Author: christophgil-guest Date: 2012-05-28 20:32:51 +0000 (Mon, 28 May 2012) New Revision: 11054
Added: trunk/packages/strap/trunk/debian/bin/strap-protein-alignment trunk/packages/strap/trunk/debian/strap-protein-alignment.1 Removed: trunk/packages/strap/trunk/debian/bin/strap trunk/packages/strap/trunk/debian/strap.1 trunk/packages/strap/trunk/debian/substvars Modified: trunk/packages/strap/trunk/debian/control trunk/packages/strap/trunk/debian/rules trunk/packages/strap/trunk/debian/strap.install trunk/packages/strap/trunk/debian/strap.links trunk/packages/strap/trunk/debian/strap.manpages Log: Deleted: trunk/packages/strap/trunk/debian/bin/strap =================================================================== --- trunk/packages/strap/trunk/debian/bin/strap 2012-05-28 18:53:10 UTC (rev 11053) +++ trunk/packages/strap/trunk/debian/bin/strap 2012-05-28 20:32:51 UTC (rev 11054) @@ -1,34 +0,0 @@ -#! /bin/sh - -echo '\033[42m\033[37m'$0'\033[0m ' -echo "See http://3d-alignment.eu/ " -echo - -. /usr/lib/java-wrappers/java-wrappers.sh -find_java_runtime java6 - -# Java option max heap size -xmx=-Xmx200M -CP=/usr/lib/java/strap-protein-alignment-1.jar: -for i in $*; do - if [ $i != ${i##-Xmx} ]; then xmx=$i; fi - if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi -done - -if [ -f /usr/bin/tm-align ]; then S3D="-s3d=tm_align"; fi - - - -echo The maximum heap size option is $xmx. -echo To change, add a program line option like -Xmx500M -echo which would set heap size to 500 Megabytes. -echo - -EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -aligner2=clustalw -probeWebProxy -stdout -askUpload $*" - -echo -echo $EXEC -echo -$EXEC - - Added: trunk/packages/strap/trunk/debian/bin/strap-protein-alignment =================================================================== --- trunk/packages/strap/trunk/debian/bin/strap-protein-alignment (rev 0) +++ trunk/packages/strap/trunk/debian/bin/strap-protein-alignment 2012-05-28 20:32:51 UTC (rev 11054) @@ -0,0 +1,34 @@ +#! /bin/sh + +echo '\033[42m\033[37m'$0'\033[0m ' +echo "See http://3d-alignment.eu/ " +echo + +. /usr/lib/java-wrappers/java-wrappers.sh +find_java_runtime java6 + +# Java option max heap size +xmx=-Xmx200M +CP=/usr/lib/java/strap-protein-alignment-1.jar: +for i in $*; do + if [ $i != ${i##-Xmx} ]; then xmx=$i; fi + if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi +done + +if [ -f /usr/bin/tm-align ]; then S3D="-s3d=tm_align"; fi + + + +echo The maximum heap size option is $xmx. +echo To change, add a program line option like -Xmx500M +echo which would set heap size to 500 Megabytes. +echo + +EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -aligner2=clustalw -probeWebProxy -stdout -askUpload $*" + +echo +echo $EXEC +echo +$EXEC + + Property changes on: trunk/packages/strap/trunk/debian/bin/strap-protein-alignment ___________________________________________________________________ Added: svn:executable + * Modified: trunk/packages/strap/trunk/debian/control =================================================================== --- trunk/packages/strap/trunk/debian/control 2012-05-28 18:53:10 UTC (rev 11053) +++ trunk/packages/strap/trunk/debian/control 2012-05-28 20:32:51 UTC (rev 11054) @@ -3,7 +3,7 @@ Priority: extra Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Christoph Gille <[email protected]> -Build-Depends: libstrap-java +Build-Depends: strap-base Standards-Version: 3.9.2 Homepage: http://3d-alignment.eu/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/strap/trunk/ @@ -11,7 +11,7 @@ Package: strap Architecture: all -Depends: libstrap-java, ${misc:Depends}, gwrite, catdoc, clustalw, tm-align, pymol, texlive-latex-base, mustang +Depends: strap-base, ${misc:Depends}, gwrite, catdoc, clustalw, tm-align, pymol, texlive-latex-base, mustang Recommends: Suggests: Enhances: clustalw, tm-align, pymol, mustang Modified: trunk/packages/strap/trunk/debian/rules =================================================================== --- trunk/packages/strap/trunk/debian/rules 2012-05-28 18:53:10 UTC (rev 11053) +++ trunk/packages/strap/trunk/debian/rules 2012-05-28 20:32:51 UTC (rev 11054) @@ -11,7 +11,7 @@ override_dh_auto_build: - test -f $(MANFILE1) && cp $(MANFILE1) debian/strap.1 + test -f $(MANFILE1) && cp $(MANFILE1) debian/strap-protein-alignment.1 override_dh_clean: dh_clean Copied: trunk/packages/strap/trunk/debian/strap-protein-alignment.1 (from rev 11032, trunk/packages/strap/trunk/debian/strap.1) =================================================================== --- trunk/packages/strap/trunk/debian/strap-protein-alignment.1 (rev 0) +++ trunk/packages/strap/trunk/debian/strap-protein-alignment.1 2012-05-28 20:32:51 UTC (rev 11054) @@ -0,0 +1,304 @@ +.TH Strap 1 "October 2011" +.SH NAME + + +Strap \- Graphical user interface to compare and align proteins by sequence and 3D-structure. +.SH Synopsis + +.B strap-protein-alignment [\fIprotein_files\fR] + +.B strap-protein-alignment [\fIalignment_files\fR] + +.B strap-protein-alignment +[\fIoptions\fR] [\fIprotein_files\fR] [\fIalignment_files\fR] [ @ \fIfile_with_list_of_protein_files\fR] + + + +.SH DESCRIPTION + +The free computer program Strap aligns proteins by sequence and +3D-structure. Strap supports the simultaneous analysis of hundreds of +proteins and integrates amino acid sequence, secondary structure, +3D-structure and genomic- and mRNA-sequence. Using standard methods, +alignments are computed automatically based on sequence and structure. +Import and export of single proteins is very easy by Drag-and-Drop. + +.SS Home-Page + +http://3d-alignment.eu/ + +http://www.bioinformatics.org/strap/ + +.SH PROGRAM PARAMETERS + +.SS Protein/alignment files + +Strap can be started with protein files or alignment files as parameters. +The following formats are supported: PDB, Swissprot, Embl, Genbank, +GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom, +Pfam, Stockholm and HSSP. + +If at least one protein file is specified, Strap will choose the +current working directory as the project directory. Otherwise the +project directory is requested at the beginning of the session. + + +Files with a leading \fB@\fR sign or preceded by a \fB@\fR sign are +interpreted as lists of files. + +\fBCurly parenthesis\fR are used for placing sequences into the same +alignment row. At the UNIX command prompt, the parentheses need to be +quoted. For example \fB'{'\fR \fIprotein1.seq protein2.seq\fR +\fB'}' '{'\fR \fIprotein3.seq protein4.seq protein5.seq \fR \fB'}'\fR +would put two proteins into the first and three proteins into the +second alignment row. If there are more than one sequences in a row, +only the top most sequence is displayed. + + + + + +.SS File Compression + +The following file compression methods are supported: .gz, .bz2 and .Z + +.SS Parts of proteins + +To display only a subset of a protein, a suffix is appended to the +protein file name. +Residue subsets are specified by an exclamation mark and a subset +expression after the protein file. Example: +"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To +refer to pdb-residue numbers use the Rasmol/Jmol syntax \fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A". + +.SH OPTIONS + +Program options start with a dash. The values \fBtrue\fR and +\fBfalse\fR can be abbreviated by \fBt\fR and \fBf\fR. The "=true" or +"=t" can be ommitted. For example \fB-noSeqres=true\fR can be written +as \fB-noSeqres=t\fR or \fB-noSeqres\fR. For most settings there is an +equivalent check-box or choice menu in the graphical user interface. + +If the Web-start script http://www.bioinformatics.org/strap/strap.php +is started, the options are given as web-variable without the leading +dash. For example for -noSeqres include \fBnoSeqres=t\fR into the +URL. + +\fB-help\fR + +Prints this text + +\fB-manual\fR + +Generates a comprehensive manual for the web browser. + +\fB\-noSeqres\fR + + Skip SEQRES lines of PDB files. + +\fB\-noIdentical\fR + +Do not load a sequence identical to an already loaded one. + +\fB\-dialog\fR=\fIJavaClassNameOfDialog\fR + +Opens a certain dialog at start. +The class name of a dialog is the tab-text can be obtained by opening the help text. + +Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot + +\fB\-script\fR=\fIURL_or_FilePath_or_ScriptText\fR + +Runs a script at start. See http://www.bioinformatics.org/strap/web/strap_script.html. +Script files in the current directory should be written with a leading +"./" like "./myScript.txt" since Strap recognizes files by the +presence of a slash and the absence of white space and colon. + +Two or more script files can be given: +-script5=\fIhttp://...../file\fR -script7=\fIhttp://...../file\fR. +The optional number suffix defines the order of consecutively executed scripts. + +Script commands can be given directly. Assume there are protein files +in PDB format loaded by Strap. The option -script="open_3D viewName, +*" would display all proteins with 3D-coordinates three-dimensionally +(See -v3d=). Scripts consisting of more than one line should be +stored in a file and the file path or URL should be given. + +Example: + +-script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *" + +\fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR + +Only needed for DAS servers that are + +\fB\-s3d\fR=\fIJavaClass\fR + +Sets the Java class to superimpose proteins. + +A short name can be used such as "tm_align" for "Superimpose_TM_align". + +Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus + +\fB\-a3d\fR=\fIJavaClass\fR + +Sets the Java class to compute structure based sequence alignments. + +Examples: -a3d=tm_align or -a3d=mapsci or -a3d=matt or -a3d=mustang + +\fB\-v3d\fR=\fIJavaClass\fR + +Sets the Java class to display 3D-structures. + +Example: -v3d=jmol or -v3d=pymol or -v3d=astex + +\fB\-aligner2\fR=\fIJavaClass\fR + +Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start. +Default value is PairAlignerNeoBioPROXY. + +Example: -aligner2=MultipleAlignerClustalW + + +\fB\-log3d\fR + +All 3D-commands which are sent to 3D-protein viewers are printed to stdout. + +\fB\-useDebian=false\fR \fB\-useDebian=true\fR + +If set to true, use the Debian packages for external programs rather +than the program versions included in Strap. For example Strap would +use /usr/bin/pymol instead of downloading and using the Pymol from +http://www.bioinformatics.org/strap/Binaries/. + +\fB\-sysProxies=true\fR or \fB-probeWebProxy=true\fR or \fB-probeWebProxy=false\fR + +See section Web proxies. + +\fB\-noCache\fR + + Do not use cached results of previous +computations. This setting can be changed in the graphical user +interface with a check-box. + +This setting influences the result of searches in growing +databases. For example consider the similarity search method +Blast. With the cache turned on, Strap would present a previously +computed Blast result even though new sequences might have been +published since last run. + +\fB\-keepFiles\fR + +Do not delete temp-files after the session. This is only important for +debugging. + +\fB\-Xmx500m\fR + +This is an option of the java command and not of Strap. +It sets the heap size to 500 Megabyte. + +\fB\-geometry=\fI666x333+11+22\fR + +Sets the size and location of the application frame to width 666, +height 333, horizontal screen position 11 and vertical position 22; + +\fB\-laf=\fIlookAndFeel\fR + +Examples: + +-laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short -laf=m) + +-laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short -laf=N) + +-laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short -laf=G) + +-laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short -laf=M) + +Also non-standard Look'n Feels can be