From: jprocter Date: Fri, 18 Jan 2013 10:50:24 +0000 (+0000) Subject: Merge branch 'JAL-1254-hotfix' into develop X-Git-Tag: Jalview_2_9~254 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=48eed205662848798c4ff2d21d3e184d135b9e83;hp=830518dd02bbe8858347dbdcf5604e47af03faf3;p=jalview.git Merge branch 'JAL-1254-hotfix' into develop --- diff --git a/.classpath b/.classpath index 6cffc21..3ec9da3 100644 --- a/.classpath +++ b/.classpath @@ -40,13 +40,13 @@ - + + - diff --git a/.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch b/.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch new file mode 100644 index 0000000..b280175 --- /dev/null +++ b/.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/.project b/.project index 5f4b511..d0dfc7e 100644 --- a/.project +++ b/.project @@ -6,23 +6,13 @@ - org.eclipse.wst.common.project.facet.core.builder - - - - org.eclipse.jdt.core.javabuilder - org.eclipse.ui.externaltools.ExternalToolBuilder - full,incremental, + org.eclipse.wst.common.project.facet.core.builder - - LaunchConfigHandle - <project>/.externalToolBuilders/Jalview Release indices [Builder].launch - @@ -31,7 +21,7 @@ LaunchConfigHandle - <project>/.externalToolBuilders/buildapplet [Builder].launch + <project>/.externalToolBuilders/Jalview Release indices [Builder].launch diff --git a/build.xml b/build.xml index 0f81af7..47a0188 100755 --- a/build.xml +++ b/build.xml @@ -91,7 +91,8 @@ - + + @@ -104,6 +105,7 @@ + @@ -133,6 +135,7 @@ + diff --git a/examples/2GIS.pdb b/examples/2GIS.pdb new file mode 100644 index 0000000..7a51ef1 --- /dev/null +++ b/examples/2GIS.pdb @@ -0,0 +1,2693 @@ +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 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 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 +ATOM 231 O6 G A 11 45.526 55.999 24.029 1.00 64.41 O +ATOM 232 N1 G A 11 44.830 57.926 25.000 1.00 64.36 N +ATOM 233 C2 G A 11 43.947 58.946 25.189 1.00 65.00 C +ATOM 234 N2 G A 11 44.297 59.851 26.098 1.00 68.08 N +ATOM 235 N3 G A 11 42.807 59.069 24.535 1.00 65.84 N +ATOM 236 C4 G A 11 42.627 58.071 23.645 1.00 65.62 C +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 +ATOM 239 OP2 A A 12 40.202 59.237 17.756 1.00 71.67 O +ATOM 240 O5' A A 12 40.736 61.612 18.310 1.00 73.09 O +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 +ATOM 245 O3' A A 12 42.666 64.736 17.314 1.00 84.06 O +ATOM 246 C2' A A 12 44.049 63.806 19.063 1.00 76.03 C +ATOM 247 O2' A A 12 44.266 65.155 19.407 1.00 74.27 O +ATOM 248 C1' A A 12 43.669 62.990 20.300 1.00 75.72 C +ATOM 249 N9 A A 12 44.223 61.636 20.328 1.00 75.30 N +ATOM 250 C8 A A 12 44.108 60.649 19.388 1.00 74.14 C +ATOM 251 N7 A A 12 44.736 59.544 19.705 1.00 74.09 N +ATOM 252 C5 A A 12 45.300 59.823 20.941 1.00 74.63 C +ATOM 253 C6 A A 12 46.096 59.060 21.819 1.00 74.42 C +ATOM 254 N6 A A 12 46.478 57.808 21.578 1.00 72.95 N +ATOM 255 N1 A A 12 46.490 59.638 22.971 1.00 74.65 N +ATOM 256 C2 A A 12 46.104 60.888 23.220 1.00 74.97 C +ATOM 257 N3 A A 12 45.361 61.704 22.480 1.00 75.87 N +ATOM 258 C4 A A 12 44.989 61.105 21.338 1.00 75.00 C +ATOM 259 P G A 13 42.588 64.456 15.747 1.00 89.08 P +ATOM 260 OP1 G A 13 41.214 63.997 15.432 1.00 89.24 O +ATOM 261 OP2 G A 13 43.757 63.599 15.410 1.00 88.56 O +ATOM 262 O5' G A 13 42.840 65.858 15.051 1.00 92.85 O +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 +ATOM 265 O4' G A 13 44.653 67.791 14.898 1.00103.90 O +ATOM 266 C3' G A 13 45.283 67.411 12.672 1.00105.04 C +ATOM 267 O3' G A 13 44.800 67.565 11.345 1.00108.37 O +ATOM 268 C2' G A 13 45.964 68.692 13.125 1.00105.26 C +ATOM 269 O2' G A 13 45.315 69.841 12.618 1.00104.89 O +ATOM 270 C1' G A 13 45.756 68.625 14.639 1.00104.73 C +ATOM 271 N9 G A 13 46.891 68.187 15.441 1.00104.87 N +ATOM 272 C8 G A 13 47.268 66.915 15.809 1.00104.80 C +ATOM 273 N7 G A 13 48.320 66.902 16.586 1.00104.77 N +ATOM 274 C5 G A 13 48.654 68.244 16.726 1.00104.42 C +ATOM 275 C6 G A 13 49.696 68.877 17.464 1.00103.88 C +ATOM 276 O6 G A 13 50.565 68.363 18.184 1.00102.76 O +ATOM 277 N1 G A 13 49.657 70.262 17.305 1.00104.10 N +ATOM 278 C2 G A 13 48.734 70.949 16.541 1.00104.31 C +ATOM 279 N2 G A 13 48.843 72.280 16.483 1.00103.88 N +ATOM 280 N3 G A 13 47.769 70.373 15.873 1.00104.42 N +ATOM 281 C4 G A 13 47.787 69.036 16.008 1.00104.66 C +ATOM 282 P A A 14 44.891 66.334 10.322 1.00111.53 P +ATOM 283 OP1 A A 14 43.610 65.588 10.429 1.00111.71 O +ATOM 284 OP2 A A 14 46.174 65.631 10.568 1.00111.96 O +ATOM 285 O5' A A 14 44.952 67.015 8.880 1.00113.37 O +ATOM 286 C5' A A 14 46.163 67.595 8.388 1.00115.63 C +ATOM 287 C4' A A 14 45.863 68.602 7.295 1.00117.25 C +ATOM 288 O4' A A 14 45.362 67.887 6.140 1.00118.63 O +ATOM 289 C3' A A 14 44.811 69.629 7.703 1.00117.39 C +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 +ATOM 294 N9 A A 14 43.165 67.322 5.573 1.00120.87 N +ATOM 295 C8 A A 14 43.339 66.006 5.934 1.00121.79 C +ATOM 296 N7 A A 14 42.327 65.231 5.622 1.00122.72 N +ATOM 297 C5 A A 14 41.418 66.095 5.023 1.00122.75 C +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 +ATOM 300 N1 A A 14 39.493 66.962 3.957 1.00122.70 N +ATOM 301 C2 A A 14 40.097 68.157 4.010 1.00122.76 C +ATOM 302 N3 A A 14 41.296 68.477 4.503 1.00122.66 N +ATOM 303 C4 A A 14 41.914 67.389 4.999 1.00122.06 C +ATOM 304 P G A 15 46.313 71.178 9.199 1.00114.09 P +ATOM 305 OP1 G A 15 47.669 70.679 8.842 1.00113.11 O +ATOM 306 OP2 G A 15 45.634 70.652 10.411 1.00113.63 O +ATOM 307 O5' G A 15 46.392 72.765 9.299 1.00110.78 O +ATOM 308 C5' G A 15 47.622 73.436 9.083 1.00106.55 C +ATOM 309 C4' G A 15 47.841 74.474 10.147 1.00104.29 C +ATOM 310 O4' G A 15 47.457 73.923 11.434 1.00103.66 O +ATOM 311 C3' G A 15 49.285 74.901 10.335 1.00103.12 C +ATOM 312 O3' G A 15 49.677 75.893 9.400 1.00102.02 O +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 +ATOM 315 C1' G A 15 48.341 74.398 12.438 1.00102.79 C +ATOM 316 N9 G A 15 49.064 73.248 12.975 1.00102.03 N +ATOM 317 C8 G A 15 48.919 71.930 12.610 1.00101.72 C +ATOM 318 N7 G A 15 49.732 71.131 13.246 1.00101.59 N +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 +ATOM 324 N2 G A 15 51.999 75.086 16.142 1.00 99.94 N +ATOM 325 N3 G A 15 50.493 74.377 14.567 1.00100.17 N +ATOM 326 C4 G A 15 50.045 73.278 13.935 1.00100.88 C +ATOM 327 P G A 16 51.026 75.682 8.551 1.00101.42 P +ATOM 328 OP1 G A 16 50.682 75.731 7.109 1.00102.83 O +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 +ATOM 331 C5' G A 16 53.321 76.916 8.702 1.00100.34 C +ATOM 332 C4' G A 16 54.036 77.485 9.896 1.00100.56 C +ATOM 333 O4' G A 16 53.436 76.981 11.111 1.00 99.81 O +ATOM 334 C3' G A 16 55.491 77.080 9.985 1.00101.38 C +ATOM 335 O3' G A 16 56.265 77.979 9.201 1.00103.43 O +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 +ATOM 339 N9 G A 16 54.369 75.375 12.509 1.00 98.45 N +ATOM 340 C8 G A 16 53.508 74.423 12.025 1.00 97.73 C +ATOM 341 N7 G A 16 53.644 73.266 12.608 1.00 96.93 N +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 +ATOM 345 N1 G A 16 56.247 73.169 15.195 1.00 96.64 N +ATOM 346 C2 G A 16 56.637 74.479 15.071 1.00 97.14 C +ATOM 347 N2 G A 16 57.623 74.875 15.890 1.00 96.62 N +ATOM 348 N3 G A 16 56.099 75.334 14.211 1.00 97.69 N +ATOM 349 C4 G A 16 55.123 74.760 13.478 1.00 97.40 C +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 +ATOM 370 P G A 18 62.500 76.096 8.807 1.00105.66 P +ATOM 371 OP1 G A 18 63.661 76.851 8.267 1.00106.51 O +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 +ATOM 375 C4' G A 18 64.199 73.117 