Regex closeparen = new Regex("}|]|<|a|b|c|d|e|f|g|h|i|j|k|l|m|n|o|p|q|r|s|t|u|v|w|x|y|z");
+
+ String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
+ : row_annotations[column - 1].displayCharacter;
+
+ boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ boolean diffdownstream = !validRes || !validEnd
+ || row_annotations[column] == null
+ || !dc.equals(row_annotations[column].displayCharacter);
+ // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
+ // If a closing base pair half of the stem, display a backward arrow
+ if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc)) )
+ {
+
+ if (diffupstream)
+ // if (validRes && column>1 && row_annotations[column-2]!=null &&
+ // dc.equals(row_annotations[column-2].displayCharacter))
+ {
+ g.fillPolygon(new int[]
+ { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x1 += 5;
+ }
+ if (diffdownstream)
+ {
+ x2 -= 1;
+ }
+ }
+ else
+ {
+
+ // display a forward arrow
+ if (diffdownstream)
+ {
+ g.fillPolygon(new int[]
+ { x2 - 5, x2 - 5, x2 }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x2 -= 5;
+ }
+ if (diffupstream)
+ {
+ x1 += 1;
+ }
+ }
+ // draw arrow body
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ }
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
// av)
public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
.equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
.length() < 2 && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(row_annotations[column].displayCharacter, x
+ g.drawString(row_annotations[column].displayCharacter
+ , x
* charWidth + charOffset, y + iconOffset);
}
g.setFont(ofont);
if (row.hasIcons)
{
char ss = validRes ? row_annotations[column].secondaryStructure
- : ' ';
- if (ss == 'S')
+ : '-';
+
+ if (ss == '(')
{
// distinguish between forward/backward base-pairing
if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
- ss = 's';
+
+ ss = ')';
+
+ }
+ }
+ if (ss == '[')
+ {
+ if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
+ {
+ ss = ']';
+
+
}
}
+ if (ss == '{')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('}') > -1)
+ {
+ ss = '}';
+
+
+ }
+ }
+ if (ss == '<')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('<') > -1)
+ {
+ ss = '>';
+
+
+ }
+ }
+ if (ss == 'A')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('a') > -1)
+ {
+ ss = 'a';
+
+
+ }
+ }
+
+ if (ss == 'B')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('b') > -1)
+ {
+ ss = 'b';
+
+ }
+ }
+
+ if (ss == 'C')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('c') > -1)
+ {
+ ss = 'c';
+
+ }
+ }
+ if (ss == 'D')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('d') > -1)
+ {
+ ss = 'd';
+
+ }
+ }
+ if (ss == '1')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('e') > -1)
+ {
+ ss = 'e';
+
+ }
+ }
+ if (ss == 'F')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('f') > -1)
+ {
+ ss = 'f';
+
+ }
+ }
+ if (ss == 'G')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('g') > -1)
+ {
+ ss = 'g';
+
+ }
+ }
+ if (ss == '2')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('h') > -1)
+ {
+ ss = 'h';
+
+ }
+ }
+ if (ss == 'I')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('i') > -1)
+ {
+ ss = 'i';
+
+ }
+ }
+ if (ss == 'J')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('j') > -1)
+ {
+ ss = 'j';
+
+ }
+ }
+ if (ss == 'K')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('k') > -1)
+ {
+ ss = 'k';
+
+ }
+ }
+ if (ss == 'L')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('l') > -1)
+ {
+ ss = 'l';
+
+ }
+ }
+ if (ss == 'M')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('m') > -1)
+ {
+ ss = 'm';
+
+ }
+ }
+ if (ss == 'N')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('n') > -1)
+ {
+ ss = 'n';
+
+ }
+ }
+ if (ss == 'O')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('o') > -1)
+ {
+ ss = 'o';
+
+ }
+ }
+ if (ss == 'P')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('p') > -1)
+ {
+ ss = 'p';
+
+ }
+ }
+ if (ss == 'Q')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('q') > -1)
+ {
+ ss = 'q';
+
+ }
+ }
+ if (ss == 'R')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('r') > -1)
+ {
+ ss = 'r';
+
+ }
+ }
+ if (ss == 'S')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('s') > -1)
+ {
+ ss = 's';
+
+ }
+ }