used. Consider tinylaf which +can be installed as a Debian package. The following two options would +apply tinylaf: + + \fB-cp=\fR/usr/share/java/tinylaf.jar +-laf=de.muntjak.tinylookandfeel.TinyLookAndFeel + +See also http://en.wikipedia.org/wiki/Look_and_feel. + +\fB\-toMultipleFasta\fR or \fB\-toClustal\fR or \fB\-toFasta\fR \fIProtein or alignment files\fR + +Loads the proteins and generates protein or ungapped multiple sequence +files with the respective format. The file paths are written to +stdout. The program terminates. + +.SS Security + +\fB\-askUpload\fR[=t/f] The user is asked each time data is uploaded +to remote servers. The user might not want unpublished sequences to be +sent to servers. + +\fB\-askExec\fR[=t/f] The user is asked when an external program is +executed. Executing native programs might be regarded as security +risk. There is a positive and a negative list which can be edited in +the menu "Security" of the Preferences-menu. + +\fB\-allowFileModification\fR According to the default policy, files +are only modified, created or deleted if they reside in the project +directory or if the file path contains "StrapAlign". This is to +prevent files to be lost. With this option file modification control +is deactivated. + +.SH PROJECT DIRECTORY + +The project directory holds information for gaps, 3D-transformations, +annotations and exported files. Usually, the protein files are also +located in the project directory. The project directory path must not +contain white space, such as "My data" or "Eigene Dateien". Therefore +the project directory can usually not be located in the home directory +on Windows-XP. + +.SH WEB-PROXY + +With the option \fB-probeWebProxy=t\fR, strap attempts to access the Web in +three different ways: (1) Directly, without Web-proxy (2) With the +settings found in the environment variable http_proxy and (3) using +the default mechanism of Java to apply the system wide settings. With the +setting \fB-probeWebProxy=f\fR, however, Strap will directly connect to the +Internet. with the option \fB-sysProxies=t\fR Strap will use the +Java-built-in mechanism to find the system wide settings, (which might +not work properly, depending on the Java system). + +.SH ALIGNMENT-FILE-EXPORT + +Supported formats are Multiple-Fasta, ClustalW, MSF, HSSP. A +colorized alignment with highlighted residue selections and secondary +structure can be exported in HTML and PDF. The colorized HTML output +can be modified in MS-Word or other text processors. The rendering +styles of the PDF output can be stored in annotations of residue +selections. + +.SH 3D-VISUALIZATION + +The following 3D-protein viewers are tightly linked with the alignment +view: Pymol, Jmol, OpenAstex. The rendering styles can be stored +within residue selections. There is a generic Rasmol like scripting +language which can be applied to all embedded visualization software. +If the desired effect can not be achieved with this generic commands, +also specific commands can be associated with residue +selections. + +.SH COPYRIGHT + +Christoph Gille \(co 1999-2011 + +License GPL + +.SH "SEE ALSO" + +A comprehensive manual is created with the option \fB-manual\fR + +.BR jalview (1) +.BR clustalx (1) +.BR seaview (1) +.BR boxshade (1) +.BR pymol (1) +.BR openastex (1) +.BR strap-text-viewer (1) Deleted: trunk/packages/strap/trunk/debian/strap.1 =================================================================== --- trunk/packages/strap/trunk/debian/strap.1 2012-05-28 18:53:10 UTC (rev 11053) +++ trunk/packages/strap/trunk/debian/strap.1 2012-05-28 20:32:51 UTC (rev 11054) @@ -1,304 +0,0 @@ -.TH Strap 1 "October 2011" -.SH NAME - - -Strap \- Graphical user interface to compare and align proteins by sequence and 3D-structure. -.SH Synopsis - -.B strap-protein-alignment [\fIprotein_files\fR] - -.B strap-protein-alignment [\fIalignment_files\fR] - -.B strap-protein-alignment -[\fIoptions\fR] [\fIprotein_files\fR] [\fIalignment_files\fR] [ @ \fIfile_with_list_of_protein_files\fR] - - - -.SH DESCRIPTION - -The free computer program Strap aligns proteins by sequence and -3D-structure. Strap supports the simultaneous analysis of hundreds of -proteins and integrates amino acid sequence, secondary structure, -3D-structure and genomic- and mRNA-sequence. Using standard methods, -alignments are computed automatically based on sequence and structure. -Import and export of single proteins is very easy by Drag-and-Drop. - -.SS Home-Page - -http://3d-alignment.eu/ - -http://www.bioinformatics.org/strap/ - -.SH PROGRAM PARAMETERS - -.SS Protein/alignment files - -Strap can be started with protein files or alignment files as parameters. -The following formats are supported: PDB, Swissprot, Embl, Genbank, -GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom, -Pfam, Stockholm and HSSP. - -If at least one protein file is specified, Strap will choose the -current working directory as the project directory. Otherwise the -project directory is requested at the beginning of the session. - - -Files with a leading \fB@\fR sign or preceded by a \fB@\fR sign are -interpreted as lists of files. - -\fBCurly parenthesis\fR are used for placing sequences into the same -alignment row. At the UNIX command prompt, the parentheses need to be -quoted. For example \fB'{'\fR \fIprotein1.seq protein2.seq\fR -\fB'}' '{'\fR \fIprotein3.seq protein4.seq protein5.seq \fR \fB'}'\fR -would put two proteins into the first and three proteins into the -second alignment row. If there are more than one sequences in a row, -only the top most sequence is displayed. - - - - - -.SS File Compression - -The following file compression methods are supported: .gz, .bz2 and .Z - -.SS Parts of proteins - -To display only a subset of a protein, a suffix is appended to the -protein file name. -Residue subsets are specified by an exclamation mark and a subset -expression after the protein file. Example: -"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To -refer to pdb-residue numbers use the Rasmol/Jmol syntax \fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A". - -.SH OPTIONS - -Program options start with a dash. The values \fBtrue\fR and -\fBfalse\fR can be abbreviated by \fBt\fR and \fBf\fR. The "=true" or -"=t" can be ommitted. For example \fB-noSeqres=true\fR can be written -as \fB-noSeqres=t\fR or \fB-noSeqres\fR. For most settings there is an -equivalent check-box or choice menu in the graphical user interface. - -If the Web-start script http://www.bioinformatics.org/strap/strap.php -is started, the options are given as web-variable without the leading -dash. For example for -noSeqres include \fBnoSeqres=t\fR into the -URL. - -\fB-help\fR - -Prints this text - -\fB-manual\fR - -Generates a comprehensive manual for the web browser. - -\fB\-noSeqres\fR - - Skip SEQRES lines of PDB files. - -\fB\-noIdentical\fR - -Do not load a sequence identical to an already loaded one. - -\fB\-dialog\fR=\fIJavaClassNameOfDialog\fR - -Opens a certain dialog at start. -The class name of a dialog is the tab-text can be obtained by opening the help text. - -Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot - -\fB\-script\fR=\fIURL_or_FilePath_or_ScriptText\fR - -Runs a script at start. See http://www.bioinformatics.org/strap/web/strap_script.html. -Script files in the current directory should be written with a leading -"./" like "./myScript.txt" since Strap recognizes files by the -presence of a slash and the absence of white space and colon. - -Two or more script files can be given: --script5=\fIhttp://...../file\fR -script7=\fIhttp://...../file\fR. -The optional number suffix defines the order of consecutively executed scripts. - -Script commands can be given directly. Assume there are protein files -in PDB format loaded by Strap. The option -script="open_3D