10.695 1.00101.12 C +ATOM 376 O4' G A 18 62.949 72.618 11.238 1.00100.63 O +ATOM 377 C3' G A 18 64.527 72.165 9.556 1.00100.12 C +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 +ATOM 382 N9 G A 18 61.557 71.174 10.058 1.00 97.34 N +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 +ATOM 388 N1 G A 18 58.790 68.401 9.575 1.00 95.75 N +ATOM 389 C2 G A 18 59.837 68.113 10.420 1.00 95.59 C +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 +ATOM 392 C4 G A 18 60.695 70.110 10.004 1.00 96.38 C +ATOM 393 P G A 19 66.529 72.627 7.927 1.00100.83 P +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 +ATOM 398 C4' G A 19 67.006 69.387 7.504 1.00 92.73 C +ATOM 399 O4' G A 19 65.677 69.803 7.898 1.00 92.37 O +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 +ATOM 481 N2 G A 22 56.779 52.662 10.534 1.00 71.19 N +ATOM 482 N3 G A 22 58.578 54.021 10.962 1.00 72.00 N +ATOM 483 C4 G A 22 59.891 54.181 10.684 1.00 72.15 C +ATOM 484 P G A 23 61.563 54.455 16.191 1.00 67.32 P +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 +ATOM 492 O3' G A 23 57.682 51.787 17.656 1.00 69.23 O +ATOM 493 C2' G A 23 56.884 51.359 15.412 1.00 64.38 C +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 +ATOM 515 O3' A A 24 62.824 50.253 18.304 1.00 71.85 O +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 +ATOM 759 C2 G A 35 60.834 67.298 3.114 1.00 77.37 C +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 +ATOM 807 P A A 38 60.393 62.448 18.155 1.00 79.26 P +ATOM 808 OP1 A A 38 60.704 61.769 19.430 1.00 80.61 O +ATOM 809 OP2 A A 38 58.991 62.817 17.844 1.00 79.34 O +ATOM 810 O5' A A 38 61.291 63.760 18.070 1.00 79.38 O +ATOM 811 C5' A A 38 62.553 63.820 18.730 1.00 81.15 C +ATOM 812 C4' A A 38 63.073 65.228 18.704 1.00 81.79 C +ATOM 813 O4' A A 38 63.352 65.593 17.331 1.00 81.63 O +ATOM 814 C3' A A 38 62.094 66.283 19.177 1.00 82.49 C +ATOM 815 O3' A A 38 62.076 66.412 20.583 1.00 84.40 O +ATOM 816 C2' A A 38 62.616 67.524 18.479 1.00 82.22 C +ATOM 817 O2' A A 38 63.767 68.030 19.123 1.00 83.01 O +ATOM 818 C1' A A 38 62.993 66.945 17.115 1.00 80.98 C +ATOM 819 N9 A A 38 61.822 66.947 16.243 1.00 78.84 N +ATOM 820 C8 A A 38 60.905 65.942 16.088 1.00 78.39 C +ATOM 821 N7 A A 38 59.915 66.249 15.289 1.00 77.70 N +ATOM 822 C5 A A 38 60.210 67.540 14.875 1.00 77.24 C +ATOM 823 C6 A A 38 59.546 68.437 14.018 1.00 77.01 C +ATOM 824 N6 A A 38 58.390 68.170 13.407 1.00 76.37 N +ATOM 825 N1 A A 38 60.117 69.640 13.812 1.00 77.26 N +ATOM 826 C2 A A 38 61.268 69.918 14.433 1.00 77.25 C +ATOM 827 N3 A A 38 61.981 69.165 15.263 1.00 77.22 N +ATOM 828 C4 A A 38 61.391 67.974 15.444 1.00 77.56 C +ATOM 829 P C A 39 60.743 66.942 21.298 1.00 86.61 P +ATOM 830 OP1 C A 39 60.919 66.819 22.766 1.00 87.75 O +ATOM 831 OP2 C A 39 59.580 66.302 20.641 1.00 86.54 O +ATOM 832 O5' C A 39 60.712 68.487 20.936 1.00 86.18 O +ATOM 833 C5' C A 39 61.720 69.347 21.428 1.00 85.71 C +ATOM 834 C4' C A 39 61.518 70.740 20.903 1.00 86.21 C +ATOM 835 O4' C A 39 61.657 70.721 19.457 1.00 85.21 O +ATOM 836 C3' C A 39 60.124 71.312 21.113 1.00 86.52 C +ATOM 837 O3' C A 39 59.927 71.874 22.399 1.00 87.69 O +ATOM 838 C2' C A 39 60.063 72.379 20.039 1.00 86.39 C +ATOM 839 O2' C A 39 60.788 73.527 20.422 1.00 87.59 O +ATOM 840 C1' C A 39 60.782 71.680 18.888 1.00 85.69 C +ATOM 841 N1 C A 39 59.790 71.009 18.040 1.00 85.17 N +ATOM 842 C2 C A 39 59.112 71.781 17.103 1.00 85.98 C +ATOM 843 O2 C A 39 59.424 72.977 16.983 1.00 88.51 O +ATOM 844 N3 C A 39 58.140 71.218 16.353 1.00 85.49 N +ATOM 845 C4 C A 39 57.847 69.928 16.510 1.00 84.91 C +ATOM 846 N4 C A 39 56.868 69.416 15.759 1.00 84.63 N +ATOM 847 C5 C A 39 58.543 69.105 17.445 1.00 84.88 C +ATOM 848 C6 C A 39 59.503 69.681 18.179 1.00 84.74 C +ATOM 849 P C A 40 58.440 71.960 23.004 1.00 87.52 P +ATOM 850 OP1 C A 40 58.530 72.443 24.403 1.00 87.13 O +ATOM 851 OP2 C A 40 57.789 70.663 22.722 1.00 88.65 O +ATOM 852 O5' C A 40 57.724 73.076 22.125 1.00 87.10 O +ATOM 853 C5' C A 40 58.160 74.423 22.184 1.00 87.69 C +ATOM 854 C4' C A 40 57.305 75.294 21.301 1.00 88.35 C +ATOM 855 O4' C A 40 57.424 74.836 19.927 1.00 88.43 O +ATOM 856 C3' C A 40 55.811 75.229 21.578 1.00 89.15 C +ATOM 857 O3' C A 40 55.427 76.080 22.652 1.00 89.80 O +ATOM 858 C2' C A 40 55.221 75.672 20.247 1.00 89.22 C +ATOM 859 O2' C A 40 55.242 77.071 20.063 1.00 90.74 O +ATOM 860 C1' C A 40 56.184 75.016 19.259 1.00 89.11 C +ATOM 861 N1 C A 40 55.680 73.714 18.791 1.00 89.08 N +ATOM 862 C2 C A 40 54.720 73.712 17.784 1.00 88.89 C +ATOM 863 O2 C A 40 54.357 74.800 17.312 1.00 88.07 O +ATOM 864 N3 C A 40 54.214 72.537 17.349 1.00 88.17 N +ATOM 865 C4 C A 40 54.640 71.394 17.881 1.00 87.25 C +ATOM 866 N4 C A 40 54.111 70.259 17.420 1.00 86.84 N +ATOM 867 C5 C A 40 55.627 71.365 18.910 1.00 87.49 C +ATOM 868 C6 C A 40 56.118 72.537 19.329 1.00 88.37 C +ATOM 869 P C A 41 54.296 75.590 23.687 1.00 91.70 P +ATOM 870 OP1 C A 41 54.317 76.506 24.848 1.00 92.23 O +ATOM 871 OP2 C A 41 54.484 74.132 23.905 1.00 92.16 O +ATOM 872 O5' C A 41 52.921 75.809 22.911 1.00 89.93 O +ATOM 873 C5' C A 41 52.470 77.118 22.601 1.00 89.57 C +ATOM 874 C4' C A 41 51.643 77.101 21.344 1.00 89.19 C +ATOM 875 O4' C A 41 52.410 76.440 20.301 1.00 89.84 O +ATOM 876 C3' C A 41 50.360 76.288 21.406 1.00 88.65 C +ATOM 877 O3' C A 41 49.269 76.984 21.992 1.00 87.24 O +ATOM 878 C2' C A 41 50.117 75.978 19.940 1.00 89.20 C +ATOM 879 O2' C A 41 49.606 77.084 19.234 1.00 90.10 O +ATOM 880 C1' C A 41 51.538 75.698 19.463 1.00 89.86 C +ATOM 881 N1 C A 41 51.817 74.263 19.619 1.00 90.67 N +ATOM 882 C2 C A 41 51.094 73.376 18.829 1.00 90.46 C +ATOM 883 O2 C A 41 50.292 73.835 18.017 1.00 90.97 O +ATOM 884 N3 C A 41 51.280 72.049 18.972 1.00 90.17 N +ATOM 885 C4 C A 41 52.155 71.592 19.865 1.00 91.13 C +ATOM 886 N4 C A 41 52.292 70.264 19.975 1.00 91.98 N +ATOM 887 C5 C A 41 52.927 72.476 20.683 1.00 91.06 C +ATOM 888 C6 C A 41 52.730 73.795 20.523 1.00 90.74 C +ATOM 889 P G A 42 48.270 76.196 22.975 1.00 87.44 P +ATOM 890 OP1 G A 42 47.291 77.141 23.567 1.00 89.10 O +ATOM 891 OP2 G A 42 49.134 75.380 23.871 1.00 88.78 O +ATOM 892 O5' G A 42 47.474 75.205 22.013 1.00 86.64 O +ATOM 893 C5' G A 42 46.541 75.702 21.061 1.00 83.77 C +ATOM 894 C4' G A 42 45.922 74.562 20.279 1.00 82.63 C +ATOM 895 O4' G A 42 46.960 73.869 19.533 1.00 81.47 O +ATOM 896 C3' G A 42 45.236 73.476 21.096 1.00 81.18 C +ATOM 897 O3' G A 42 43.883 73.838 21.383 1.00 79.00 O +ATOM 898 C2' G A 42 45.304 72.282 20.150 1.00 81.50 C +ATOM 899 O2' G A 42 44.294 72.313 19.164 1.00 82.78 O +ATOM 900 C1' G A 42 46.671 72.484 19.489 1.00 81.61 C +ATOM 901 N9 G A 42 47.741 71.774 20.181 1.00 81.64 N +ATOM 902 C8 G A 42 48.763 72.326 20.911 1.00 81.07 C +ATOM 903 N7 G A 42 49.539 71.435 21.463 1.00 81.18 N +ATOM 904 C5 G A 42 49.003 70.221 21.061 1.00 81.25 C +ATOM 905 C6 G A 42 49.410 68.898 21.358 1.00 81.50 C +ATOM 906 O6 G A 42 50.354 68.526 22.067 1.00 81.74 O +ATOM 907 N1 G A 42 48.589 67.959 20.740 1.00 81.55 N +ATOM 908 C2 G A 42 47.512 68.257 19.943 1.00 81.83 C +ATOM 909 N2 G A 42 46.847 67.214 19.438 1.00 82.10 N +ATOM 910 N3 G A 42 47.119 69.488 19.664 1.00 81.24 N +ATOM 911 C4 G A 42 47.904 70.414 20.254 1.00 81.41 C +ATOM 912 P G A 43 43.122 73.181 22.637 1.00 79.16 P +ATOM 913 OP1 G A 43 41.728 73.681 22.656 1.00 80.54 O +ATOM 914 OP2 G A 43 43.981 73.361 23.831 1.00 80.58 O +ATOM 915 O5' G A 43 43.054 71.627 22.294 1.00 78.89 O +ATOM 916 C5' G A 43 42.267 71.158 21.205 1.00 76.22 C +ATOM 917 C4' G A 43 42.432 69.665 