+ if (ss == 'T')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('t') > -1)
+ {
+ ss = 't';
+
+ }
+ }
+ if (ss == 'U')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('u') > -1)
+ {
+ ss = 'u';
+
+ }
+ }
+ if (ss == 'V')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('v') > -1)
+ {
+ ss = 'v';
+
+ }
+ }
+ if (ss == 'W')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('w') > -1)
+ {
+ ss = 'w';
+
+ }
+ }
+ if (ss == 'X')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('x') > -1)
+ {
+ ss = 'x';
+
+ }
+ }
+ if (ss == 'Y')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('y') > -1)
+ {
+ ss = 'y';
+
+ }
+ }
+ if (ss == 'Z')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('z') > -1)
+ {
+ ss = 'z';
+
+ }
+ }
if (!validRes || (ss != lastSS))
{
if (x > -1)
iconOffset, startRes, column, validRes, validEnd);
break;
- case 'S': // Stem case for RNA secondary structure
- case 's': // and opposite direction
- drawStemAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
+ case '(': // Stem case for RNA secondary structure
+ case ')': // and opposite direction
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+// case 'S': // Stem case for RNA secondary structure
+// case 's': // and opposite direction
+// drawStemAnnot(g, row_annotations, lastSSX, x, y,
+// iconOffset, startRes, column, validRes, validEnd);
break;
-
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case '1':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case '2':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'S':
+ case 's':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+ //System.out.println(lastSS);
+ Color nonCanColor= getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
startRes, column, validRes, validEnd);
break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case '1':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case '2':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+ //System.out.println(lastSS);
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g,nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
default:
drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
startRes, column, validRes, validEnd);
private final Color HELIX_COLOUR = Color.red;
private final Color STEM_COLOUR = Color.blue;
+
+ private Color sdNOTCANONICAL_COLOUR;
public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
int x, int y, int iconOffset, int startRes, int column,
x += charWidth;
}
}
+
+
+ Color getNotCanonicalColor(char lastss)
+ {
+ switch (lastss)
+ {
+ case '{':
+ case '}':
+ return Color.cyan;
+
+ case '[':
+ case ']':
+ return Color.green;
+
+ case '>':
+ case '<':
+ return Color.magenta;
+
+ case 'A':
+ case 'a':
+ return Color.orange;
+
+ case 'B':
+ case 'b':
+ return Color.pink;
+
+ case 'C':
+ case 'c':
+ return Color.red;
+
+ case 'D':
+ case 'd':
+ return Color.yellow;
+
+ case '1':
+ case 'e':
+ return Color.black;
+
+ case 'F':
+ case 'f':
+ return Color.darkGray;
+
+ case 'G':
+ case 'g':
+ return Color.gray;
+
+ case '2':
+ case 'h':
+ return Color.lightGray;
+
+ case 'I':
+ case 'i':
+ return Color.white;
+
+ case 'J':
+ case 'j':
+ return Color.cyan;
+
+ case 'K':
+ case 'k':
+ return Color.magenta;
+
+ case 'L':
+ case 'l':
+ return Color.orange;
+
+ case 'M':
+ case 'm':
+ return Color.red;
+
+ case 'N':
+ case 'n':
+ return Color.yellow;
+
+ case 'O':
+ case 'o':
+ return Color.pink;
+
+ case 'P':
+ case 'p':
+ return Color.black;
+
+ case 'Q':
+ case 'q':
+ return Color.blue;
+
+ case 'R':
+ case 'r':
+ return Color.cyan;
+
+ case 'S':
+ case 's':
+ return Color.magenta;
+
+ case 'T':
+ case 't':
+ return Color.darkGray;
+
+ case 'U':
+ case 'u':
+ return Color.yellow;
+
+ case 'V':
+ case 'v':
+ return Color.blue;
+
+ case 'W':
+ case 'w':
+ return Color.orange;
+
+ case 'X':
+ case 'x':
+ return Color.magenta;
+
+ case 'Y':
+ case 'y':
+ return Color.blue;
+
+ case 'Z':
+ case 'z':
+ return Color.blue;
+
+ default :
+ System.out.println("This is not a interaction");
+ return null;
+
+ }
+ }
}
+
+
+
public static final int TCOFFEE = 15;
+ public static final int RNAINTERACTION = 16;
+
/**
* index of first colourscheme (includes 'None')
*/
{
ret = PURINEPYRIMIDINE;
}
+
+ else if (name.equalsIgnoreCase("RNA Interaction type"))
+ {