viewName, -*" would display all proteins with 3D-coordinates three-dimensionally -(See -v3d=). Scripts consisting of more than one line should be -stored in a file and the file path or URL should be given. - -Example: - --script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *" - -\fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR - -Only needed for DAS servers that are - -\fB\-s3d\fR=\fIJavaClass\fR - -Sets the Java class to superimpose proteins. - -A short name can be used such as "tm_align" for "Superimpose_TM_align". - -Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus - -\fB\-a3d\fR=\fIJavaClass\fR - -Sets the Java class to compute structure based sequence alignments. - -Examples: -a3d=tm_align or -a3d=mapsci or -a3d=matt or -a3d=mustang - -\fB\-v3d\fR=\fIJavaClass\fR - -Sets the Java class to display 3D-structures. - -Example: -v3d=jmol or -v3d=pymol or -v3d=astex - -\fB\-aligner2\fR=\fIJavaClass\fR - -Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start. -Default value is PairAlignerNeoBioPROXY. - -Example: -aligner2=MultipleAlignerClustalW - - -\fB\-log3d\fR - -All 3D-commands which are sent to 3D-protein viewers are printed to stdout. - -\fB\-useDebian=false\fR \fB\-useDebian=true\fR - -If set to true, use the Debian packages for external programs rather -than the program versions included in Strap. For example Strap would -use /usr/bin/pymol instead of downloading and using the Pymol from -http://www.bioinformatics.org/strap/Binaries/. - -\fB\-sysProxies=true\fR or \fB-probeWebProxy=true\fR or \fB-probeWebProxy=false\fR - -See section Web proxies. - -\fB\-noCache\fR - - Do not use cached results of previous -computations. This setting can be changed in the graphical user -interface with a check-box. - -This setting influences the result of searches in growing -databases. For example consider the similarity search method -Blast. With the cache turned on, Strap would present a previously -computed Blast result even though new sequences might have been -published since last run. - -\fB\-keepFiles\fR - -Do not delete temp-files after the session. This is only important for -debugging. - -\fB\-Xmx500m\fR - -This is an option of the java command and not of Strap. -It sets the heap size to 500 Megabyte. - -\fB\-geometry=\fI666x333+11+22\fR - -Sets the size and location of the application frame to width 666, -height 333, horizontal screen position 11 and vertical position 22; - -\fB\-laf=\fIlookAndFeel\fR - -Examples: - --laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short -laf=m) - --laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short -laf=N) - --laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short -laf=G) - --laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short -laf=M) - -Also non-standard Look'n Feels can be used. Consider tinylaf which -can be installed as a Debian package. The following two options would -apply tinylaf: - - \fB-cp=\fR/usr/share/java/tinylaf.jar --laf=de.muntjak.tinylookandfeel.TinyLookAndFeel - -See also http://en.wikipedia.org/wiki/Look_and_feel. - -\fB\-toMultipleFasta\fR or \fB\-toClustal\fR or \fB\-toFasta\fR \fIProtein or alignment files\fR - -Loads the proteins and generates protein or ungapped multiple sequence -files with the respective format. The file paths are written to -stdout. The program terminates. - -.SS Security - -\fB\-askUpload\fR[=t/f] The user is asked each time data is uploaded -to remote servers. The user might not want unpublished sequences to be -sent to servers. - -\fB\-askExec\fR[=t/f] The user is asked when an external program is -executed. Executing native programs might be regarded as security -risk. There is a positive and a negative list which can be edited in -the menu "Security" of the Preferences-menu. - -\fB\-allowFileModification\fR According to the default policy, files -are only modified, created or deleted if they reside in