21.035 1.00 73.95 C +ATOM 918 O4' G A 43 43.825 69.361 20.731 1.00 73.16 O +ATOM 919 C3' G A 43 42.147 68.845 22.284 1.00 72.25 C +ATOM 920 O3' G A 43 40.760 68.556 22.410 1.00 70.37 O +ATOM 921 C2' G A 43 42.934 67.568 22.021 1.00 72.79 C +ATOM 922 O2' G A 43 42.252 66.676 21.167 1.00 72.66 O +ATOM 923 C1' G A 43 44.169 68.108 21.301 1.00 73.72 C +ATOM 924 N9 G A 43 45.326 68.263 22.176 1.00 74.90 N +ATOM 925 C8 G A 43 45.959 69.425 22.531 1.00 75.68 C +ATOM 926 N7 G A 43 46.978 69.231 23.326 1.00 76.53 N +ATOM 927 C5 G A 43 47.014 67.856 23.511 1.00 76.40 C +ATOM 928 C6 G A 43 47.904 67.046 24.278 1.00 77.11 C +ATOM 929 O6 G A 43 48.872 67.395 24.964 1.00 77.75 O +ATOM 930 N1 G A 43 47.576 65.697 24.188 1.00 77.74 N +ATOM 931 C2 G A 43 46.535 65.187 23.456 1.00 77.07 C +ATOM 932 N2 G A 43 46.377 63.863 23.507 1.00 75.92 N +ATOM 933 N3 G A 43 45.705 65.927 22.731 1.00 77.52 N +ATOM 934 C4 G A 43 46.002 67.244 22.807 1.00 76.21 C +ATOM 935 P C A 44 40.195 67.977 23.797 1.00 69.28 P +ATOM 936 OP1 C A 44 38.714 67.902 23.774 1.00 70.40 O +ATOM 937 OP2 C A 44 40.874 68.768 24.857 1.00 71.31 O +ATOM 938 O5' C A 44 40.754 66.488 23.872 1.00 68.86 O +ATOM 939 C5' C A 44 40.391 65.506 22.905 1.00 66.43 C +ATOM 940 C4' C A 44 41.060 64.188 23.236 1.00 63.86 C +ATOM 941 O4' C A 44 42.501 64.360 23.212 1.00 61.55 O +ATOM 942 C3' C A 44 40.764 63.664 24.631 1.00 62.52 C +ATOM 943 O3' C A 44 39.610 62.844 24.610 1.00 63.93 O +ATOM 944 C2' C A 44 41.970 62.790 24.921 1.00 61.24 C +ATOM 945 O2' C A 44 41.822 61.512 24.348 1.00 60.87 O +ATOM 946 C1' C A 44 43.089 63.572 24.232 1.00 60.02 C +ATOM 947 N1 C A 44 43.846 64.470 25.117 1.00 57.66 N +ATOM 948 C2 C A 44 44.654 63.921 26.119 1.00 56.64 C +ATOM 949 O2 C A 44 44.654 62.698 26.294 1.00 55.06 O +ATOM 950 N3 C A 44 45.410 64.740 26.872 1.00 56.82 N +ATOM 951 C4 C A 44 45.372 66.056 26.665 1.00 57.91 C +ATOM 952 N4 C A 44 46.153 66.830 27.420 1.00 58.97 N +ATOM 953 C5 C A 44 44.533 66.641 25.676 1.00 57.75 C +ATOM 954 C6 C A 44 43.788 65.821 24.938 1.00 57.21 C +ATOM 955 P A A 45 38.915 62.435 25.990 1.00 67.24 P +ATOM 956 OP1 A A 45 37.920 61.357 25.739 1.00 66.87 O +ATOM 957 OP2 A A 45 38.473 63.720 26.574 1.00 68.09 O +ATOM 958 O5' A A 45 40.101 61.855 26.886 1.00 64.88 O +ATOM 959 C5' A A 45 40.493 60.486 26.806 1.00 61.73 C +ATOM 960 C4' A A 45 41.533 60.188 27.856 1.00 60.43 C +ATOM 961 O4' A A 45 42.672 61.053 27.651 1.00 58.62 O +ATOM 962 C3' A A 45 41.106 60.425 29.294 1.00 60.22 C +ATOM 963 O3' A A 45 40.583 59.206 29.787 1.00 62.36 O +ATOM 964 C2' A A 45 42.432 60.692 29.984 1.00 58.55 C +ATOM 965 O2' A A 45 43.085 59.476 30.257 1.00 60.38 O +ATOM 966 C1' A A 45 43.194 61.456 28.902 1.00 57.88 C +ATOM 967 N9 A A 45 43.076 62.911 28.943 1.00 57.39 N +ATOM 968 C8 A A 45 42.160 63.673 28.261 1.00 56.72 C +ATOM 969 N7 A A 45 42.351 64.962 28.378 1.00 55.38 N +ATOM 970 C5 A A 45 43.445 65.058 29.218 1.00 55.87 C +ATOM 971 C6 A A 45 44.141 66.154 29.716 1.00 56.96 C +ATOM 972 N6 A A 45 43.820 67.421 29.438 1.00 57.41 N +ATOM 973 N1 A A 45 45.196 65.909 30.525 1.00 57.38 N +ATOM 974 C2 A A 45 45.510 64.636 30.807 1.00 56.39 C +ATOM 975 N3 A A 45 44.925 63.522 30.402 1.00 56.23 N +ATOM 976 C4 A A 45 43.888 63.803 29.596 1.00 56.50 C +ATOM 977 P A A 46 39.689 59.199 31.111 1.00 66.16 P +ATOM 978 OP1 A A 46 39.133 57.830 31.270 1.00 64.50 O +ATOM 979 OP2 A A 46 38.779 60.365 30.994 1.00 65.42 O +ATOM 980 O5' A A 46 40.701 59.506 32.306 1.00 67.24 O +ATOM 981 C5' A A 46 41.462 58.484 32.965 1.00 66.66 C +ATOM 982 C4' A A 46 42.341 59.140 34.004 1.00 66.99 C +ATOM 983 O4' A A 46 43.028 60.224 33.349 1.00 67.35 O +ATOM 984 C3' A A 46 41.625 59.765 35.195 1.00 67.72 C +ATOM 985 O3' A A 46 41.669 58.959 36.376 1.00 68.21 O +ATOM 986 C2' A A 46 42.564 60.890 35.577 1.00 69.03 C +ATOM 987 O2' A A 46 43.607 60.394 36.401 1.00 72.13 O +ATOM 988 C1' A A 46 43.082 61.336 34.209 1.00 66.39 C +ATOM 989 N9 A A 46 42.276 62.348 33.564 1.00 62.89 N +ATOM 990 C8 A A 46 41.084 62.169 32.918 1.00 62.52 C +ATOM 991 N7 A A 46 40.653 63.243 32.308 1.00 62.67 N +ATOM 992 C5 A A 46 41.614 64.200 32.605 1.00 62.01 C +ATOM 993 C6 A A 46 41.747 65.544 32.251 1.00 61.96 C +ATOM 994 N6 A A 46 40.877 66.192 31.482 1.00 64.57 N +ATOM 995 N1 A A 46 42.823 66.214 32.714 1.00 62.07 N +ATOM 996 C2 A A 46 43.697 65.565 33.480 1.00 62.26 C +ATOM 997 N3 A A 46 43.684 64.298 33.881 1.00 63.14 N +ATOM 998 C4 A A 46 42.603 63.665 33.400 1.00 62.84 C +ATOM 999 P C A 47 42.413 57.528 36.388 1.00 67.72 P +ATOM 1000 OP1 C A 47 42.629 56.988 35.028 1.00 70.69 O +ATOM 1001 OP2 C A 47 41.663 56.714 37.372 1.00 70.77 O +ATOM 1002 O5' C A 47 43.856 57.748 37.034 1.00 64.73 O +ATOM 1003 C5' C A 47 44.558 56.596 37.540 1.00 62.38 C +ATOM 1004 C4' C A 47 46.022 56.881 37.836 1.00 60.75 C +ATOM 1005 O4' C A 47 46.726 57.283 36.632 1.00 57.34 O +ATOM 1006 C3' C A 47 46.301 58.002 38.819 1.00 61.65 C +ATOM 1007 O3' C A 47 46.215 57.517 40.147 1.00 66.33 O +ATOM 1008 C2' C A 47 47.730 58.398 38.472 1.00 58.98 C +ATOM 1009 O2' C A 47 48.710 57.539 39.015 1.00 59.79 O +ATOM 1010 C1' C A 47 47.729 58.226 36.961 1.00 56.15 C +ATOM 1011 N1 C A 47 47.460 59.483 36.270 1.00 52.42 N +ATOM 1012 C2 C A 47 48.401 60.504 36.371 1.00 52.13 C +ATOM 1013 O2 C A 47 49.423 60.304 37.044 1.00 51.95 O +ATOM 1014 N3 C A 47 48.179 61.672 35.738 1.00 50.89 N +ATOM 1015 C4 C A 47 47.062 61.832 35.031 1.00 51.44 C +ATOM 1016 N4 C A 47 46.861 62.994 34.431 1.00 52.10 N +ATOM 1017 C5 C A 47 46.091 60.804 34.911 1.00 51.28 C +ATOM 1018 C6 C A 47 46.326 59.658 35.541 1.00 51.11 C +ATOM 1019 P C A 48 45.766 58.513 41.317 1.00 69.35 P +ATOM 1020 OP1 C A 48 45.485 57.695 42.529 1.00 67.22 O +ATOM 1021 OP2 C A 48 44.703 59.395 40.751 1.00 67.82 O +ATOM 1022 O5' C A 48 47.058 59.411 41.569 1.00 67.80 O +ATOM 1023 C5' C A 48 48.244 58.859 42.135 1.00 66.18 C +ATOM 1024 C4' C A 48 49.242 59.962 42.373 1.00 65.53 C +ATOM 1025 O4' C A 48 49.635 60.527 41.099 1.00 62.77 O +ATOM 1026 C3' C A 48 48.679 61.145 43.136 1.00 66.13 C +ATOM 1027 O3' C A 48 48.741 60.923 44.527 1.00 71.49 O +ATOM 1028 C2' C A 48 49.582 62.286 42.698 1.00 63.22 C +ATOM 1029 O2' C A 48 50.818 62.332 43.383 1.00 63.14 O +ATOM 1030 C1' C A 48 49.807 61.927 41.231 1.00 60.44 C +ATOM 1031 N1 C A 48 48.843 62.587 40.347 1.00 55.14 N +ATOM 1032 C2 C A 48 49.088 63.893 39.966 1.00 54.49 C +ATOM 1033 O2 C A 48 50.090 64.465 40.414 1.00 55.34 O +ATOM 1034 N3 C A 48 48.233 64.509 39.125 1.00 52.59 N +ATOM 1035 C4 C A 48 47.161 63.865 38.679 1.00 51.17 C +ATOM 1036 N4 C A 48 46.362 64.510 37.843 1.00 50.44 N +ATOM 1037 C5 C A 48 46.871 62.531 39.070 1.00 52.11 C +ATOM 1038 C6 C A 48 47.732 61.933 39.898 1.00 54.08 C +ATOM 1039 P A A 49 47.654 61.613 45.471 1.00 74.04 P +ATOM 1040 OP1 A A 49 47.893 61.129 46.859 1.00 75.80 O +ATOM 1041 OP2 A A 49 46.338 61.389 44.821 1.00 75.26 O +ATOM 1042 O5' A A 49 48.017 63.156 45.395 1.00 72.61 O +ATOM 1043 C5' A A 49 49.222 63.621 45.964 1.00 73.43 C +ATOM 1044 C4' A A 49 49.383 65.087 45.696 1.00 74.37 C +ATOM 1045 O4' A A 49 49.425 65.301 44.263 1.00 73.83 O +ATOM 1046 C3' A A 49 48.229 65.975 46.115 1.00 76.55 C +ATOM 1047 O3' A A 49 48.233 66.240 47.513 1.00 80.22 O +ATOM 1048 C2' A A 49 48.525 67.223 45.299 1.00 75.25 C +ATOM 1049 O2' A A 49 49.601 67.966 45.824 1.00 76.33 O +ATOM 1050 C1' A A 49 48.953 66.608 43.969 1.00 73.01 C +ATOM 1051 N9 A A 49 47.835 66.511 43.031 1.00 71.22 N +ATOM 1052 C8 A A 49 47.031 65.426 42.781 1.00 71.73 C +ATOM 1053 N7 A A 49 46.081 