+ ret = RNAINTERACTION;
+ }
// else if (name.equalsIgnoreCase("Covariation"))
// {
// ret = COVARIATION;
{
index = TCOFFEE;
}
+ else if (cs instanceof RNAInteractionColourScheme)
+ {
+ index = RNAINTERACTION;
+ }
+
+
/*
* else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
*/
ret = "T-Coffee Scores";
break;
+
+ case RNAINTERACTION:
+ ret = "RNA Interaction type";
+
+ break;
/*
* case COVARIATION: ret = "Covariation";
*
case TCOFFEE:
cs = new TCoffeeColourScheme(coll);
- // case COVARIATION:
- // cs = new CovariationColourScheme(annotation);
+ break;
+
+ case RNAINTERACTION:
+ cs = new RNAInteractionColourScheme();
+ break;
+
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
// break;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+ package jalview.schemes;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+
+public class RNAInteractionColourScheme extends ResidueColourScheme{
+ public RNAInteractionColourScheme()
+ {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c)
+ {
+ // System.out.println("called"); log.debug
+ return colors[ResidueProperties.nucleotideIndex[c]];
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color currentColour;
+ if ((threshold == 0) || aboveThreshold(c, j))
+ {
+ try
+ {
+ currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+ } catch (Exception ex)
+ {
+ return Color.white;
+ }
+ }
+ else
+ {
+ return Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+ }
static
{
toRNAssState = new Hashtable();
- toRNAssState.put(")", "S");
- toRNAssState.put("(", "S");
+ toRNAssState.put(")", "(");
+ toRNAssState.put("(", "(");
+ toRNAssState.put("]", "[");
+ toRNAssState.put("[", "[");
+ toRNAssState.put("{", "{");
+ toRNAssState.put("}", "{");
+ toRNAssState.put(">", ">");
+ toRNAssState.put("<", ">");
+ toRNAssState.put("A", "A");
+ toRNAssState.put("a", "A");
+ toRNAssState.put("B", "B");
+ toRNAssState.put("b", "B");
+ toRNAssState.put("C", "C");
+ toRNAssState.put("c", "C");
+ toRNAssState.put("D", "D");
+ toRNAssState.put("d", "D");
+ toRNAssState.put("1", "1");
+ toRNAssState.put("e", "1");
+ toRNAssState.put("F", "F");
+ toRNAssState.put("f", "F");
+ toRNAssState.put("G", "G");
+ toRNAssState.put("g", "G");
+ toRNAssState.put("2", "2");
+ toRNAssState.put("h", "2");
+ toRNAssState.put("I", "I");
+ toRNAssState.put("i", "I");
+ toRNAssState.put("J", "J");
+ toRNAssState.put("j", "J");
+ toRNAssState.put("K", "K");
+ toRNAssState.put("k", "K");
+ toRNAssState.put("L", "L");
+ toRNAssState.put("l", "L");
+ toRNAssState.put("M", "M");
+ toRNAssState.put("m", "M");
+ toRNAssState.put("N", "N");
+ toRNAssState.put("n", "N");
+ toRNAssState.put("O", "O");
+ toRNAssState.put("o", "O");
+ toRNAssState.put("P", "P");
+ toRNAssState.put("p", "P");
+ toRNAssState.put("Q", "Q");
+ toRNAssState.put("q", "Q");
+ toRNAssState.put("R", "R");
+ toRNAssState.put("r", "R");
+ toRNAssState.put("S", "S");
+ toRNAssState.put("s", "S");
+ toRNAssState.put("T", "T");
+ toRNAssState.put("t", "T");
+ toRNAssState.put("U", "U");
+ toRNAssState.put("u", "U");
+ toRNAssState.put("V", "V");
+ toRNAssState.put("v", "V");
+ toRNAssState.put("W", "W");
+ toRNAssState.put("w", "W");
+ toRNAssState.put("X", "X");
+ toRNAssState.put("x", "X");
+ toRNAssState.put("Y", "Y");
+ toRNAssState.put("y", "Y");
+ toRNAssState.put("Z", "Z");
+ toRNAssState.put("z", "Z");
+
}
/**
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.getProperty().put("CHAIN",chaincode);
seq.addPDBId(pdbr);
}
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.ws;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.List;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.mime.HttpMultipartMode;
+import org.apache.http.entity.mime.MultipartEntity;
+import org.apache.http.entity.mime.content.FileBody;
+import org.apache.http.entity.mime.content.InputStreamBody;
+import org.apache.http.entity.mime.content.StringBody;
+import org.apache.http.impl.client.DefaultHttpClient;
+
+/**
+ * Helpful procedures for working with services via HTTPClient
+ * @author jimp
+ *
+ */
+public class HttpClientUtils
+{
+ /**
+ * do a minimal HTTP post with URL-Encoded parameters passed in the Query
+ * string
+ *
+ * @param postUrl
+ * @param vals
+ * @return Reader containing content, if any, or null if no entity returned.