the project -directory or if the file path contains "StrapAlign". This is to -prevent files to be lost. With this option file modification control -is deactivated. - -.SH PROJECT DIRECTORY - -The project directory holds information for gaps, 3D-transformations, -annotations and exported files. Usually, the protein files are also -located in the project directory. The project directory path must not -contain white space, such as "My data" or "Eigene Dateien". Therefore -the project directory can usually not be located in the home directory -on Windows-XP. - -.SH WEB-PROXY - -With the option \fB-probeWebProxy=t\fR, strap attempts to access the Web in -three different ways: (1) Directly, without Web-proxy (2) With the -settings found in the environment variable http_proxy and (3) using -the default mechanism of Java to apply the system wide settings. With the -setting \fB-probeWebProxy=f\fR, however, Strap will directly connect to the -Internet. with the option \fB-sysProxies=t\fR Strap will use the -Java-built-in mechanism to find the system wide settings, (which might -not work properly, depending on the Java system). - -.SH ALIGNMENT-FILE-EXPORT - -Supported formats are Multiple-Fasta, ClustalW, MSF, HSSP. A -colorized alignment with highlighted residue selections and secondary -structure can be exported in HTML and PDF. The colorized HTML output -can be modified in MS-Word or other text processors. The rendering -styles of the PDF output can be stored in annotations of residue -selections. - -.SH 3D-VISUALIZATION - -The following 3D-protein viewers are tightly linked with the alignment -view: Pymol, Jmol, OpenAstex. The rendering styles can be stored -within residue selections. There is a generic Rasmol like scripting -language which can be applied to all embedded visualization software. -If the desired effect can not be achieved with this generic commands, -also specific commands can be associated with residue -selections. - -.SH COPYRIGHT - -Christoph Gille \(co 1999-2011 - -License GPL - -.SH "SEE ALSO" - -A comprehensive manual is created with the option \fB-manual\fR - -.BR jalview (1) -.BR clustalx (1) -.BR seaview (1) -.BR boxshade (1) -.BR pymol (1) -.BR openastex (1) -.BR strap-text-viewer (1) Modified: trunk/packages/strap/trunk/debian/strap.install =================================================================== --- trunk/packages/strap/trunk/debian/strap.install 2012-05-28 18:53:10 UTC (rev 11053) +++ trunk/packages/strap/trunk/debian/strap.install 2012-05-28 20:32:51 UTC (rev 11054) @@ -1,2 +1,2 @@ -debian/bin/strap usr/bin +debian/bin/strap-protein-alignment usr/bin debian/strap.desktop usr/share/applications Modified: trunk/packages/strap/trunk/debian/strap.links =================================================================== --- trunk/packages/strap/trunk/debian/strap.links 2012-05-28 18:53:10 UTC (rev 11053) +++ trunk/packages/strap/trunk/debian/strap.links 2012-05-28 20:32:51 UTC (rev 11054) @@ -1,2 +1 @@ -usr/bin/strap usr/bin/strap-protein-alignment -usr/share/man/man1/strap.1 usr/share/man/man1/strap-protein-alignment.1 +usr/share/man/man1/strap-protein-alignment.1 usr/share/man/man1/strap.1 Modified: trunk/packages/strap/trunk/debian/strap.manpages =================================================================== --- trunk/packages/strap/trunk/debian/strap.manpages 2012-05-28 18:53:10 UTC (rev 11053) +++ trunk/packages/strap/trunk/debian/strap.manpages 2012-05-28 20:32:51 UTC (rev 11054) @@ -1 +1 @@ -debian/strap.1 +debian/strap-protein-alignment.1 Deleted: trunk/packages/strap/trunk/debian/substvars =================================================================== --- trunk/packages/strap/trunk/debian/substvars 2012-05-28 18:53:10 UTC (rev 11053) +++ trunk/packages/strap/trunk/debian/substvars 2012-05-28 20:32:51 UTC (rev 11054) @@ -1 +0,0 @@ -misc:Depends= _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