65.663 41.907 1.00 70.51 N +ATOM 1054 C5 A A 49 46.280 66.989 41.550 1.00 69.33 C +ATOM 1055 C6 A A 49 45.599 67.839 40.664 1.00 69.09 C +ATOM 1056 N6 A A 49 44.545 67.453 39.944 1.00 69.34 N +ATOM 1057 N1 A A 49 46.044 69.110 40.540 1.00 69.39 N +ATOM 1058 C2 A A 49 47.106 69.484 41.260 1.00 70.23 C +ATOM 1059 N3 A A 49 47.833 68.775 42.123 1.00 70.98 N +ATOM 1060 C4 A A 49 47.360 67.522 42.226 1.00 69.91 C +ATOM 1061 P G A 50 46.846 66.209 48.339 1.00 82.72 P +ATOM 1062 OP1 G A 50 47.164 66.087 49.785 1.00 82.86 O +ATOM 1063 OP2 G A 50 45.964 65.198 47.703 1.00 81.94 O +ATOM 1064 O5' G A 50 46.219 67.654 48.091 1.00 81.41 O +ATOM 1065 C5' G A 50 45.935 68.105 46.777 1.00 84.37 C +ATOM 1066 C4' G A 50 45.652 69.584 46.784 1.00 86.37 C +ATOM 1067 O4' G A 50 45.672 70.042 45.399 1.00 85.92 O +ATOM 1068 C3' G A 50 44.276 69.971 47.302 1.00 88.18 C +ATOM 1069 O3' G A 50 43.942 70.325 48.632 1.00 92.03 O +ATOM 1070 C2' G A 50 43.367 70.206 46.117 1.00 86.73 C +ATOM 1071 O2' G A 50 42.687 71.428 46.274 1.00 86.89 O +ATOM 1072 C1' G A 50 44.351 70.323 44.948 1.00 84.88 C +ATOM 1073 N9 G A 50 43.925 69.272 44.029 1.00 81.15 N +ATOM 1074 C8 G A 50 44.114 67.917 44.173 1.00 79.88 C +ATOM 1075 N7 G A 50 43.441 67.213 43.306 1.00 79.00 N +ATOM 1076 C5 G A 50 42.810 68.160 42.516 1.00 78.27 C +ATOM 1077 C6 G A 50 41.925 67.995 41.442 1.00 78.52 C +ATOM 1078 O6 G A 50 41.491 66.941 40.959 1.00 78.22 O +ATOM 1079 N1 G A 50 41.521 69.220 40.921 1.00 78.77 N +ATOM 1080 C2 G A 50 41.922 70.445 41.387 1.00 78.84 C +ATOM 1081 N2 G A 50 41.425 71.512 40.756 1.00 79.59 N +ATOM 1082 N3 G A 50 42.748 70.610 42.398 1.00 78.54 N +ATOM 1083 C4 G A 50 43.143 69.435 42.917 1.00 78.68 C +ATOM 1084 P A A 51 42.880 69.415 49.453 1.00 96.02 P +ATOM 1085 OP1 A A 51 42.446 70.195 50.660 1.00 95.76 O +ATOM 1086 OP2 A A 51 43.467 68.046 49.625 1.00 96.17 O +ATOM 1087 O5' A A 51 41.609 69.253 48.500 1.00 94.71 O +ATOM 1088 C5' A A 51 40.743 68.118 48.626 1.00 93.44 C +ATOM 1089 C4' A A 51 39.313 68.526 48.358 1.00 92.36 C +ATOM 1090 O4' A A 51 38.931 69.502 49.358 1.00 90.16 O +ATOM 1091 C3' A A 51 39.090 69.216 47.018 1.00 92.54 C +ATOM 1092 O3' A A 51 38.742 68.280 46.002 1.00 96.31 O +ATOM 1093 C2' A A 51 37.939 70.159 47.316 1.00 90.20 C +ATOM 1094 O2' A A 51 36.698 69.487 47.304 1.00 89.63 O +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 +ATOM 1097 C8 A A 51 40.528 71.680 49.247 1.00 80.40 C +ATOM 1098 N7 A A 51 41.164 72.817 49.124 1.00 78.33 N +ATOM 1099 C5 A A 51 40.236 73.652 48.517 1.00 77.49 C +ATOM 1100 C6 A A 51 40.296 74.995 48.117 1.00 75.83 C +ATOM 1101 N6 A A 51 41.375 75.764 48.279 1.00 75.08 N +ATOM 1102 N1 A A 51 39.199 75.530 47.539 1.00 76.02 N +ATOM 1103 C2 A A 51 38.118 74.757 47.382 1.00 77.71 C +ATOM 1104 N3 A A 51 37.939 73.479 47.718 1.00 78.31 N +ATOM 1105 C4 A A 51 39.049 72.981 48.287 1.00 79.42 C +ATOM 1106 P A A 52 39.515 68.317 44.596 1.00 97.90 P +ATOM 1107 OP1 A A 52 39.960 66.929 44.294 1.00 98.51 O +ATOM 1108 OP2 A A 52 40.520 69.410 44.687 1.00 97.41 O +ATOM 1109 O5' A A 52 38.395 68.749 43.546 1.00 98.75 O +ATOM 1110 C5' A A 52 38.737 69.495 42.378 1.00100.86 C +ATOM 1111 C4' A A 52 37.985 70.804 42.367 1.00101.84 C +ATOM 1112 O4' A A 52 38.002 71.359 43.705 1.00100.72 O +ATOM 1113 C3' A A 52 38.535 71.905 41.465 1.00102.80 C +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 +ATOM 1118 N9 A A 52 39.367 73.140 44.269 1.00 97.90 N +ATOM 1119 C8 A A 52 40.197 72.318 44.981 1.00 96.81 C +ATOM 1120 N7 A A 52 41.251 72.923 45.460 1.00 96.75 N +ATOM 1121 C5 A A 52 41.110 74.232 45.031 1.00 96.25 C +ATOM 1122 C6 A A 52 41.900 75.370 45.216 1.00 95.31 C +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 +ATOM 1126 N3 A A 52 39.505 75.511 43.719 1.00 96.85 N +ATOM 1127 C4 A A 52 39.955 74.381 44.291 1.00 97.01 C +ATOM 1128 P A A 53 38.666 72.624 38.930 1.00108.87 P +ATOM 1129 OP1 A A 53 37.810 72.491 37.721 1.00108.36 O +ATOM 1130 OP2 A A 53 40.093 72.223 38.866 1.00109.37 O +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 +ATOM 1142 N7 A A 53 41.870 74.045 41.382 1.00110.63 N +ATOM 1143 C5 A A 53 42.720 74.990 41.938 1.00110.94 C +ATOM 1144 C6 A A 53 43.826 74.875 42.795 1.00111.51 C +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 +ATOM 1162 N1 U A 54 44.348 73.146 38.309 1.00 95.04 N +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 +ATOM 1170 P G A 55 47.525 74.791 34.471 1.00 97.86 P +ATOM 1171 OP1 G A 55 48.367 75.702 33.647 1.00 97.40 O +ATOM 1172 OP2 G A 55 46.754 73.696 33.816 1.00 97.86 O +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 +ATOM 1271 N1 C A 59 50.164 61.434 25.444 1.00 55.90 N +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 +ATOM 1280 OP1 C A 60 52.566 57.477 20.623 1.00 60.10 O +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 +ATOM 1291 N1 C A 60 49.075 62.919 20.594 1.00 63.39 N +ATOM 1292 C2 C A 60 48.741 64.252 20.458 1.00 63.93 C +ATOM 1293 O2 C A 60 47.699 64.537 19.859 1.00 66.02 O +ATOM 1294 N3 C A 60 49.552 65.196 20.975 1.00 64.43 N +ATOM 1295 C4 C A 60 50.669 64.837 21.602 1.00 64.08 C +ATOM 1296 N4 C A 60 51.437 65.800 22.106 1.00 64.35 N +ATOM 1297 C5 C A 60 51.045 63.476 21.743 1.00 63.45 C +ATOM 1298 C6 C A 60 50.228 62.556 21.229 1.00 63.91 C +ATOM 1299 P A A 61 50.069 59.698 16.181 1.00 61.03 P +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 +ATOM 1321 P A A 62 46.873 53.710 16.473 1.00 53.92 P +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 +ATOM 1337 C6 A A 62 52.743 50.373 13.029 1.00 53.85 C +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 +ATOM 1341 N3 A A 62 50.576 49.358 11.532 1.00 53.66 N +ATOM 1342 C4 A A 62 50.426 50.169 12.589 1.00 55.03 C +ATOM 1343 P U A 63 45.533 47.735 15.702 1.00 53.62 P +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 +ATOM 1597 P A A 75 43.733 17.113 13.257 1.00 71.98 P +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 diff --git a/lib/VARNAv3-9-dev.jar b/lib/VARNAv3-9-dev.jar deleted file mode 100644 index 6ae57bf..0000000 Binary files a/lib/VARNAv3-9-dev.jar and /dev/null differ diff --git a/lib/VARNAv3-9.jar b/lib/VARNAv3-9.jar new file mode 100644 index 0000000..86ac411 Binary files /dev/null and b/lib/VARNAv3-9.jar differ diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index 8bfd7b5..ccf68bb 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -21,6 +21,14 @@ import java.io.*; 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.*; @@ -50,7 +58,6 @@ public class PDBViewer extends JInternalFrame implements Runnable public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains, AlignmentPanel ap, String protocol) - { this.pdbentry = pdbentry; this.seq = seq; diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index a6ad951..95dec13 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -22,8 +22,10 @@ import java.util.*; 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 { @@ -57,7 +59,7 @@ public class PDBfile extends jalview.io.AlignFile id = safeName(getDataName()); chains = new Vector(); - + ArrayList rna=new ArrayList(), prot=new ArrayList(); PDBChain tmpchain; String line = null; boolean modelFlag = false; @@ -156,6 +158,8 @@ public class PDBfile extends jalview.io.AlignFile 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()); @@ -170,16 +174,43 @@ public class PDBfile extends jalview.io.AlignFile // 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"); @@ -193,7 +224,73 @@ public class PDBfile extends jalview.io.AlignFile } } } - + private void processPdbFileWithJmol(ArrayList prot) throws Exception + { + // process prot sequence with Jmol to get annotated alignment. + // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP); + } + private void processPdbFileWithAnnotate3d(ArrayList 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 ochains, AlignmentI al, String dnaOrProtein) + { + if (al!