+ * @throws IOException
+ * @throws ClientProtocolException
+ * @throws Exception
+ */
+ public static BufferedReader doHttpUrlPost(String postUrl,
+ List<NameValuePair> vals) throws ClientProtocolException,
+ IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ public static BufferedReader doHttpMpartFilePost(String postUrl,
+ List<NameValuePair> vals, String fparm,File file, String mtype) throws ClientProtocolException,
+ IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE);
+ for (NameValuePair nvp:vals)
+ {
+ mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
+ }
+
+ FileBody fb = new FileBody(file, mtype!=null ? mtype : "application/octet-stream");
+ mpe.addPart(fparm, fb);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+ public static BufferedReader doHttpMpartInputstreamPost(String postUrl,
+ List<NameValuePair> vals, String fparm,String fname, InputStream is, String mtype) throws ClientProtocolException,
+ IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.STRICT);
+ for (NameValuePair nvp:vals)
+ {
+ mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
+ }
+
+ InputStreamBody fb = (mtype!=null) ? new InputStreamBody(is, fname, mtype) : new InputStreamBody(is, fname);
+ mpe.addPart(fparm, fb);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+}
import jalview.datamodel.Alignment;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import java.util.Vector;
import com.stevesoft.pat.Regex;
import jalview.datamodel.AlignmentI;
+import jalview.io.FormatAdapter;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
*/
public AlignmentI getSequenceRecords(String queries) throws Exception
{
-
+ AlignmentI pdbfile = null;
Vector result = new Vector();
String chain = null;
String id = null;
try
{
- PDBfile pdbfile = new PDBfile(file,
- jalview.io.AppletFormatAdapter.FILE);
- for (int i = 0; i < pdbfile.chains.size(); i++)
+ pdbfile = new FormatAdapter().readFile(file,
+ jalview.io.AppletFormatAdapter.FILE, "PDB");
+ if (pdbfile != null)
{
- if (chain == null
- || ((PDBChain) pdbfile.chains.elementAt(i)).id
- .toUpperCase().equals(chain))
+ for (SequenceI pdbcs : pdbfile.getSequences())
{
- PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
- // Get the Chain's Sequence - who's dataset includes any special
- // features added from the PDB file
- SequenceI sq = pdbchain.sequence;
- // Specially formatted name for the PDB chain sequences retrieved from
- // the PDB
- sq.setName(jalview.datamodel.DBRefSource.PDB + "|" + id + "|"
- + sq.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
- * entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable());
- * entry.getProperty().put("chains", pdbchain.id + "=" + sq.getStart()
- * + "-" + sq.getEnd()); sq.getDatasetSequence().addPDBId(entry);
- */
- // Add PDB DB Refs
- // We make a DBRefEtntry because we have obtained the PDB file from a
- // verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- // information
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),
- getDbVersion(), id + pdbchain.id);
- sq.addDBRef(dbentry);
- // and add seuqence to the retrieved set
- result.addElement(sq.deriveSequence());
+ String chid = null;
+ // Mapping map=null;
+ for (PDBEntry pid : (Vector<PDBEntry>) pdbcs.getPDBId())
+ {
+ if (pid.getFile() == file)
+ {
+ chid = (String) pid.getProperty().get("CHAIN");
+
+ }
+ ;
+
+ }
+ if (chain == null
+ || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim()) || (chain
+ .trim().length() == 0 && chid.equals("_")))))
+ {
+ pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
+ + "|" + pdbcs.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" +
+ * sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from
+ // a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ DBRefEntry dbentry = new DBRefEntry(getDbSource(),
+ getDbVersion(), (chid == null ? id : id + chid));
+ // dbentry.setMap()
+ pdbcs.addDBRef(dbentry);
+ }
+ else
+ {
+ // remove this sequence from the alignment - since it's not from the
+ // right chain
+ pdbfile.deleteSequence(pdbcs);
+ }
}
}
-
- if (result.size() < 1)
+ if (pdbfile == null || pdbfile.getHeight() < 1)
{
throw new Exception("No PDB Records for " + id + " chain "
+ ((chain == null) ? "' '" : chain));
