[med-svn] [Git][med-team/gentle][master] 2 commits: Updated upstream repository to https://github.com/GENtle-persons/gentle-m
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Mon Jul 31 16:24:45 BST 2023
Steffen Möller pushed to branch master at Debian Med / gentle
Commits:
e6fec562 by Steffen Moeller at 2023-07-31T17:15:14+02:00
Updated upstream repository to https://github.com/GENtle-persons/gentle-m
- - - - -
45d1a367 by Steffen Moeller at 2023-07-31T17:23:53+02:00
Fix to open HTML files from within GENtle.
Needed to show online help.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/HelpDoesNotWork.patch
- debian/patches/series
- + debian/patches/strcpy_unreserved.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+gentle (1.9+cvs20100605+dfsg1-13) UNRELEASED; urgency=medium
+
+ * Increased size of char[]s (factor 10) to
+ - accomodate longer sequence lines and/or
+ - avoid compiler warnings.
+ * Now opening website with /usr/bin/open (provided e.g. by xdg-utils)
+ * Update of upstream repository.
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 31 Jul 2023 14:44:40 +0200
+
gentle (1.9+cvs20100605+dfsg1-12) unstable; urgency=medium
* Added more patches to eradicate compiler warnings on font selection.
=====================================
debian/control
=====================================
@@ -20,6 +20,7 @@ Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends}
Recommends: clustalw
+Suggests: xdg-utils
Description: suite to plan genetic cloning
GENtle is a software for DNA and amino acid editing, database management,
plasmid maps, restriction and ligation, alignments, sequencer data
=====================================
debian/copyright
=====================================
@@ -1,7 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: GENtle
Upstream-Contact: Magnus Manske <magnusmanske+gentle at googlemail.com>
-Source: https://github.com/magnusmanske/gentle-m
+Source: https://github.com/GENtle-persons/gentle-m
Files-Excluded: */clustalw
*/tinyxml
*/.cvsignore
=====================================
debian/patches/HelpDoesNotWork.patch
=====================================
@@ -0,0 +1,90 @@
+Index: gentle2/main.cpp
+===================================================================
+--- gentle2.orig/main.cpp
++++ gentle2/main.cpp
+@@ -420,7 +420,7 @@ int MyApp::OnExit ()
+ // return 0;
+ }
+
+-void MyApp::launchBrowser ( wxString url )
++void MyApp::launchBrowser ( const wxString url )
+ {
+ // wxMessageBox ( url ) ;
+ // if ( wxLaunchDefaultBrowser ( url ) ) return ;
+@@ -432,18 +432,18 @@ void MyApp::launchBrowser ( wxString url
+ \brief Returns the command line to invoke the browser.
+ \param command The URL/file.
+ */
+-wxString MyApp::getHTMLCommand ( wxString command )
++wxString MyApp::getHTMLCommand ( const wxString command )
+ {
+ #ifdef __WXMAC__
+ return _T("open ") + command ;
+-#endif
++#else
+ wxString ret ;
+ ret = getFileFormatCommand ( command , _T("html") ) ;
+ if ( ret.IsEmpty() ) ret = getFileFormatCommand ( command , _T("htm") ) ;
+ if ( !ret.IsEmpty() ) return ret ;
+-
+ // Fallback
+ #ifdef __WXMSW__
++ wxPrintf(stderr,"E getHTMLCommand: Running backup code to assign application to HTML-formatted file.");
+ wxRegKey regKey;
+ wxString idName(_T("HKEY_CLASSES_ROOT\\.html"));
+ regKey.SetName(idName);
+@@ -459,8 +459,15 @@ wxString MyApp::getHTMLCommand ( wxStrin
+ q += _T(" \"") + command + _T("\"") ;
+ return q ;
+ #else
++#ifdef __DEBIAN__
++ return _T("open ") + command ;
++#else
++ wxPrintf(stderr,"E getHTMLCommand: Returning empty string as command top open HTML file.");
+ return _T("") ;
+ #endif
++#endif
++#endif
++
+ }
+
+ /** \fn MyApp::getFileFormatCommand ( wxString command )
+@@ -468,7 +475,7 @@ wxString MyApp::getHTMLCommand ( wxStrin
+ \param type The file ending to find the application for.
+ \param file The URL/file.
+ */
+-wxString MyApp::getFileFormatCommand ( wxString type , wxString file )
++wxString MyApp::getFileFormatCommand ( const wxString type , const wxString file )
+ {
+ wxFileType *ft = mtm.GetFileTypeFromExtension ( type ) ;
+ if ( !ft ) return _T("") ;
+@@ -479,7 +486,7 @@ wxString MyApp::getFileFormatCommand ( w
+ \brief Returns the application associated with a file type. Windows only.
+ \param type The file ending to find the application for.