=null && al.getHeight()>0) + { + ArrayList matches=new ArrayList(); + ArrayList aligns=new ArrayList(); + + 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-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. */ package jalview.analysis; - import java.util.*; import java.awt.*; @@ -267,16 +266,11 @@ public class AlignSeq } /** - * 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 */ @@ -289,6 +283,14 @@ public class AlignSeq 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) { @@ -302,7 +304,7 @@ public class AlignSeq * 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) @@ -920,6 +922,98 @@ public class AlignSeq } /** + * 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 as1 = new ArrayList(), as2 = new ArrayList(); + 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 diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java index e386e5c..1583f84 100644 --- a/src/jalview/analysis/Rna.java +++ b/src/jalview/analysis/Rna.java @@ -54,12 +54,12 @@ public class Rna { 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()) @@ -69,7 +69,7 @@ public class Rna } Object temp = stack.pop(); pairs.addElement(temp); - pairs.addElement(i); + pairs.addElement(i); } i++; diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 08bb3fd..32a4e29 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -59,11 +59,15 @@ public class StructureFrequency */ 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; @@ -84,15 +88,26 @@ public class StructureFrequency 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 { @@ -101,9 +116,11 @@ public class StructureFrequency 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 { @@ -114,7 +131,7 @@ public class StructureFrequency s = '-'; } - if (s != '(') + if (s != '(' && s != '[') { if (s == '-') { @@ -123,41 +140,57 @@ public class StructureFrequency } 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++; } @@ -170,9 +203,14 @@ public class StructureFrequency residueHash.put(PAIRPROFILE, pairs); } - + if (wooble==true) + { count = values['(']; - + } + if (wooble==false) + { + count = values['[']; + } residueHash.put(MAXCOUNT, new Integer(count)); residueHash.put(MAXRESIDUE, maxResidue); @@ -187,12 +225,19 @@ public class StructureFrequency } 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[][] diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 0f0ba4e..4d574d6 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,3753 +1,3767 @@ -/* - * 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 . - */ -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 sg = new Vector(); - 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 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; - } - -} +/* + * 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 . + */ +package jalview.appletgui; + +import jalview.analysis.AAFrequency; +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.SequenceCollectionI; +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.RNAInteractionColourScheme; +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 == RNAInteractionColour) + { + changeColour(new RNAInteractionColourScheme()); + } + 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 sg = new Vector(); + 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 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 RNAInteractionColour = 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); + RNAInteractionColour.setLabel("Purine/Pyrimidine"); + RNAInteractionColour.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); + 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(RNAInteractionColour); + 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; + } + +} diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 5e4569a..1c63f7f 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -17,6 +17,10 @@ */ 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; @@ -66,6 +70,7 @@ public class Jalview } }); } + protected static boolean proteine; /** * main class for Jalview application @@ -515,8 +520,28 @@ public class Jalview // 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", @@ -589,7 +614,8 @@ public class Jalview desktop.setInBatchMode(false); } } - + + private static void startUsageStats(final Desktop desktop) { /** @@ -901,6 +927,21 @@ public class Jalview * @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; @@ -1039,4 +1080,7 @@ class FeatureFetcher { return queued == 0 && running == 0; } + + + }; diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 0a8e087..ea13922 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -20,9 +20,12 @@ package jalview.datamodel; 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! * @@ -49,6 +52,8 @@ public class AlignmentAnnotation /** DOCUMENT ME!! */ public Annotation[] annotations; + + /** * RNA secondary structure contact positions @@ -240,7 +245,37 @@ public class AlignmentAnnotation 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; @@ -273,7 +308,36 @@ public class AlignmentAnnotation 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) { @@ -508,7 +572,7 @@ public class AlignmentAnnotation { if (annotations[i] != null) { - annotations[i].displayCharacter = ""; + annotations[i].displayCharacter = "X"; } } } @@ -973,7 +1037,7 @@ public class AlignmentAnnotation { 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); @@ -1034,5 +1098,4 @@ public class AlignmentAnnotation { this.calcId = calcId; } - } diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java index 73611bd..042e0f7 100755 --- a/src/jalview/datamodel/Annotation.java +++ b/src/jalview/datamodel/Annotation.java @@ -38,6 +38,8 @@ public class Annotation /** DOCUMENT ME!! */ public float value; + + // add visual cues here @@ -62,6 +64,7 @@ public class Annotation description = desc; secondaryStructure = ss; value = val; + } /** @@ -105,6 +108,7 @@ public class Annotation secondaryStructure = that.secondaryStructure; value = that.value; colour = that.colour; + } /** @@ -115,6 +119,10 @@ public class Annotation */ public Annotation(float val) { - this(null, null, ' ', val); + this(null, null, ' ', val,null); } + + + + } diff --git a/src/jalview/datamodel/SecondaryStructureAnnotation.java b/src/jalview/datamodel/SecondaryStructureAnnotation.java new file mode 100644 index 0000000..5c3eae9 --- /dev/null +++ b/src/jalview/datamodel/SecondaryStructureAnnotation.java @@ -0,0 +1,31 @@ +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. + */ +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 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 + + } + +} diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java new file mode 100644 index 0000000..b0adb45 --- /dev/null +++ b/src/jalview/ext/paradise/Annotate3D.java @@ -0,0 +1,34 @@ +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 vals = new ArrayList(); + 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 vals = new ArrayList(); + vals.add(new BasicNameValuePair("pdbid", pdbid)); + return HttpClientUtils.doHttpUrlPost( + "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d", + vals); + } + +} diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java