stopQuery();
throw (ex);
}
-
- SequenceI[] results = new SequenceI[result.size()];
- for (int i = 0, j = result.size(); i < j; i++)
- {
- results[i] = (SequenceI) result.elementAt(i);
- result.setElementAt(null, i);
- }
- return new Alignment(results);
+ return pdbfile;
}
/*
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.ws.jws1;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.InputStreamParser;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLEncoder;
+
+public class Annotate3D
+{
+ // protected BufferedReader in;
+ // protected BufferedWriter out;
+
+ public Annotate3D()
+ {
+ System.out.println("Annotate3D");
+ // try {
+ // Create a URL for the desired page
+ // String id = "1HR2";
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
+ // in = new BufferedReader(new InputStreamReader(url.openStream()));
+ // String str;
+ // OutputStream out1 = null;
+ // out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
+ // while ((str = in.readLine()) != null) {
+ // System.out.println(str);
+ // out.write(str);
+ // }
+ // in.close();
+ // out.close();
+ // } catch (MalformedURLException e) {
+ // } catch (IOException e) {
+ // }
+ }
+
+ public AlignmentI getRNAMLFor(final FileParse source) throws IOException
+ {
+ try
+ {
+ StringBuffer sb = new StringBuffer();
+
+ Reader fpr = source.getReader();
+ int p = 0;
+ char[] cbuff = new char[2048];
+ while ((p = fpr.read(cbuff)) > 0)
+ {
+ for (int i = 0; i < p; i++)
+ {
+ sb.append(cbuff[i]);
+ }
+ }
+
+ FileParse fp = new InputStreamParser(
+ jalview.ext.paradise.Annotate3D.getRNAMLForPDBFileAsString(sb
+ .toString()), source.getDataName());
+ AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+ return nal;
+ } catch (Throwable x)
+ {
+ if (x instanceof IOException)
+ {
+ throw ((IOException) x);
+ }
+ else
+ {
+ throw new IOException(
+ "Unexpected exception when handling RNAML translation of PDB data",
+ x);
+ }
+ }
+ }
+
+ public Annotate3D(String path) throws InterruptedException
+ {
+ System.out.println("Annotate3D");
+ try
+ {
+ // //URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
+ // System.out.println("Step1");
+ // FileReader r = new FileReader(inFile);
+ // BufferedReader in = new BufferedReader(r);
+ // StringBuffer content = new StringBuffer();
+ // System.out.println("Step2");
+ // while(in.readLine()!=null){
+ // content.append(in.readLine());
+ // //System.out.println("Step3"+in.readLine());
+ // }
+ //
+ // String data = URLEncoder.encode("data", "UTF-8") + "=" +
+ // URLEncoder.encode(content.toString(), "UTF-8");
+ // for (int i=0;i<data.length();i++)
+ // {
+ // System.out.print(data.charAt(i));
+ // }
+
+ // String data = "width=50&height=100";
+
+ // // Send the request
+ // FileReader r = new FileReader(path);
+ // BufferedReader in = new BufferedReader(r);
+ // StringBuffer content = new StringBuffer();
+ // System.out.println("Step1");
+ // while(in.readLine()!=null){
+ // content.append(in.readLine());
+ //
+ // }
+ // System.out.println("Step2");
+ // String data = URLEncoder.encode("data", "UTF-8") + "=" +
+ // URLEncoder.encode(content.toString(), "UTF-8");
+ // System.out.println("Step2");
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
+ // DataInputStream is = new DataInputStream(url.openStream());
+ // String str;
+ // while ((str = is.readLine()) != null) {
+ // System.out.println(str);
+ // //out.write(str);
+ // }
+ FileReader r = new FileReader(path);
+ BufferedReader in = new BufferedReader(r);
+ String content = "";
+ String str;
+
+ while ((str = in.readLine()) != null)
+ {
+ // System.out.println(str);
+
+ content = content + str;
+ }
+ System.out.println("pdbfile=" + content.toString());
+ System.out.println("capacité=" + content.length());
+ String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
+ System.out.println("param=" + paramfile);
+ URL url = new URL(
+ "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+ + content);
+ BufferedReader is = new BufferedReader(new InputStreamReader(
+ url.openStream()));
+ String str4;
+ while ((str4 = is.readLine()) != null)
+ {
+ System.out.println(str4);
+ // out.write(str);
+ }
+ in.close();
+ is.close();
+
+ // HttpURLConnection connection = (HttpURLConnection)url.openConnection();
