added stricter compilation requirements and fixed resulting errors

[mothur.git] / Mothur.xcodeproj / project.pbxproj

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index f5bc8ad01ae02e054c66ca4d87ea6d1b0ba478e8..7959c798a10a0e1745559369e95bbb5d77347f7f 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -77,6 +77,9 @@
                37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; };
                37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; };
                37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */; };
+               37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */; };
+               37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */; };
+               37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */; };
                37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */; };
                37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C753CD0FB3415200DBD02E /* distancecommand.cpp */; };
                37D928550F21331F001D4494 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927B80F21331F001D4494 /* ace.cpp */; };
@@ -321,6 +324,12 @@
                37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = SOURCE_ROOT; };
                37B73C741004BEFD008C4B41 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = "<group>"; };
                37B73C751004BEFD008C4B41 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = "<group>"; };
+               37B73CA41004D89A008C4B41 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = "<group>"; };
+               37B73CA51004D89A008C4B41 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = "<group>"; };
+               37B73CBE1004EB38008C4B41 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = "<group>"; };
+               37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = "<group>"; };
+               37B73CCD1004F5E0008C4B41 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = "<group>"; };
+               37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = "<group>"; };
                37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = SOURCE_ROOT; };
                37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = SOURCE_ROOT; };
                37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = SOURCE_ROOT; };
@@ -783,6 +792,8 @@
                                3749273E0FD5956B0031C06B /* getrabundcommand.cpp */,
                                3749271B0FD58C840031C06B /* getsabundcommand.h */,
                                3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
+                               37B73CA41004D89A008C4B41 /* getseqscommand.h */,
+                               37B73CA51004D89A008C4B41 /* getseqscommand.cpp */,
                                375873F10F7D64800040F377 /* heatmapcommand.h */,
                                375873F00F7D64800040F377 /* heatmapcommand.cpp */,
                                378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
@@ -813,6 +824,8 @@
                                372E126F0F26365B0095CF7E /* readotucommand.cpp */,
                                37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
                                37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
+                               37B73CBE1004EB38008C4B41 /* removeseqscommand.h */,
+                               37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */,
                                7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
                                7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
                                371B30B30FD7EE67000414CA /* screenseqscommand.h */,
@@ -825,6 +838,8 @@
                                37D928460F21331F001D4494 /* summarycommand.cpp */,
                                37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
                                37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
+                               37B73CCD1004F5E0008C4B41 /* systemcommand.h */,
+                               37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */,
                                211C38370F961E1F00FEE541 /* treegroupscommand.h */,
                                211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
                                7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */,
@@ -1117,6 +1132,9 @@
                                7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */,
                                379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */,
                                37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */,
+                               37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */,
+                               37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */,
+                               37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -1176,11 +1194,20 @@
                                );
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
+                               GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
-                               GCC_WARN_PEDANTIC = NO;
+                               GCC_WARN_MISSING_PARENTHESES = YES;
+                               GCC_WARN_PEDANTIC = YES;
+                               GCC_WARN_UNUSED_FUNCTION = YES;
+                               GCC_WARN_UNUSED_PARAMETER = NO;
+                               GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               OTHER_CPLUSPLUSFLAGS = "";
+                               OTHER_CPLUSPLUSFLAGS = (
+                                       "-ansi",
+                                       "-pedantic",
+                                       "-wall",
+                               );
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
                                WARNING_CFLAGS = "";