+ */
+-wxString MyApp::getFileFormatApplication ( wxString type )
++wxString MyApp::getFileFormatApplication ( const wxString type )
+ {
+ #ifdef __WXMSW__
+ wxRegKey regKey;
+Index: gentle2/main.h
+===================================================================
+--- gentle2.orig/main.h
++++ gentle2/main.h
+@@ -185,12 +185,12 @@ class MyApp : public wxApp
+ virtual void init_txt ( wxString lang , wxString csv , wxHashString *target = NULL , int ln = 1 ) ;
+ virtual void do_my_ass ( bool b , wxString msg = _T("") ) ;
+ virtual void do_my_log ( wxString function , wxString msg = _T("") ) ;
+- virtual wxString getHTMLCommand ( wxString command ) ; ///< Returns the command line for running a browser
+- virtual wxString getFileFormatApplication ( wxString type ) ; ///< Returns application associated with a file type
+- virtual wxString getFileFormatCommand ( wxString type , wxString file ) ; ///< Returns the command line for running this file
++ virtual wxString getHTMLCommand ( const wxString command ) ; ///< Returns the command line for running a browser
++ virtual wxString getFileFormatApplication ( const wxString type ) ; ///< Returns application associated with a file type
++ virtual wxString getFileFormatCommand ( const wxString type , const wxString file ) ; ///< Returns the command line for running this file
+ virtual wxString get_GENtle_version () ; ///< Returns the GENtle version string
+ virtual wxString getLocalDBname () ; ///< Returns the filename of the default local database
+- virtual void launchBrowser ( wxString url ) ;
++ virtual void launchBrowser ( const wxString url ) ;
+
+ MyFrame *frame; ///< The application frame
+ wxMimeTypesManager mtm ; ///< The MIME types manager
=====================================
debian/patches/series
=====================================
@@ -13,3 +13,5 @@ DoNotShowBoxAboutMarkersLoading.patch
ExpandOverridesAll.patch
YetAnotherMissingReturn.patch
YetAnotherPenSelection.patch
+strcpy_unreserved.patch
+HelpDoesNotWork.patch
=====================================
debian/patches/strcpy_unreserved.patch
=====================================
@@ -0,0 +1,77 @@
+Index: gentle2/ureadseq.c
+===================================================================
+--- gentle2.orig/ureadseq.c
++++ gentle2/ureadseq.c
+@@ -101,7 +101,7 @@ struct ReadSeqVars {
+ boolean allDone, done, filestart, addit;
+ FILE *f;
+ long linestart;
+- char s[256], *sp;
++ char s[256*10+42], *sp; // to reduce the chance to run into unallocated memory
+
+ //int (*isseqchar)();
+ int (*isseqchar)(int c);
+@@ -183,16 +183,16 @@ Local void countseq(char *s, struct Read
+ }
+
+
+-Local void addinfo(char *s, struct ReadSeqVars *V)
++Local void addinfo(const char * const s, struct ReadSeqVars * const V)
+ {
+- char s2[256], *si;
+- boolean saveadd;
++ char s2[256*10+42+314]; // needs to be long enough to accept V->s
+
+- si = s2;
+- while (*s == ' ') s++;
+- sprintf(si, " %d) %s\n", V->nseq, s);
++ char * const si = s2;
++ const char *stmp=s;
++ while (*stmp == ' ') stmp++;
++ snprintf(si, sizeof(s2)-1, " %d) %s\n", V->nseq, stmp); // skipping prefix of spaces
+
+- saveadd = V->addit;
++ const boolean saveadd = V->addit;
+ V->addit = true;
+ V->isseqchar = isAnyChar;
+ addseq( si, V);
+@@ -1565,7 +1565,7 @@ short writeSeq(FILE *outf, const char *s
+ /* dump sequence to standard output */
+ {
+ const short kSpaceAll = -9;
+-#define kMaxseqwidth 250
++#define kMaxseqwidth 2500
+
+ boolean baseonlynum= false; /* nocountsymbols -- only count true bases, not "-" */
+ short numline = 0; /* only true if we are writing seq number line (for interleave) */
+@@ -1577,10 +1577,10 @@ short writeSeq(FILE *outf, const char *s
+
+ short linesout = 0, seqtype = kNucleic;
+ long i, j, l, l1, ibase;
+- char idword[31], endstr[10];
++ char idword[31+42], endstr[10+42];
+ char seqnamestore[128], *seqname = seqnamestore;
+ char s[kMaxseqwidth], *cp;
+- char nameform[10], numform[10], nocountsymbols[10];
++ char nameform[10+42], numform[10+42], nocountsymbols[10+42];
+ unsigned long checksum = 0, checktotal = 0;
+
+ gPretty.atseq++;
+@@ -1592,7 +1592,7 @@ short writeSeq(FILE *outf, const char *s
+ sscanf( seqname, "%30s", idword);
+ sprintf(numform, "%ld", seqlen);
+ numwidth= strlen(numform)+1;
+- nameform[0]= '\0';
++ nameform[0]= 0;
+
+ if (strstr(seqname,"checksum") != NULL) {
+ cp = strstr(seqname,"bases");
+@@ -1602,7 +1602,7 @@ short writeSeq(FILE *outf, const char *s
+ }
+ }
+
+- strcpy( endstr,"");
++ endstr[0]=0;
+ l1 = 0;
+
+ if (outform == kGCG || outform == kMSF)
View it on GitLab: https://salsa.debian.org/med-team/gentle/-/compare/402644f2dadb21a375681687237dd7b24807bc42...45d1a36770719ad4fb58279dcef37418d3b0b285
--
View it on GitLab: https://salsa.debian.org/med-team/gentle/-/compare/402644f2dadb21a375681687237dd7b24807bc42...45d1a36770719ad4fb58279dcef37418d3b0b285
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