+ // connection.setRequestMethod("POST" );
+ // connection.setRequestProperty("data", path );
+ // //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
+ // BufferedReader input = new BufferedReader(new
+ // InputStreamReader(connection.getInputStream()));
+ // //DataInputStream input = new
+ // DataInputStream(connection.getInputStream());
+ // String c;
+ // while((c=input.readLine())!=null){
+ // System.out.print(c);
+ // }
+ // input.close();
+ // BufferedReader in1 = new BufferedReader(is);
+
+ // OutputStream out1 = null;
+ // System.out.println("Step3");
+ // BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
+ // "temp.rnaml"));
+ //
+ // in.close();
+ // out.close();
+
+ // return;
+
+ // System.out.println(data.length());
+ // System.out.println("step2");
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
+ // System.out.println("step3");
+ // URLConnection conn = url.openConnection();
+ // conn.setDoOutput(true);
+ // OutputStreamWriter writer = new
+ // OutputStreamWriter(conn.getOutputStream());
+
+ // write parameters
+ // writer.write(data);
+ // writer.flush();
+
+ // Get the response
+ // StringBuffer answer = new StringBuffer();
+ // //BufferedReader reader = new BufferedReader(new
+ // InputStreamReader(conn.getInputStream()));
+ // //String line;
+ // while ((line = reader.readLine()) != null) {
+ // answer.append(line);
+ // System.out.println(line);
+ // }
+ // writer.close();
+ // reader.close();
+
+ // Output the response
+
+ } catch (MalformedURLException ex)
+ {
+ ex.printStackTrace();
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ // in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ // String str;
+
+ // out = new FileOutputStream("temp.rnaml");
+ // out = new BufferedWriter(new FileWriter("temp.rnaml"));
+
+ // while ((str = in.readLine()) != null) {
+ // System.out.println(str);
+ // out.write(str);
+ // System.out.println(str);
+ // in.close();
+
+ // out.close();
+ // } catch (MalformedURLException e) {
+ // } catch (IOException e) {
+ // }
+ //
+ // }
+
+ // public BufferedWriter getReader()
+ // {
+ // System.out.println("The buffer");
+
+ // return out;
+
+ // }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.analysis;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Test the alignment -> Mapping routines
+ * @author jimp
+ *
+ */
+public class TestAlignSeq
+{
+
+ SequenceI s1,s2,s3;
+ /**
+ * @throws java.lang.Exception
+ */
+ @Before
+ public void setUp() throws Exception
+ {
+ s1 = new Sequence("Seq1","ASDFAQQQRRRSSS");
+ s1.setStart(3);
+ s2 = new Sequence("Seq2","ASDFA");
+ s2.setStart(5);
+ s3 = new Sequence("Seq1","SDFAQQQSSS");
+
+ }
+
+ @Test
+ /**
+ * simple test that mapping from alignment corresponds identical positions.
+ */
+ public void TestGetMappingForS1()
+ {
+ jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
+ System.out.println("s1: "+as.getAStr1());
+ System.out.println("s2: "+as.getAStr2());
+
+ Mapping s1tos2=as.getMappingFromS1(false);
+ System.out.println(s1tos2.getMap().toString());
+ for (int i=s2.getStart();i<s2.getEnd();i++)
+ {
+ System.out.println("Position in s2: "+i +" maps to position in s1: "+s1tos2.getPosition(i));
+ assertTrue("",s2.getCharAt(i)==s1.getCharAt(s1tos2.getPosition(i)));
+ }
+ }
+
+}
--- /dev/null
+/**
+ *
+ */
+package jalview.ext.jmol;
+
+import static org.junit.Assert.*;
+
+import java.util.Vector;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Test;
+
+/**
+ * @author jimp
+ *
+ */
+public class PDBFileWithJmolTest
+{
+
+ @Test
+ public void test() throws Exception
+ {
+ PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", jalview.io.AppletFormatAdapter.FILE);
+ Vector<SequenceI> seqs=jtest.getSeqs();
+
+ assertTrue("No sequences extracted from testfile\n"+(jtest.hasWarningMessage() ? jtest.getWarningMessage(): "(No warnings raised)"), seqs!=null && seqs.size()>0);
+ for (SequenceI sq:seqs)
+ {
+ AlignmentI al = new Alignment(new SequenceI[] { sq});
+ if (!al.isNucleotide())
+ {
+ assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);
+ }
+ }
+ }
+
+}
--- /dev/null
+package jalview.ext.paradise;
+
+import static org.junit.Assert.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ext.paradise.Annotate3D;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