index 527a847..21f626f 100644 --- a/src/jalview/ext/varna/VarnaCommands.java +++ b/src/jalview/ext/varna/VarnaCommands.java @@ -1,167 +1,157 @@ -/* - * 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 . - */ -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 str = new ArrayList(); - 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; - } - -} +/* + * 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 . + */ +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 jalview.util.Comparison; + +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 str = new ArrayList(); + 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; + } + +} diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index 1a4c7ac..70e68ee 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -17,17 +17,28 @@ */ 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; @@ -64,12 +75,23 @@ public class AppVarna extends JInternalFrame implements 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 rnaList = new ArrayList(); 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(); @@ -80,6 +102,7 @@ public class AppVarna extends JInternalFrame implements 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)"); @@ -87,7 +110,7 @@ public class AppVarna extends JInternalFrame implements { 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, @@ -100,13 +123,16 @@ public class AppVarna extends JInternalFrame implements // 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); @@ -121,6 +147,7 @@ public class AppVarna extends JInternalFrame implements getBounds().width, getBounds().height); this.pack(); showPanel(true); + System.out.println("Sortie initialisation VANRA"); } public String replaceOddGaps(String oldStr) @@ -136,6 +163,7 @@ public class AppVarna extends JInternalFrame implements public RNA trimRNA(RNA rna, String name) { ShiftList offset = new ShiftList(); + RNA rnaTrim = new RNA(name); try { @@ -398,4 +426,18 @@ public class AppVarna extends JInternalFrame implements } + @Override + public void onTranslationChanged() + { + // TODO Auto-generated method stub + + } + + @Override + public void onZoomLevelChanged() + { + // TODO Auto-generated method stub + + } + } diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java index 81452af..61c44c2 100644 --- a/src/jalview/gui/AppVarnaBinding.java +++ b/src/jalview/gui/AppVarnaBinding.java @@ -43,20 +43,14 @@ import java.util.List; 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; @@ -146,16 +140,19 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding { // super("VARNA in Jalview"); initVarna(seq, struc); + } public AppVarnaBinding(ArrayList rnaList) { + // super("VARNA in Jalview"); initVarnaEdit(rnaList); } private void initVarna(String seq, String str) { + DefaultListModel dlm = new DefaultListModel(); DefaultListSelectionModel m = new DefaultListSelectionModel(); @@ -188,6 +185,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding try { + vp = new VARNAPanel("0", "."); _RNA1.setRNA(seq, str); _RNA1.drawRNARadiate(vp.getConfig()); @@ -216,6 +214,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding private void initVarnaEdit(ArrayList rnaInList) { + DefaultListModel dlm = new DefaultListModel(); int marginTools = 40; @@ -239,7 +238,8 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding 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()); } @@ -249,10 +249,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding try { + vp = new VARNAPanel("0", "."); for (int i = 0; i < rnaInList.size(); i++) { rnaInList.get(i).drawRNARadiate(vp.getConfig()); + } } catch (ExceptionNonEqualLength e) { @@ -801,7 +803,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding 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) @@ -931,6 +938,20 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding // TODO Auto-generated method stub } + + @Override + public void onZoomLevelChanged() + { + // TODO Auto-generated method stub + + } + + @Override + public void onTranslationChanged() + { + // TODO Auto-generated method stub + + } } /* diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java index 6896863..979a2e2 100644 --- a/src/jalview/gui/AssociatePdbFileWithSeq.java +++ b/src/jalview/gui/AssociatePdbFileWithSeq.java @@ -18,6 +18,14 @@ 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; @@ -69,6 +77,7 @@ public class AssociatePdbFileWithSeq { entry.setId(pdbfile.id); } + } catch (java.io.IOException ex) { ex.printStackTrace(); @@ -78,5 +87,4 @@ public class AssociatePdbFileWithSeq sequence.getDatasetSequence().addPDBId(entry); return entry; } - } diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 877aebb..db7c32c 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -912,7 +912,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements .getSelectedFile().getParent()); String format = null; - if (chooser.getSelectedFormat().equals("Jalview")) + if (chooser.getSelectedFormat()!=null && chooser.getSelectedFormat().equals("Jalview")) { format = "Jalview"; } diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 1a367c5..075374a 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -23,6 +23,14 @@ import java.awt.*; 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.*; @@ -70,6 +78,7 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); // protected JRadioButtonMenuItem covariationColour = new // JRadioButtonMenuItem(); @@ -192,6 +201,7 @@ public class PopupMenu extends JPopupMenu 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++) @@ -280,11 +290,23 @@ public class PopupMenu extends JPopupMenu 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); @@ -310,6 +332,7 @@ public class PopupMenu extends JPopupMenu 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); @@ -446,6 +469,11 @@ public class PopupMenu extends JPopupMenu { purinePyrimidineColour.setSelected(true); } + + else if (sg.cs instanceof RNAInteractionColourScheme) + { + RNAInteractionColour.setSelected(true); + } /* * else if (sg.cs instanceof CovariationColourScheme) { * covariationColour.setSelected(true); } @@ -1113,9 +1141,9 @@ public class PopupMenu extends JPopupMenu 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); @@ -1278,6 +1306,16 @@ public class PopupMenu extends JPopupMenu 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) { @@ -1465,6 +1503,11 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void RNAInteractionColour_actionPerformed() + { + getGroup().cs = new RNAInteractionColourScheme(); + refresh(); + } /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 6c1a343..81d0ae4 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -65,6 +65,8 @@ public abstract class AlignFile extends FileParse */ 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(); } /** diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 11f5adb..85ea8e0 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -38,7 +38,7 @@ public class AppletFormatAdapter */ 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 @@ -52,7 +52,7 @@ public class AppletFormatAdapter * 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 @@ -66,8 +66,8 @@ public class AppletFormatAdapter * 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" // }; @@ -78,7 +78,7 @@ public class AppletFormatAdapter */ public static final String[] READABLE_FNAMES = new String[] { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", - "Stockholm" };// , + "Stockholm","RNAML" };// , // "SimpleBLAST" // }; @@ -227,7 +227,9 @@ public class AppletFormatAdapter } 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")) { @@ -237,7 +239,11 @@ public class AppletFormatAdapter { afile = new SimpleBlastFile(inFile, type); } - + else if (format.equals("RNAML")) + { + afile = new RnamlFile(inFile, type); + } + Alignment al = new Alignment(afile.getSeqsAsArray()); afile.addAnnotations(al); @@ -292,7 +298,7 @@ public class AppletFormatAdapter * * @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 @@ -344,6 +350,10 @@ public class AppletFormatAdapter { afile = new StockholmFile(source); } + else if (format.equals("RNAML")) + { + afile = new RnamlFile(source); + } else if (format.equals("SimpleBLAST")) { afile = new SimpleBlastFile(source); @@ -451,6 +461,11 @@ public class AppletFormatAdapter { afile = new AMSAFile(alignment); } + else if (format.equalsIgnoreCase("RNAML")) + { + afile = new RnamlFile(); + } + else { throw new Exception( diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java index 0c0d186..0e964b3 100755 --- a/src/jalview/io/FastaFile.java +++ b/src/jalview/io/FastaFile.java @@ -19,6 +19,7 @@ package jalview.io; import java.io.*; + import jalview.datamodel.*; /** diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 975a1a3..27b4944 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -17,12 +17,18 @@ */ 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 { @@ -252,7 +258,7 @@ public class FileLoader implements Runnable // load } loadtime = -System.currentTimeMillis(); - Alignment al = null; + AlignmentI al = null; if (format.equalsIgnoreCase("Jalview")) { @@ -298,7 +304,7 @@ public class FileLoader implements Runnable error = format + "\n" + error; } } - + if ((al != null) && (al.getHeight() > 0)) { if (viewport != null) diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index b06edc5..1cdd95d 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -131,6 +131,13 @@ public class IdentifyFile break; } + + if ((data.indexOf("<") > -1)) + { + reply = "RNAML"; + + break; + } if ((data.length() < 1) || (data.indexOf("#") == 0)) { @@ -159,6 +166,8 @@ public class IdentifyFile break; } + + else if (data.indexOf(">") > -1) { // FASTA, PIR file or BLC file diff --git a/src/jalview/io/InputStreamParser.java b/src/jalview/io/InputStreamParser.java new file mode 100644 index 0000000..19cbad9 --- /dev/null +++ b/src/jalview/io/InputStreamParser.java @@ -0,0 +1,54 @@ +/* + * 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 . + */ +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(); + } + +} diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index 0fae4ee..abdfed0 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -348,7 +348,7 @@ public class JPredFile extends AlignFile * @param args * DOCUMENT ME! */ - public static void main(String[] args) + public static void main(String[] args) { try { diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java index 527312b..c5ef4f7 100755 --- a/src/jalview/io/PfamFile.java +++ b/src/jalview/io/PfamFile.java @@ -20,6 +20,7 @@ package jalview.io; import java.io.*; import java.util.*; + import jalview.datamodel.*; import jalview.util.*; diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java index de0d8a3..39f367b 100755 --- a/src/jalview/io/PileUpfile.java +++ b/src/jalview/io/PileUpfile.java @@ -57,6 +57,7 @@ public class PileUpfile extends MSFfile * * @throws IOException * DOCUMENT ME! + */ public PileUpfile(String inFile, String type) throws IOException { diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java new file mode 100644 index 0000000..122e6e1 --- /dev/null +++ b/src/jalview/io/RnamlFile.java @@ -0,0 +1,179 @@ +/* + * 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 . + */ +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 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 -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; + } +} diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 669181a..b0d3c8b 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -1,688 +1,294 @@ -/* - * 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 . - */ -/* - * 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 - * #=GF TN 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 number DE - * DEscription DR ; ; Database Reference OS - * OrganiSm (species) OC Organism Classification (clade, etc.) - * LO 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; } - */ -} +/* + * 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 . + */ +/* + * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk + */ +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.FileReader; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Vector; + +import com.stevesoft.pat.Regex; + +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; +import fr.orsay.lri.varna.factories.RNAFactory; +import fr.orsay.lri.varna.models.rna.RNA; + +// 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"); + protected ArrayList result; + + public String id; + + 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 + { + FileReader fr = null; + fr = new FileReader(inFile); + + BufferedReader r = new BufferedReader(fr); + result = null; + try + { + result = RNAFactory.loadSecStrStockholm(r); + } catch (ExceptionUnmatchedClosingParentheses umcp) + { + errormessage = "Unmatched parentheses in annotation. Aborting (" + + umcp.getMessage() + ")"; + throw new IOException(umcp); + } + // DEBUG System.out.println("this is the secondary scructure:" + // +result.size()); + SequenceI[] seqs = new SequenceI[result.size()]; + for (int i = 0; i < result.size(); i++) + { + // DEBUG System.err.println("Processing i'th sequence in Stockholm file") + RNA current = result.get(i); + + String seq = current.getSeq(); + String rna = current.getStructDBN(true); + // DEBUG System.out.println(seq); + // DEBUG System.err.println(rna); + int begin = 0; + int end = seq.length() - 1; + id = safeName(getDataName()); + 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)); + this.annotations.addElement(align); + } + this.setSeqs(seqs); + + } + + 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; + } + /** + * 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; + } +} \ No newline at end of file diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index b523763..5858f86 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -138,6 +138,8 @@ public class GAlignFrame extends JInternalFrame protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); // protected JRadioButtonMenuItem covariationColour = new // JRadioButtonMenuItem(); @@ -453,7 +455,7 @@ public class GAlignFrame extends JInternalFrame colours.add(purinePyrimidineColour); // colours.add(covariationColour); colours.add(tcoffeeColour); - + colours.add(RNAInteractionColour); setColourSelected(jalview.bin.Cache .getDefault("DEFAULT_COLOUR", "None")); @@ -531,6 +533,11 @@ public class GAlignFrame extends JInternalFrame purinePyrimidineColour.setSelected(true); break; + + case ColourSchemeProperty.RNAINTERACTION: + RNAInteractionColour.setSelected(true); + + break; /* * case ColourSchemeProperty.COVARIATION: * covariationColour.setSelected(true); @@ -910,14 +917,22 @@ public class GAlignFrame extends JInternalFrame }); 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() { @@ -1873,6 +1888,7 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); colourMenu.add(purinePyrimidineColour); + colourMenu.add(RNAInteractionColour); // colourMenu.add(covariationColour); colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); @@ -1882,7 +1898,7 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); - colourMenu.add(rnahelicesColour); + colourMenu.add(rnahelicesColour); calculateMenu.add(sort); calculateMenu.add(calculateTree); calculateMenu.addSeparator(); @@ -2267,6 +2283,11 @@ public class GAlignFrame extends JInternalFrame protected void purinePyrimidineColour_actionPerformed(ActionEvent e) { } + + protected void RNAInteractionColour_actionPerformed(ActionEvent e) + { + } + /* * protected void covariationColour_actionPerformed(ActionEvent e) { } diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index a3af237..5742337 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -126,6 +126,7 @@ public class GDesktop extends JFrame */ private void jbInit() throws Exception { + FileMenu.setText("File"); HelpMenu.setText("Help"); VamsasMenu.setText("Vamsas"); diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index ab27d8a..65f65bb 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -69,6 +69,7 @@ public class AnnotationRenderer // 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)) @@ -85,6 +86,7 @@ public class AnnotationRenderer } else { + // display a forward arrow if (diffdownstream) { @@ -142,6 +144,65 @@ public class AnnotationRenderer */ 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, @@ -454,7 +515,8 @@ public class AnnotationRenderer .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); @@ -463,15 +525,284 @@ public class AnnotationRenderer 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) @@ -488,12 +819,78 @@ public class AnnotationRenderer 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) @@ -558,6 +955,67 @@ public class AnnotationRenderer 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); @@ -637,6 +1095,8 @@ public class AnnotationRenderer 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, @@ -1018,4 +1478,135 @@ public class AnnotationRenderer 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; + + } + } } + + + diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 47dbde2..4132f32 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -86,6 +86,8 @@ public class ColourSchemeProperty public static final int TCOFFEE = 15; + public static final int RNAINTERACTION = 16; + /** * index of first colourscheme (includes 'None') */ @@ -166,6 +168,11 @@ public class ColourSchemeProperty { ret = PURINEPYRIMIDINE; } + + else if (name.equalsIgnoreCase("RNA Interaction type")) + { + ret = RNAINTERACTION; + } // else if (name.equalsIgnoreCase("Covariation")) // { // ret = COVARIATION; @@ -239,6 +246,12 @@ public class ColourSchemeProperty { index = TCOFFEE; } + else if (cs instanceof RNAInteractionColourScheme) + { + index = RNAINTERACTION; + } + + /* * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; } */ @@ -333,6 +346,11 @@ public class ColourSchemeProperty ret = "T-Coffee Scores"; break; + + case RNAINTERACTION: + ret = "RNA Interaction type"; + + break; /* * case COVARIATION: ret = "Covariation"; * @@ -484,8 +502,14 @@ public class ColourSchemeProperty 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; diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java new file mode 100644 index 0000000..42f4feb --- /dev/null +++ b/src/jalview/schemes/RNAInteractionColourScheme.java @@ -0,0 +1,82 @@ +/* + * 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 . + */ + 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; + } + } diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index fa4260f..0ca155a 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1341,8 +1341,67 @@ public class ResidueProperties 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"); + } /** diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index 804595b..14ace19 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -430,6 +430,7 @@ public class DBRefUtils ref = new DBRefEntry(locsrc, version, pdbid + chaincode); PDBEntry pdbr = new PDBEntry(); pdbr.setId(pdbid); + pdbr.getProperty().put("CHAIN",chaincode); seq.addPDBId(pdbr); } } diff --git a/src/jalview/ws/HttpClientUtils.java b/src/jalview/ws/HttpClientUtils.java new file mode 100644 index 0000000..740b669 --- /dev/null +++ b/src/jalview/ws/HttpClientUtils.java @@ -0,0 +1,142 @@ +/* + * 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 . + */ +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 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 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 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; + } + } +} diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index b432dff..219008d 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -20,6 +20,7 @@ package jalview.ws.dbsources; import jalview.datamodel.Alignment; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; +import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import java.util.Vector; @@ -30,6 +31,7 @@ import MCview.PDBfile; import com.stevesoft.pat.Regex; import jalview.datamodel.AlignmentI; +import jalview.io.FormatAdapter; import jalview.ws.ebi.EBIFetchClient; import jalview.ws.seqfetcher.DbSourceProxy; @@ -93,7 +95,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy */ public AlignmentI getSequenceRecords(String queries) throws Exception { - + AlignmentI pdbfile = null; Vector result = new Vector(); String chain = null; String id = null; @@ -127,45 +129,61 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy 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) 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)); @@ -175,14 +193,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy 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; } /* diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java new file mode 100644 index 0000000..a30a9a1 --- /dev/null +++ b/src/jalview/ws/jws1/Annotate3D.java @@ -0,0 +1,266 @@ +/* + * 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 . + */ +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. + */ +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 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); + } + } + } + +} diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java new file mode 100644 index 0000000..1ed46f4 --- /dev/null +++ b/test/jalview/ext/paradise/TestAnnotate3D.java @@ -0,0 +1,102 @@ +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"); + } + } + } + } +} diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java index 3147054..6d11ebe 100644 --- a/test/jalview/io/TCoffeeScoreFileTest.java +++ b/test/jalview/io/TCoffeeScoreFileTest.java @@ -26,7 +26,15 @@ import java.io.FileNotFoundException; 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 { @@ -34,7 +42,7 @@ 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()); @@ -56,7 +64,7 @@ public class TCoffeeScoreFileTest { @Test - public void testWrongFile() { + public void testWrongFile() { try { TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE); assertFalse(result.isValid()); @@ -173,7 +181,7 @@ public class TCoffeeScoreFileTest { } @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()); diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java new file mode 100644 index 0000000..f5913e6 --- /dev/null +++ b/test/jalview/ws/PDBSequenceFetcherTest.java @@ -0,0 +1,37 @@ +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 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); + } + } + +}