+import java.io.BufferedReader;
+import java.io.File;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import MCview.PDBfile;
+
+import compbio.util.FileUtil;
+
+public class TestAnnotate3D
+{
+
+ @Test
+ public void testIdVsContent() throws Exception
+ {
+ BufferedReader id = (BufferedReader) Annotate3D
+ .getRNAMLForPDBId("2GIS");
+ assertTrue("Didn't retrieve 2GIS by id.", id != null);
+ BufferedReader file = (BufferedReader) Annotate3D
+ .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
+ "examples/2GIS.pdb")));
+ assertTrue("Didn't retrieve using examples/2GIS.pdb.", file != null);
+ String iline, fline;
+ do
+ {
+ iline = id.readLine();
+ fline = file.readLine();
+ if (iline != null)
+ System.out.println(iline);
+ if (fline != null)
+ System.out.println(fline);
+
+ assertTrue("Results differ for ID and file upload based retrieval",
+ ((iline == fline && iline == null) || (iline != null
+ && fline != null && iline.equals(fline))));
+
+ } while (iline != null);
+ }
+
+ /**
+ * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
+ * Annotate3d vs those extracted by Jalview from the originl PDB file
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testPDBfileVsRNAML() throws Exception
+ {
+ PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+ Assert.assertTrue(pdbf.isValid());
+ StringBuffer sb = new StringBuffer();
+ // Comment - should add new FileParse constructor like new FileParse(Reader
+ // ..). for direct reading
+ BufferedReader br = new BufferedReader(
+ Annotate3D.getRNAMLForPDBFileAsString(FileUtil
+ .readFileToString(new File("examples/2GIS.pdb"))));
+ String line;
+ while ((line = br.readLine()) != null)
+ {
+ sb.append(line + "\n");
+ }
+ assertTrue("No data returned by Annotate3D", sb.length() > 0);
+ AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ FormatAdapter.PASTE, "RNAML");
+
+ assertTrue("No alignment returned.", al != null);
+ assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
+ for (SequenceI sq : al.getSequences())
+ {
+ {
+ SequenceI struseq = null;
+ String sq_ = new String(sq.getSequence()).toLowerCase();
+ for (SequenceI _struseq : pdbf.getSeqsAsArray())
+ {
+ if (new String(_struseq.getSequence()).toLowerCase().equals(sq_))
+ {
+ struseq = _struseq;
+ break;
+ }
+ }
+ if (struseq == null)
+ {
+ Assert.fail("Couldn't find this sequence in original input:\n"
+ + new FastaFile().print(new SequenceI[]
+ { sq }) + "\n\nOriginal input:\n"
+ + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
+ }
+ }
+ }
+ }
+}
import java.io.IOException;
import java.util.List;
+import javax.xml.parsers.ParserConfigurationException;
+
import org.junit.Test;
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
public class TCoffeeScoreFileTest {
final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
@Test
- public void testReadHeader() throws IOException, FileNotFoundException {
+ public void testReadHeader() throws IOException {
TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
@Test
- public void testWrongFile() {
+ public void testWrongFile() {
try {
TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
assertFalse(result.isValid());
}
@Test
- public void testHeightAndWidthWithResidueNumbers() throws IOException {
+ public void testHeightAndWidthWithResidueNumbers() throws Exception {
String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
assertTrue(result.isValid());
--- /dev/null
+package jalview.ws;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBSequenceFetcherTest
+{
+
+ @Before
+ public void setUp() throws Exception
+ {
+ }
+
+ @Test
+ public void testRnaSeqRetrieve() throws Exception
+ {
+ List<DbSourceProxy> sps = new SequenceFetcher(false)
+ .getSourceProxy("PDB");
+ AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
+ assertTrue(response!=null);
+ assertTrue(response.getHeight()==1);
+ for (SequenceI sq:response.getSequences())
+ {
+ assertTrue("No annotation transfered to sequence.",sq.getAnnotation().length>0);
+ assertTrue("No PDBEntry on sequence.",sq.getPDBId().size()>0);
+ assertTrue("No RNA annotation on sequence.", sq.getRNA()!=null);
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff